University of Southern California Dissertations and Theses

The S. pombe Mst1 histone acetyltransferase is required for genome stability

(USC Thesis Other)

The S. pombe Mst1 histone acetyltransferase is required for genome stability

PDF

Download

Open document

Flip pages

Download a page range

Download transcript

Copy asset link

Request this asset

Transcript (if available)

Content THE S. POMBE MST1 HISTONE ACETYLTRANSFERASE IS REQUIRED FOR
GENOME STABILITY

by
Rebecca Lynn Nugent

A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree of
DOCTOR OF PHILOSOPHY
(MOLECULAR BIOLOGY)

August 2010

Copyright 2010 Rebecca Lynn Nugent

ii

Acknowledgments

This process has been a journey of personal and scientific discovery. I am
grateful for the lessons my advisor Susan Forsburg taught me along the way. Susan
quickly learns the strengths and weakness of her students. She tailors her management to
each individual, allowing for the maximum professional and personal growth. For me,
this meant she took a very cocky 22-year old and developed a professional scientist. She
did this through giving me enough space to fail, while guiding me through technical
roadblocks and the inevitable hypothesis failure.
Will Dolan had a large influence on me joining Susan’s lab and I am grateful for
his presence during my first year here. JiPing Yuan’s patience and friendship helped me
through many difficult years. Pao-Chen Li gave me so much of her time and valuable
advice; I am lucky to be her labmate and friend. Lab members Anthony, Angel, Doug,
Sarah, Lin, Ruben, Marc, Nimna, Tara, Morgan and Amanda have peppered my time
here and each taught me something unique and long-lasting. I’ve made wonderful life
long friends here: Alison, Laura and Meghna. I look forward to years of ginspirations to
come with them.
I would not be here without the unconditional support from my family. There are
not enough positive, wonderful things to say about my parents, Terry and Dick, which
could do any justice to the love and support they give me. My sister Kristin has always
been a source of support and an ear for when I just needed to talk. I love them all very
much.

iii

Finally I would like to thank my husband Phil for his sacrifices these past six
years. He hustled and worked jobs he didn’t like so we could live comfortably with an
adorable cat named Jade (whom he hates and is allergic to). Without pipetting, working at
the bench or knowing any molecular biology, he deserves a portion of this degree.

Chapter 2 is a partial reprint from Gomez et al, Genetics 2008 in which Eliana Gomez
was the first author and I was the second. Susan Forsburg directed and supervised the
research that was the basis for this chapter.

Chapter 3 is a full reprint of Nugent et al BMC Genomics 2010, in which I was the co-
first author. This work was done in collaboration with Tony Wright’s lab at the
Karolinska Institutet in Sweden and Chris Seidel’s group at the Stower’s institute. Author
contributions are clearly stated in the chapter. Susan Forsburg directed and supervised the
research that was the basis for this chapter.

iv

Table of Contents

Acknowledgments ii
List of Tables vi
List of Figures vii
Abstract ix
Chapter 1: Introduction 1
Chapter 2: Characterizing Mst1 in the DNA damage repair
and response pathway 21
2.1 Introduction 21
2.2 Results 22
2.3 Discussion 32
2.4 Materials and Methods 36

Chapter 3: Expression profiling of S. pombe acetyltransferase
mutants identifies redundant pathways of gene regulation 41
3.1 Overview 41
3.2 Background 41
3.3 Results 45
3.4 Discussion 87
3.5 Conclusions 94
3.6 Methods 95
3.7 Author Contributions 100
3.8 External Contributions 100

Chapter 4: Chapter 4: The S. pombe histone acetyltransferase Mst1
is necessary for proper centromere architecture. 101
4.1 Chapter 4 Abstract 101
4.2 Introduction 101
4.3 Results 103
4.4 Discussion 113
4.5 Materials and Methods 115

v

Bibliography 120

Appendices: 142
Appendix A: Differentially expressed genes (1.7 fold)
in HAT mutants 142
Appendix B: Creation of Histone H4 K5R K8R K12R mutant 208
B.1 Purpose 208
B.2 Histone H4 KR Mutant Construction 208

vi

List of Tables

Table 1.1: Common Histone modifications and Protein Domains 3
Table 1.2: MYST and GNAT Histone acetyltransferases 6
Table 1.3: NuA4 members in S. cerevisae, and S. pombe. 9
Table 2.1: Genes isolated by 2-hybrid screening. 23
Table 2.2: Genetic interactions between mst1
ts
and other mutants 26
Table 2.3: Strains used in chapter 2 36
Table 3.1: Differentially regulated genes in single HAT mutants 49
Table 3.2: GO terms differentially regulated in HAT mutants. 51
Table 3.3: Differentially regulated genes (3.25 fold) in the triple HAT mutant. 59
Table 3.4: Differentially expressed genes (3.25 fold) in double HAT mutants. 62
Table 3.5: Genes with 2 fold change in gene expression after exposure to salt. 70
Table 3.6: Differentially expressed genes in mst1
ts
. 84
Table 3.7: Strains used in chapter 3 95
Table 4.1: Strains used in chapter 4 115
Table 4.2: Primers used in chapter 4 117
Table A.1: Differentially expressed genes (1.7 fold) in HAT mutants 142
Table B.1: Primers used in Appendix B 210

vii

List of Figures

Figure 1.1: The S. pombe centromere 15
Figure 2.1: Confirmation of yeast two-hybrid results 24
Figure 2.2: mst1
ts
genetic interactions 27
Figure 2.3: Damage sensitivity of mst1-L344S 28
Figure 2.4: Mst1 is necessary for proper checkpoint activation. 30
Figure 2.5: Rad22YFP foci 32
Figure 3.1: Characterization of mutant phenotypes 46
Figure 3.2: Overlapping expression in different mutants 58
Figure 3.3: Validation of microarray results by qPCR. 61
Figure 3.4: Salt response is redundantly regulated by multiple
HAT families. 70
Figure 3.5: Histone H3 acetylation is differentially affected by
different HAT mutants. 85
Figure 3.6: Venn diagram of differentially down and up-regulated
GO terms of mst1
ts
mutant compared to single, double, and triple
HAT mutants 87
Figure 4.1: mst1 mutants cells show evidence for chromosome
segregation defects 104

Figure 4.2: mst1
ts
shows a selective defect in gene silencing
at the central core 106
Figure 4.3: The kinetochore does not localize to the centromere in the
absence of Mst1 107

Figure 4.4: Histone H4 acetylation is differentially affected
by Mst1 and Clr6 108

Figure 4.5: mst1
ts
does not exhibit genetic interactions with
central core specific histone deacetylases 109

viii

Figure 4.6: Histone H4 acetylation patterns at the central core 111

Figure 4.7: Kinetochore localization in mutants with only
one copy of histone H4. 112

Figure B.1 H4K5R K8R K12R plasmid (pRLN101). 209

Figure B.2 Sequence alignment of wild-type histone H4
and h4kr mutant 210

ix

Abstract

Within the cell DNA exists as chromatin, a complex mass of nucleic acids and
proteins. Chromatin is highly structured and is compacted through the interaction of
double stranded DNA with histone proteins, to form a nucleosome. Histones are post-
translationally modified on the amino acids of their N-terminal tails to create a heritable
epigenetic code. Histone acetylation regulates the interaction between DNA and histones
in nucleosomes. Histone acetyltransferases are the enzymes that transfer acetyl groups on
to histones.
S. pombe (Sp) Mst1 is a member of the MYST family of histone
acetyltransferases (HATs) and is the likely orthologue of human TIP60 and S. cerevisiae
Esa1 (KAT5). The MYST family of HATs has roles in transcriptional regulation and
DNA damage repair. I show SpMst1 is necessary for response to DNA damage. Mst1
was found to interact with a wide-variety of proteins through a yeast 2-hybrid
experiment: I confirmed the interaction of Mst1 and Rad22. I also found evidence for
increased endogenous DNA damage in mst1 mutant cells. I show Mst1 functions within
DNA damage checkpoint pathway.
I found that MYST and GNAT family HATs have significant functional overlap
in regards to induced cellular stress, transcription and acetylation targets. Specifically the
MYST family HAT SpMst2 and GNAT family HAT SpGcn5 each acetylate histone H3
lysine 14.

x

Finally I show that histone acetylation is necessary for proper centromere
architecture. Mst1 is genetically placed to function at the central core of the centromere.
In the absence of Mst1 the kinetochore, localization is disrupted. The kinetochore is a
complex of proteins that link the chromosomes and microtubules during cytokinesis. Data
suggest this is related to histone H4 acetylation.

1

Chapter One: Introduction

Histone Acetyltransferases (HATs) transfer acetyl groups to the histone tails to create an
epigenetic code. They are highly conserved throughout eukaryotes. Histone
acetyltransferases are grouped into families based on their conserved domains and
functions. My work has focused on characterizing the MYST and GNAT family histone
acetyltransferases in S. pombe. I have particularly examined the essential MYST family
HAT Mst1, studying its role in DNA damage repair, transcription and chromosome
segregation. I also studied the overlap of MYST and GNAT family HATs in transcription
and DNA damage response. This introduction will present an overview of DNA structure,
the enzymes that modify it and the cellular processes affected.

Section I: Chromatin and dynamics

1.1.1 Nuclear Structure of DNA
Within the cell, DNA is highly structured and organized. 147 base pairs of DNA
are wrapped around basic proteins called histones to create a nucleosome. A nucleosome
is composed of four distinct histone proteins. Histones H2A and H2B are present as two
dimers and H3 and H4 form a tetramer (OUDET et al. 1975). The nucleosomes are the
core component of chromatin, which is the densely compacted material that makes up
chromosomes. This structure allows the cells to regulate many DNA transactions.
2

Chromatin can be broadly classified as heterochromatin and euchromatin, and
these terms refer to the level of DNA compaction. It was originally defined in Drosophila
Melongaster after DNA staining revealed certain regions of the chromatin stained darker
(heterochromatin) than other regions (euchromatin) (rev in (PASSARGE 1979)).
Subsequent research showed heterochromatin is densely packed DNA and
transcriptionally silenced while euchromatin is less dense and transcriptionally active (rev
in (WEGEL and SHAW 2005)). Chromatin is regulated spatially. as heterochromatin is
located physically near the nuclear peripheries and active euchromatin is in the center of
the nucleus (TADDEI et al. 2004). The structural and spatial regulations are each
influenced by their nucleosomal environment, more specifically by their histones and
their modifications.

1.1.2 Histones and histone modifications
The four core histones H2A, H2B, H3 and H4 are evolutionarily well conserved
through eukaryotes (THATCHER and GOROVSKY 1994). Histones are composed of two
distinct parts: a globular domain that is wrapped by the DNA, and N-terminal tails that
protrude outside. There are also C-terminal tails for some histones. Histones are post-
translationally modified on amino acid residues. These modifications are chemical groups
that can alter the interaction of the histone and the DNA. This can allow for regulation of
the interaction, making the DNA to histone bond tighter as found in heterochromatin, or
looser as in euchromatin (rev in (JENUWEIN and ALLIS 2001)). These modifications also
act to bring context to the many diverse regions of the chromosomes, as proteins have
domains that bind specific modifications. This allows for targeted functions, as in the
3

case of transcription and replication (rev in (JENUWEIN and ALLIS 2001)). Table 1.1 lists
common histone modifications and the protein domains that bind them.
There are many different covalent modifications found on histones (see Table
1.1), but this work will focus on the most well studied: protein acetylation. The acetyl
groups are often dynamic and spatially influence one another either on neighboring
amino acid residues of the same histone or on other histone tails.

Table 1.1: Common Histone modifications (LATHAM and DENT 2007) and Protein
Domains
Modification
Amino Acid
residue(s)

Protein Domain Histone Target Reference
Acetylation Lysine (K)

Bromodomain
acetylated lysine
residues
(MUJTABA et al.
2007)
biotinylation Lysine (K)

Chromodomain
methylated lysines
on histone tails
(JACOBS et al.
2001)
Sumoylation Lysine (K)

WD40 repeat
dimethylated
histone tails
(WYSOCKA et
al. 2005)
Methylation
Lysine (K),
Arginine (R)

Tudor domain
methylated
arginine and
methylated
histones
(COTE and
RICHARD 2005)
ubiquitylnation Lysine (K)

PHD finger
Histone 3 lysine 4
trimethylation

citrullination Arginine (R)

phosphorylation
Serine (S),
Threonine
(T)

Isomerization Proline (P)

Acetylation is associated with active transcription and DNA damage repair and is
one of the most well studied modifications. Acetyl groups are negatively charged and
modify lysine residues on each of the four core histone proteins. It was first discovered
that histones were negatively charged and that this activated RNA production
(transcription) in 1964 (ALLFREY et al. 1964). Presumably the negatively charged DNA
and acetyl group repel each other causing the nucleosome/DNA interactions to relax.
4

Histones located in promoter regions of highly transcribed genes are hyperacetylated
(KURDISTANI et al. 2004; ROBERT et al. 2004). Histone acetylation is also found flanking
DNA double strand breaks (TAMBURINI and TYLER 2005).
Biotinylation is a less well-known modification found on histones H2A, H3 and
H4. It is found in heterochromatic regions of the chromosomes (CAMPOREALE et al.
2007). Sumolyation occurs on all four core histone tails and is associated with repressed
transcription (NATHAN et al. 2006).
Methyl groups can be chemically added to either lysine or arginine residues.
Uniquely they can be added in a mono, di or tri manner on amino acid residues (LATHAM
and DENT 2007). Histone methylation is commonly found in areas of transcriptional
repression or silenced regions of the chromosome. (MILLAR and GRUNSTEIN 2006;
NAKAYAMA et al. 2001; RICE et al. 2003).
Ubiquitylnation of histone tails can be either in a mono or poly state. The most
common site of histone ubiquitination is histone H2A Lys (K) 119, which makes up 5-
15% of H2A (GOLDKNOPF et al. 1975). Subsequent research showed both histone H2A
and H2B are ubiquitinated (rev in (WEAKE and WORKMAN 2008). This modification has
roles in transcriptional regulation and DNA damage repair. Citrullination is a
modification arising from the deimination of the arginine. This chemical reaction is
mediated by Peptidylarginine deiminase (PAD) enzymes and this occurs on all four core
histones (NAKASHIMA et al. 2002). Recent work shows that citrullination is a
euchromatic mark as increased citrullination is correlated with chromosome
decondensation (WANG et al. 2009). Proline isomerization is a modification not well
5

studied, although recent reports indicate it is involved in the proper regulation of
transcription (NELSON et al. 2006).
Phosphorylation occurs on serines on all four histone cores. Phosphorylation of
H2A, specifically at serine 129 in yeasts (NAKAMURA et al. 2004), is necessary for DNA
damage repair (FERNANDEZ-CAPETILLO et al. 2004; THATCHER and GOROVSKY 1994).
Other sites of phosporylation mark cell cycle dynamics and regulate formation of
heterochromatin and transcription (AHN et al. 2005; BAKER and GRANT 2007; BARBER et
al. 2004; KLOC et al. 2008; ZHANG et al. 2006).
Variants of H2A and H3 histones are incorporated into specific regions of the
chromosome where they fulfill specialized functions (rev in (HENIKOFF and AHMAD
2005)). The most well studied histone H3 variant is CenpA. CenpA (spCnp1) is
evolutionarily conserved and localizes to the centromere (rev in (SMITH 2002)). The
presence of CenpA defines the centromere, and is essential for spindle association and
chromosome segregation. Other H3 variants, such as H3.1 and H3.3 are associated with
transcriptional elongation and other activities.
H2A variants fall into a number of categories. MacroH2A and H2A-Bbd are
found in vertebrates and are associated with inactive X-chromosomes (CHADWICK and
WILLARD 2001). H2Az (SpPht1) is a conserved from yeasts to humans, and is found at
promoter regions of genes throughout species (RAISNER et al. 2005; SCHONES et al. 2008;
WHITE et al. 1988). Histone H2Az is also necessary to promote the proper boundaries
between heterochromatic and euchromatic regions (MENEGHINI et al. 2003; ZOFALL et al.
2009).H2Ax is a histone variant that is randomly assembled throughout the genome but is
specifically phosphorylated at sites of DNA double strand breaks (rev in (FERNANDEZ-
6

CAPETILLO et al. 2004)). Yeasts do not have this histone variant; instead their H2A
contains phospho-acceptor sites in the C-Terminus that are characteristic of H2Ax.
Drosophila melanogaster has a combined H2Ax-H2Az variant called H2Av.

Section II: Histone acetyltransferases
The enzymes that transfer acetyl groups to histones are called histone
acetyltransferases (HATs). To counter the histone acetyltransferase there are classes of
enzymes with the opposing function, the histone deacetylaces (HDACs) (GALLINARI et
al. 2007) which makes acetylation a reversible switch. This thesis focuses on the function
of histone acetyltransferases within S. pombe.

Table 1.2: Representative MYST and GNAT Histone acetyltransferases
KAT Family homologs Acetylation targets Cellular Functions
KAT 5
SpMst1
ScEsa1
hTip60
H4 K 5, 8, 12, 16
H2Az, H2A K 4, 7
Essential for viability;
DNA damage repair;
transcription
KAT 2
SpGcn5
ScGcn5
dGcn5 H3 K 9, 14, 23, 36
Transcription; DNA
damage repair

1.2.1 Histone Acetyltransferase families.
There are two separate categories of HATs: Type A are located in the nucleus and
B in the cytoplasm (STERNER and BERGER 2000). Within S. pombe there are four major
HAT families: GNAT, MYST, TAF
II
250, ATF2. The GNAT and MYST family of HATs
have known roles in DNA damage repair, transcription and chromosome structure (rev in
(STERNER and BERGER 2000; UTLEY and COTE 2003). My thesis project focuses on the
GNAT and MYST family HATs, so for the purpose of this introduction we will focus on
7

them. There is a push in the field to reclassify most HATs as lysine acetyltransferases
(KATs), with a standard name for homologs across species. This is due to the fact that
many histone acetyltransferases acetylate non histone targets. The number given to the
KAT, aka KAT5, corresponds to the order in which they were discovered (ALLIS et al.
2007). For the purpose of this thesis these enzymes will be referred to as HATs and the
KAT designation will be used when applicable.
The GNAT (Gcn5 related N-acetyltransferase) family is named after the most
well-studied HAT, Gcn5 (Kat2 (Allis et al. 2007)). Gcn5 is well conserved from yeast to
humans: a deletion of the budding yeast gcn5 is rescued by expressing the human Gcn5
(WANG et al. 1997). It was originally isolated as a transcriptional activator
(Georgakopoulos and Thireos 1992) in yeast and later identified as a histone
acetyltransferase (BROWNELL et al. 1996).
The MYST family is named after the founding members MOZ, Ybf2/Sas3, Sas2,
and Tip60, named so because these enzymes all have a homologous domain (BORROW et
al. 1996; UTLEY and COTE 2003). hTip60 (Tat-interacting protein) was originally isolated
as an HIV-Tat interacting protein (KAMINE et al. 1996). hMoz was originally isolated as
a fusion protein with CBP (CREB-binding protein) in a t(8; 16)(p11; q13) translocation,
which occurs commonly in acute myeloid leukemia (BORROW et al. 1996). ScSas2 and
ScSas3 (something about silencing) were found in a genetic screen that assayed for
epigenetic silencing defective mutants (REIFSNYDER et al. 1996). Later, based on a
BLAST search of the complete genome, S. pombe was found to have two MYST HATs,
SpMst1 and SpMst2 (GOMEZ et al. 2005). The highly conserved MYST domain contains
an acetyl-CoA binding domain, many of the MYST family members also have a zinc
8

finger (UTLEY and COTE 2003) either defined by sequence or structure (YAN et al.
2000).
It is clear that MYST homologues not only share a common defining domain, but
also overlap in their functions. From the MYST family HATs there are three proteins that
show very strong homology to each other. These are the KAT5 (ALLIS et al. 2007) HATs
SpMst1, ScEsa1, and hTip60.

1.2.2 HAT Complexes
Most histone acetyltransferases function within a larger protein complex
(CARROZZA et al. 2003). These complexes have the catalytic HAT as the core catalytic
component and other proteins are exchanged in and out of the complex depending on the
context of the cell. Many of the transient proteins are shared between different chromatin
modifying complexes (SHEVCHENKO et al. 2008), yet each complex has a unique and
specific function in the cell. Many of the transient members of these complexes have
specialized protein domains that allows them to bind specific regions of the chromatin.
Common protein domains and their histone modification specificities are listed in table 1.
The residues these domains bind to are commonly associated with a biological function
and therefore leads to the catalytic HAT being targeted to specific regions of the genome.
Gcn5 is the catalytic HAT in a larger protein complex, named SAGA (GRANT et
al. 1997) after the founding members Spt-Ada-Gcn5-acetyltransferase. Spt proteins were
originally isolated in a yeast genetic screen looking for suppressor of Ty, a
retrotransposon, by Fred Winston in the 1980s (WINSTON et al. 1984). These proteins
have a range of functions within the cell, but most have to do with transcription
9

elongation or chromatin remodeling (YAMAGUCHI et al. 2001). Ada (alteration/deficiency
in activation.) was found in a budding yeast screen assaying for mutants that were
defective in expressing a toxic Gal4-VP16 plasmid (BERGER et al. 1992) and are involved
in activating transcription. In addition to the members above, SAGA also contains TATA
binding protein-associated factors (TAF
II
s) (GRANT et al. 1998). The SAGA complex,
like Gcn5, is highly conserved from yeast to humans (HELMLINGER et al. 2008). For a
complete list of SAGA members see (BAKER and GRANT 2007).
The KAT5 HATs all operate within the NuA4 (nucleosome acetyltransferase of
histone H4). ScEsa1 and SpMst1 are the catalytic subunits for the NuA4 in yeasts
(ALLARD et al. 1999; SHEVCHENKO et al. 2008). The NuA4 complex houses the catalytic
KAT5 HATs from yeast to humans. Remarkably, like most HAT containing complexes,
the proteins that are associated are well conserved throughout species (DOYON and COTE
2004). The members of the NuA4 complexes are listed in table 1.3.

Table 1.3: NuA4 members in S. cerevisae, and S. pombe. (DOYON et al. 2004;
SHEVCHENKO et al. 2008)
Budding
Yeast Essential? Citation
Other
Complex
Fission
Yeast
Essent
ial? Citation
Other
Complex
Tra1 Yes
(Saleh et
al. 1998)
Astra,
Saga Tra2
unkno
wn
Vid21 No
(Auger et
al. 2008) Vid21
unkno
wn n/a
Epl1 Yes
(Galarne
au et al.
2000) Epl1
unkno
wn n/a
Arp4 Yes
(Galarne
au et al.
2000;
Harata et
al. 1994)
Swr1,
Ino80 Alp5 Yes
Minoda
et al.
2005)
Ino80,
Swr1
Swc4 Swr1 Swc4 n/a Swr1
Esa1 Yes (Clarke Mst1 Yes (Gomez
Table 1.3: Continued 10

et al.
1999;
Smith et
al. 1998)
et al.
2005)
Yaf9 No
(Zhang
et al.
2004) Swr1 Yaf9 No n/a Swr1
Act1 Yes
(Shortle
et al.
1982)
Swr1,
Ino80 Act1
Ino80,
Swr1
Eaf3 No
(Reid et
al. 2004) Rpd3S Alp13 No
(Nakaya
ma et
al.
2003)(K
IM et al.
2010)
Clr6(smal
l)
Yng2 No
(Krogan
et al.
2004) Png1 No
(Chen
et al.)
Eaf7 No
(Krogan
et al.
2004) Eaf7
Yap1 No
(Moye-
Rowley
et al.
1989)
Pap1
(caf3) No
(Benko
et al.
1997)
Eaf5 No
(Krogan
et al.
2004)
No
homology
Eaf6 No
(Doyon
and Cote
2004;
Mitchell
et al.
2008)
No
homology
Bdf1 No
(Liu et
al. 2007) Swr1
No
homology
Bdc1 No

Unlike most HAT complexes, the NuA4 has two distinct complexes, the piccolo complex
and the larger NuA4 (BOUDREAULT et al. 2003). The piccolo complex, in budding yeast,
includes the catalytic subunit ScEsa1 and also ScEpl1 (GALARNEAU et al. 2000) and
ScYng2 (CHOY et al. 2001). These proteins are necessary for hisonte H4 acetylation and
enhances the complex’s recognition of nucleosomes (BERNDSEN et al. 2007; SELLECK et
al. 2005). Work in budding yeast shows that ScEaf1 (SpVid21) is the only subunit of the
complex not shared with other chromatin modifying complexes. In the absence of ScEaf1
11

the NuA4 complex dissociates (AUGER et al. 2008; MITCHELL et al. 2008). I will
generally refer to the HAT catalytic subunit interchangeably with the complexes in which
they operate. When applicable, specific complex members will be identified as having
unique phenotypes that aid in the functions and understanding of the catalytic HATs.

1.2.3 Histone Specificity
Each HAT family, and the subfamilies that exist within them, has specific lysine
residue targets that it acetylates. Some specificities can overlap, as this thesis will
investigate in chapter 3. This can lead to functional redundancies not only between
different HATs in a common family, but also in HATs from different families.
hTip60 was found to acetylate lysine residues on histones H3, H4 and H2A with a
preference towards histone H4 (KIMURA and HORIKOSHI 1998; YAMAMOTO and
HORIKOSHI 1997). ScEsa1 acetylates histone H4 preferentially, but also acetylates H3 and
H2A (CLARKE et al. 1999; SMITH et al. 1998). SpMst1 can acetylate all four histones in
an in vitro HAT assay (GOMEZ et al. 2008). In chapter 4 I will examine Mst1 targets
more closely. In S. pombe the other MYST family HAT SpMst2 acetylates histone
H4K16 and this thesis will explore the role it plays in histone H3 acetylation in chapter 3
(GOMEZ et al. 2005). Across species, Gcn5 has specificity towards histone H3 lysine
residues, H3K9, H3K14, H3K18 in vivo (KOUZARIDES 2007).

1.2.4 Essential HATs
In lower eukaryotes like S. cerevisae and S. pombe, Gcn5 is not essential,
however in higher eukaryotes, including mice, deletion of Gcn5 causes apoptosis and
12

embryonic lethality (XU et al. 2000). In fruit flies, the absence of Gcn5 prevents
metamorphosis resulting in death (CARRE et al. 2005). These phenotypes could be due to
the extended N-terminal tail in Gcn5 homologs in higher eukaryotes (XU et al. 1998).
Work from Sharon Dent’s lab shows two telomere associated factors, Trf1 and Pot1 are
lost from the telomere in a conditional Gcn5 knockout. They speculate that this is a direct
effect from Gcn5 and the SAGA complex, and not due to histone acetylation(ATANASSOV
et al. 2009).
Each of the KAT5 HATs are essential for viability. Mice with Tip60 homozygous
deletions die before implantation (GORRINI et al. 2007), however, the heterozygous
deletion mice are viable. These heterozygous mice, though, have elevated rates of
lymphomas, suggesting that Tip60 suppresses tumorigenesis in vivo. hTip60
knockdowns using siRNA show that cells arrest at the G2/M transition of the cell cycle
(DOYON et al. 2006). ScEsa1 temperature sensitive mutants shifted to the non-permissive
temperature also arrest at the G2/M transition of the cell cycle and this is dependent on
the DNA damage checkpoint ScRad9. These temperature mutants also show mitotic
defects as seen by improper DNA segregation (CLARKE et al. 1999). Through a spore
germination experiment, ∆mst1 exhibits a disordered mitosis, like ESA1 mutants.
However, analysis of mst1 temperature sensitive mutants shifted to the non-permissive
temperature indicates that SpMst1 does not have a cell cycle arrest phenotype like
ScEsa1and hTip60 (GOMEZ et al. 2008). Intriguingly, recent work suggests that ScEsa1’s
essential function may not be through acetylation. Work in M. Mitchell Smith’s lab made
point mutations in the catalytic MYST domain, these mutants were viable and showed
specific sensitivities to DNA damaging agents (DECKER et al. 2008). It is unclear what
13

exact cellular process(es) these individual HATs affect that make them essential for
viability. However it is clear that HATs function in all major aspects of cell life.

1.2.5 In vivo functions of histone acetyltransferases
1.2.5.1 Transcription
There is a strong correlation between histone acetylation and promoter activation.
Many highly transcribed genes are hyperacetylated on histones H3 and H4 at their
promoter regions and are euchromatic (WIREN et al. 2005). Many of the members of the
GNAT family were originally isolated as transcription activators. Elongator (ScElp3), a
GNAT family HAT, was originally isolated as a subunit of the RNA polymerase
holoenzyme complex (OTERO et al. 1999). This finding, at its name, suggests a role in
elongation, not promoter function.ESA1 mutants are defective in transcriptional silencing
of the ribosomal DNA (rDNA) and at the telomeres (CLARKE et al. 2006). ScGcn5 and
the Ada proteins were each found in genetic screens isolating transcriptionally
incompetent mutants (BERGER et al. 1992; GEORGAKOPOULOS and THIREOS 1992). The
canonical rule in the field was that HATs always activate transcription. However, recent
data collected by DNA microarrays to study gene expression found few differentially
expressed genes in a Sp∆gcn5 strain and there was as much repressed transcription as
activated (HELMLINGER et al. 2008; JOHNSSON et al. 2006). This indicates that there are
either multiple HATs that acetylate the same histone residues or multiple HATs
redundantly regulate transcription through the different lysine residues. This subject will
be explored in Chapter 3. Transcriptional activation and silencing is closely linked to
14

chromatin structure because RNA polymerase and associating factors need a euchromatic
environment to gain access to promoter regions.

1.2.5.2 Chromatin structure and maintenance
Within genomes, there are regions of conserved structure across species. The
centromere and telomere are heterochromatic and gene coding regions are euchromatic.
Histone deacetylaces (HDACs) and histone methyltransferases (HMTs) promote
constitutive heterochromatic regions at the centromere and telomere (ELGIN and GREWAL
2003). The MYST family HATs SpMst2 and ScSas2 negatively regulate telomere
silencing through acetylating histone H4 lysine 16 antagonistically with the HDAC
SpSir2 (FREEMAN-COOK et al. 2005; GOMEZ et al. 2005; SUKA et al. 2002). H4K16 is a
modification that is found in regions transitioning from heterochromatin to euchromatin.
In fruit flies the MYST family HAT MOF (males absent

on the first) is necessary for
dosage compensation of the X chromosome through acetylation of histone H4 lysine 16
(AKHTAR and BECKER 2000). ScEsa1 regulates the silencing of rDNA genes(CLARKE et
al. 2006).
The pombe centromere is composed of three distinct regions: an outer repeat (otr),
an inner repeat (imr) and central core (cnt) (see figure 1.1) (HALDAR and KAMAKAKA
2006). The otr region is highly heterochromatic, while the central core is not. The
heterochromatic structure is necessary for proper chromosome segregation as mutants
that disrupt the heterochromatin formation display improper segregation (rev in
(ALLSHIRE and KARPEN 2008)). The heterochromatin is mediated through histone H3K9
methylation by the methylase Clr4 (BANNISTER et al. 2001). This histone modification
15

recruits heterochromatin protein 1 (Swi6/HP1) which works in a feedback loop the
methylase Clr4 (NONAKA et al. 2002). Heterochromatin is prevented from spreading into
the central core through tRNA genes (rev in (HALDAR and KAMAKAKA 2006)).

Figure1.1 The S. pombe centromere (adapted from (HALDAR and KAMAKAKA 2006)).

The histone variant CenpA (SpCnp1) operates within the central core region.
Cenp-A defines the central core and is necessary for the kintochore to bind in this region
(MELLONE and ALLSHIRE 2003) Recently researchers showed another histone variant
H2Az (SpPht1) is specifically located in the inner core in a histone chaperone deletion
background (BUCHANAN et al. 2009). A histone chaperone deposits histones into the
chromatin. The SWR1 and NuA4 complexes work together to acetylate and deposit
H2Az into the chromosome (KIM et al. 2009; KROGAN et al. 2004). In S. pombe cells,
∆pht1 cells exhibit chromosome entaglements and defective chromosome silencing.
Studies using a pht1 mutant with the acetylated lysine residues mutated to arginine show
similar phenotypes (HOU et al. ; KIM et al. 2009). This data, combined with chromosome
segregation defects seen in the Sp∆mst1 mutant, suggests that histone acetylation plays a
direct role in maintaining proper centromere architecture, this will be explored further for
SpMst1 in chapter 4.

16

1.2.5.3 DNA replication
DNA replication is a well-controlled process that must occur once during the cell
cycle. This is accomplished by strict regulation of where replication starts, a DNA origin,
and factors that keeps the DNA polymerases processing through properly and reloading
after damage. A novel MYST family member in humans and in Drosophila was found
through a yeast two-hybrid screen that looked for Orc1 (origin replication complex 1)
binding partners: histone acetyltransferase bound to Orc1 (Hbo1) (IIZUKA and STILLMAN
1999). Subsequent research showed the hHbo1 binds hMcm2 through hHbo1’s zinc
finger (BURKE et al. 2001) and that hHbo1 is necessary for replication origin licensing
which leads to proper loading of MCMs to the chromosome (IIZUKA et al. 2006; MIOTTO
and STRUHL ; WU and LIU 2008). Like hHbo1, many MYST family members are
necessary for some aspect of proper replication or replication restart. SpMst1 and SpMst2
are sensitive to the drug hydroxyurea (HU), a drug that depletes the cell of
deoxyribonucleotides, stalling replication, and genetically interacts with mutants required
for proper replication (GOMEZ et al. 2005). SpMst1 also physically interact with MCMs.
Mutations in the ScEsa1 and genes in the S. cerevisiae NuA4 complex cause cells to be
sensitive to hydroxyurea and show prolonged levels of Rad53 phosphorylation during S
phase, indicating they sustain DNA replication under stress (CHOY and KRON 2002;
LOTTERSBERGER et al. 2007).

1.2.5.4 DNA damage repair
Following DNA damage, there is a signal cascade of kinase checkpoint proteins,
and specific histone modifications recruit repair proteins to the damage site (rev (VAN
17

ATTIKUM and GASSER 2009). Histones H3 and H4 are hyperacetylated at DNA double
strand breaks and ScEsa1 and ScGcn5 are recruited to those breaks (TAMBURINI and
TYLER 2005). Yeast mutants lacking histone H4 N-terminal tails, where damage specific
acetylation occurs, are hypersensitive to DNA damaging agents (DOWNS et al. 2004). In
2002, work from Christman’s group showed ScEsa1 was essential for DNA damage
repair, specifically by acetylating histone H4 (BIRD et al. 2002). Work done in mouse
embryonic fibroblasts with conditional knockouts of the NuA4 member TRRAP showed
that acetylation of chromatin near breaks is required for the DNA to relax and allow
repair proteins to bind (MURR et al. 2005). ESA1 and mst1 mutants both show sensitivity
to drugs that induce DNA damage (BIRD et al. 2002; GOMEZ et al. 2008). Point
mutations in the catalytic MYST domain of ScESA1 are viable but show sensitivity to
DNA damaging agents (DECKER et al. 2008). This suggests that ScEsa1’s essential role
within the cell is independent of histone acetylation required for proper DNA repair.
In 2001, Brand et al showed that a hGcn5-containing complex in human HeLa
cells was recruited to sites of UV damaged DNA and where it acetylated histone H3
(BRAND et al. 2001). This function is conserved as ScGcn5 participates nucleotide
excision repair (NER) in yeast (YU et al. 2005). ScHAT1 also contributes to DNA repair,
specifically through recombination following a break, blurring the canonical rule that
type-B HATs reside, and therefore, function solely in the cytoplasm (QIN and PARTHUN
2002).
However, the obvious question that arises is how do the histone acetyltransferases
get recruited to sites of DNA damage? This is mediated in part through the
phosphorylation signal cascade from the DNA damage checkpoint. When DNA damage
18

occurs, the MRN protein complex binds the site of damage. This then recruits the
conserved checkpoint protein ATM (spRad3) (ataxia telangiectasia, mutated) (VAN
ATTIKUM and GASSER 2009). ATM is a kinase, with many different targets in vivo. One
such target is H2Ax, which is phosphorylated by ATM on serine 139 in human cells and
localizes to areas of breaks (REDON et al. 2002). Yeasts lack the H2Ax variant, but H2A
is phosphorylated at serine 129 with the same effect (NAKAMURA et al. 2005). Proteins
located in the NuA4 complex, specifically ScArp4 (SpAlp5), bind H2Ax (H2Ap), and
that binding enhances the NuA4’s catalytic activity (DOWNS et al. 2004).

1.2.6 Non-histone acetylation targets
Currently there are only a handful non-histone targets known for histone
acetyltransferases. hTip60 acetylates the DNA repair checkpoint protein ATM and p53
(SUN et al. 2005; TANG et al. 2006). This acetylation is essential for activation of ATM
after DNA double strand breaks. Intriguingly hATM and hTip60 form a complex in vivo
and the hTip60 in this complex is distinct from the NuA4 as shown through a co-
immunoprecipitation (SUN et al. 2005). In budding yeast the synthetic lethality of a
Sc∆sas3 Sc∆gcn5 double deletion mutant is thought to be due to the fact they redundantly
acetylate a non-histone target (HOWE et al. 2001). Work in budding yeast identified non-
chromatin targets for the NuA4 complex. Researchers identified targets using a yeast
proteome microarray on a FAST (nitrocellulose) slide. They found 91 proteins that were
acetylated and found that these candidates had gene ontology (GO) terms from
metabolism to cell cycle progression to stress response (LIN et al. 2009). This explains
work done earlier showing the NuA4 complex has genetic interactions with many
19

different cytosolic functional groups (MITCHELL et al. 2008). This was independently
confirmed when investigators identified enzymes in human cells that process cellular
metabolism, such as intermediates in the TCA cycle, urea cycle, fatty acid metabolism to
name a few, that were acetylated (ZHAO et al. 2010). At this time, the lysine
acetyltransferases responsible have not been identified. As technology advances and
proteome arrays become more readily available I expect the number of non-chromatin
targets to increase significantly.

Section III: Summary
Histone acetylation is linked to many chromosome activities including replication,
repair, transcription, and assembly of specialized domains such as centromeres and
telomeres. In this dissertation I characterize roles associated with the essential MYST
family HAT Mst1 in S. pombe. To do that I have completed three distinct projects
characterizing Mst1.
Chapter 2 results from collaborative work I preformed in the initial molecular
characterization of mst1
ts
. I showed mst1 mutant cells have defects in DNA damage
response leading to sensitivity to many different DNA damaging agents. I also
characterized the role Mst1 has in the DNA damage checkpoint response.
Chapter 3 studies the functional redundancies between two major HAT families in
yeast, MYST and GNAT, and is a reprint of Nugent et al BMC Genomics 2010. This
work was done in collaboration with Tony Wright’s lab at the Karolinska Institutet in
Sweden and Chris Seidel’s group at the Stower’s institute. Author contributions are stated
in the beginning of the chapter. We found that MYST and GNAT HATs, specifically
20

Gcn5 and Mst2, overlap in histone lysine specificity and are redundant in response to
DNA damage and transcription. Interestingly, Mst1 does not have a strong
transcriptional fingerprint, consistent with this HAT playing a role in non-transcriptional
activities.
Finally, chapter four introduces a novel role for Mst1 dependent acetylation for
proper kinetochore localization and chromosome segregation.

21

Chapter 2: Characterizing Mst1 in the DNA damage repair and response pathway

2.1 Introduction:
In 2002 exciting work showed ScEsa1 was necessary for viability after exposure
to DNA damaging drugs (BIRD et al. 2002). Later work showed histone acetylation is
correlated with proper repair of DNA damage. Histone H4 and H3 tails are
hyperacetylated at DNA double strand breaks and ScEsa1 and the major Histone H3 HAT
ScGcn5 are recruited specifically to those breaks (TAMBURINI and TYLER 2005). Work
done with the NuA4 complex member Trrap in human cells showed histone acetylation is
essential for allowing repair proteins to gain access to the DNA break (MURR et al.
2005).
At sites of DNA breaks there is the phosphorylation of histone H2A in lower
eukaryotes and in higher eukaryotes the histone variant H2Ax is phosphorylated. Histone
H2A is phosphorylated on Serine 129 in S. pombe by the damage checkpoint proteins
SpRad3 and SpTel1(NAKAMURA et al. 2004). This phosphorylation is important for repair
for DNA damage and also acts as a signal for repair proteins. ScArp4 a budding yeast
member of the NuA4 complex binds phospho-H2A. Not only does that guide the NuA4
to the site of damage to acetylate the region surrounding the break, but the ScArp4
interaction strengthens the enzymatic activity of the catalytic HAT ScEsa1 (DOWNS et al.
2004).
Histone acetylation is not the only role for the KAT5 enzymes in DNA damage
repair. hTip60 has two well known non-histone targets, the tumor suppressing protein
p53 and the DNA damage checkpoint ATM (SUN et al. 2005; SYKES et al. 2006; TANG et
22

al. 2006). The Tip60 dependent acetylation activates ATM, this is essential for ATM to
respond to DNA damage (SUN et al. 2005). In S. pombe, when damage occurs, Rad3
(hATR/M) is activated and this leads to a phosphorylation signal cascade resulting in
halting the cell cycle and repairing the damage. If damage occurs in S phase, Cds1 is
activated, if the damage occurs in G2 then Chk1 is activated. S. pombe does not have a
direct p53 homolog. Chk1 activation is dependent on Rad3 phosphorylation. However,
through a complementary pathway Crb2 is directed to sites of damage through histone
H4 methylation and H2A phosphorylation (DU et al. 2006). These overlapping pathways
(Crb2 is also phosphorylated by Rad3) activate Chk1 and retain it at the site of damage
(reviewed in (GAME and CHERNIKOVA 2009).
Here I characterize the role of the essential MYST family HAT Mst1 in DNA
damage repair and response. By using an isolated temperature sensitive allele (GOMEZ et
al. 2008) I assayed the role Mst1 has in replication restart, DNA damage repair and
chromosome segregation. I examined the role that DNA damage checkpoint proteins and
their activation may have in these phenotypes. I also find that in the absence of Mst1 cells
have higher levels of endogenous DNA damage than wild-type cells. I conclude that
Mst1 is necessary for the proper repair of DNA damage in fission yeast.

2.2 Results
2.2.1 Identification of Mst1 interaction partners by two-hybrid screening
To determine SpMst1 functions, Eliana Gomez performed a yeast 2-hybrid
experiment to identify additional proteins that SpMst1 interacts with. The interacting
gene products are summarized in table 2.1:
23

Table 2.1: Genes isolated by 2-hybrid screening. ß -gal is a qualitative measure of the
degree of activation in the 2-hybrid system.
ß-Gal Gene Function
+ bud6/fat1
+
Actin interacting protein (ScBUD6/AIP3 homolog) (GLYNN et al.
2001)
+ cbh1
+
one of three fission yeast CENP-B proteins. Required for
heterochromatin function. No S. cerevisiae homologue. (BAUM and
CLARKE 2000; NAKAGAWA et al. 2002)
+ hip1
+
HIRA histone chaperone (ScHIR1 homolog) (BLACKWELL et al. 2004)
++ msc1
+
High copy suppressor of ∆chk; E3 ubiquitin ligase and putative
demethylase (AHMED et al. 2004; DUL and WALWORTH 2007) No S.
cerevisiae homologue.
++ rad22
+
homologous recombination protein (ScRAD52 homolog) (OSTERMANN
et al. 1993)
+ res2/pct1
+
Transcription factor, forms a complex with Cdc10 (ScMBP1 homolog)
(MIYAMOTO et al. 1994)
+ sec18
+
putative vesicle membrane fusion protein; uncharacterized ScSec18
homologue. ORF: SPAC1834.11c.
++ skb1
+
arginine methyltransferase (ScHSL7 homolog) (GILBRETH et al. 1996)
++ taf111
+
Transcription factor; putative TFIID subunit required for sexual
development SPAC2G11.14 (UENO et al. 2001)

2.2.2 Validation of 2-hybrid screening
To confirm the yeast 2-hybrid results in vivo, I performed co-
immunoprecipitations between Mst1 and tagged versions of the interacting proteins. I
over-expressed tagged Mst1, either Mst1-HA or Mst1-V5, in the presence and absence of
tagged 2-hybrid targets. I performed soluble immunoprecipitations (IPs) on these cells,
pulling down either Mst1 or the tagged 2-hybrid targets. As seen in Figure 2-1 I found
Mst1 interacted with Rad22-YFP convincingly. SpRad22 (ScRad52) is a homologous
recombination protein (OSTERMANN et al. 1993) that localizes to sites of dsDNA breaks
in vivo (MEISTER et al. 2005).
24

Fig 2.1 Confirmation of yeast two-hybrid results. The western blots above are co-
immunoprecipitations of the identified yeast two-hybrid proteins and Mst1-V5.

When I precipitated Hip1-pk and Cbh1-gfp, using V5 and Gfp respectively, I
found Mst1-HA and Mst1-V5 was also pulled down, although less convincingly. The
presence of a Mst1-tagged band in a wild-type untagged target protein background (non-
specific pull-down) makes these results unclear, this was true with the reverse pulling out
Mst1-HA and looking for Hip1-pk. Hip1 is a HIRA family histone chaperone that
promotes proper chromatin formation and has phenotypes at the centromere (BLACKWELL
Input IP HA
Msc1-HA
Mst1-V5
+
+
+
+
+
-
+
+
+
- +
-
+
- -
-
-
-
anti-HA
anti-V5
Input IP V5
Skb1-HA
Mst1-V5
+
+
+
-
+
+
+
- +
-
+
- -
-
-
-
anti-HA
anti-V5
anti-GFP
anti-V5
Input IP GFP
Rad22-GFP
Mst1-V5
+
+
+
-
+
+
+
- +
-
+
-
-
-
-
-
Input IP V5
Hip1-Pk
Mst1-HA
+
+
+
-
+
+
+
- +
-
+
-
-
-
-
-
anti-HA
anti-V5
Input IP V5
Hip1-Pk
Mst1-HA
+
+
+
-
+
+
+
- +
-
+
-
-
-
-
-
Input IP GFP
Cbh1-GFP
Mst1-V5
+ + + + -
-
- -
+ - + - +
+
- -
25

et al. 2004). Cbh1 is one of two Cenp-B orthologues in S. pombe (NAKAGAWA et al.
2002). In higher eukaryotes Cenp-B is localized to the kinetochore regions of the
centromere and in S pombe Cbh1 recruits heterochromatin proteins to the centromere
(COOKE et al. 1990; NAKAGAWA et al. 2002). There is a strong possibility that Mst1
interacts with these proteins on the chromatin. However, chromatin immunoprecipitations
were not successful due to technical difficulties and therefore it is unconfirmed iff these
proteins interact on chromatin.
Attempts to co-IP Mst1 with Msc1 and Skb1 were negative. Msc1 is a multi-copy
suppressor of Chk1 (AHMED et al. 2004) and is an E3 ubiquitin ligase (DUL and
WALWORTH 2007). It is also a member of the SWR complex, which in budding yeast
works with the NuA4 complex to acetylate and deposit the histone variant H2Az
(KROGAN et al. 2003; SHEVCHENKO et al. 2008). Skb1 is a methyltransferase that is
required for viability after hyperosmotic shock (BAO et al. 2001). However, as discussed
before, it is unclear if the lack of in vivo interaction is due to a transient interaction, an
interaction on the chromatin, or if the yeast two-hybrid gave false positives

2.2.3 Mst1 genetic interactions
In addition to the physical interactions identified in the yeast two hybrid screen
both Eliana Gomez and I found that Mst1 has many genetic interactions. These genes
span the functional groups of DNA replication, DNA damage repair and centromere
heterochromatin formation. For a complete list see table 2.2.

26

Table 2.2: genetic interactions between mst1
ts
and other mutants. Double mutants
were constructed and growth rate relative to the single mutants was assessed by streaking
and/or frogging at different temperatures.
Gene Function double mutant phenotype
DNA replication
mcm2ts
mcm4ts
mcm7ts
orp1ts
pol1ts
hsk1ts
∆rad2

MCM helicase
MCM helicase
MCM helicase
ORC subunit
DNA polymerase a
Cdc7 kinase
FEN endonuclease

reduced permissive temperature
reduced permissive temperature
reduced permissive temperature
reduced permissive temperature
reduced permissive temperature
reduced permissive temperature
no effect
DSB repair
∆rad32
∆rad50
∆rhp51
∆rqh1
∆rti1

MRE11
RAD50
RAD51
SGS1/Blm helicase
Rad52 homologue

no effect
reduced permissive temperature
reduced permissive temperature
no effect
no effect
Chromatin
∆cbh1
∆clr3
∆clr4
∆hip1
∆msc1
∆mst2
∆swi6
∆pht1

CENP-B homologue
histone deacetylase
histone methyltransferase
HIRA homologue
putative demethylase
MYST acetyltransferase
HP1 homologue
Histone variant

no effect
reduced permissive temperature
reduced permissive temperature
no effect
no effect
no effect
reduced permissive temperature
no effect
Other
∆skb1
∆taz1

arginine methyltransferase
telomere binding protein

no effect
no effect

As seen in Figure 2.2 the synthetic phenotype is seen as a reduction in viability at a
previously permissive temperature for the double mutants versus the single mutant
parents. While most mst1
ts
interactions were with genes involved in DNA replication,
there were also interactions with genes necessary for proper centromere formation and
DNA double strand break repair.
27

Figure 2.2: mst1
ts
genetic interactions. Double mutants were constructed and serial
dilutions were performed at different temperatures to characterize any synthetic
interactions. Equivalent numbers of exponentially growing cells were diluted fivefold and
incubated at the indicated temperatures (GOMEZ et al. 2008).

2.2.4 Mst1 damage sensitivities
Mst1 homologs in yeast and humans are required for proper DNA damage
response (BIRD et al. 2002; IKURA et al. 2000). This combined with the yeast two hybrid
interactions prompted me to next look at the role of Mst1 in the DNA damage response
25°C 28°C 32°C 36°C
WT
mst1ts
hsk1ts
mst1ts hsk1ts
rhp51
mst1ts rhp51
WT
mst1ts
orp1ts
mst1ts orp1ts
pol1ts
mst1ts pol1ts
WT
mst1ts
swi6
mst1ts swi6
WT
mst1ts
clr3
mst1ts clr3
clr4
mst1ts clr4
mcm2ts
mst1ts mcm2ts
A
B
C
D
28

pathway. Using the temperature sensitive allele isolated using a homologous mutation
from budding yeast (CLARKE et al. 1999; GOMEZ et al. 2008), Eliana found and I later
confirmed that mst1 mutants were sensitive to an array of DNA damaging agents (Figure
2-3). mst1 mutant cells are sensitive to hydroxyurea, which causes replication fork
stalling, MMS, an alkylating agent that causes DNA double strand breaks, and are
slightly sensitive to camptothecin (CPT), which causes double strand breaks in S phase.
mst1 mutant cells were also highly sensitive to thiabendazole (TBZ), a spindle pole
poison that disrupts chromosome segregation.

Figure 2.3: Damage sensitivity of mst1-L344S. (A) mst1 sensitivity relative to DNA-
damaging agents. Exponentially growing cells were diluted fivefold on YES plates with
the indicated drugs and grown 4 days at 29°. (B) mst1 is sensitive to thibendazole.
Exponentially growing cells were diluted fivefold on YES plates and grown 3 days at
32°. (C) mst1 ∆cds1 is sensitive to MMS. Exponentially growing cells were diluted
fivefold on YES and YES with indicated drug plates and grown 3 days at 32°

Eliana made double mutants of mst1
ts
∆cds1 and mst1
ts
∆chk1. I used those mutants
to ask if the sensitivity mst1 mutants exhibit to DNA damaging agents reflected a role of
Mst1 in the DNA damage checkpoint pathway. The double mutants grew normally and
there were no synthetic phenotypes during asynchronous growth. I next tested viability
on chronic exposure to drugs causing damage. Per previously published results ∆cds1
29

mutants were highly sensitive to hydroxyurea and ∆chk1 mutants were sensitive to MMS
(FRANCESCONI et al. 1997; LINDSAY et al. 1998). When I assayed the mst1
ts
∆chk1
mutants they were similar in sensitivities to either single mutant parent. Unexpectedly
though I found that mst1∆cds1 cells were very sensitive to MMS, more so than either
single mutant alone (Figure 2.3). This indicates that Mst1 may function in the Chk1 arm
of the DNA damage response pathway.

2.2.5 DNA damage checkpoint activation
After observing the mst1∆cds1 MMS phenotype, I then asked if the checkpoint
was activated during acute damage. I monitored activation of the damage checkpoint by
observing phosphorylation –dependent mobility shift of Chk1 HA in SDS-PAGE
followed by western blot. Previous work showed that activated Chk1 runs as a doublet on
a SDS-PAGE gel. (PANKRATZ and FORSBURG 2005), I exposed wild-type and mst1
ts
cells
to MMS for 45 minutes then assayed for Chk1 activation. I found that in wild-type cells
Chk1-HA does indeed show a mobility shift as seen in the slower moving upper band
(Figure 2-4). However in multiple isolates of mst1
ts
Chk1-HA strains, there is no upper
band. There is, however, a faster moving unidentified band below the Chk1-HA
unmodified band: at this time, the nature of this band is unknown. Therefore I conclude
Chk1 phosphorylation after exposure to MMS in a mst1
ts
background is impaired.
30

Figure 2.4 Mst1 is necessary for proper checkpoint activation. A. Chk1 activation
after 4 hrs exposure to MMS at 32°. B. Cds1 activation after exposure to HU at the
indicated times.

We next asked if Cds1 activation was impaired in the absence of Mst1. Cds1-HA is
activated through phosphorylation which translates as an upwards smear on an SDS-page
gel. We added hydroxyurea and harvested cells at 0, 15 minutes, 30 minutes, 1 hr and 2
hrs. In WT cells there is an obvious upwards smear starting at 30 minutes. However in
mst1
ts
cells the kinetics are delayed, with the shift occurring at 1 hr. I conclude that the
Cds1 checkpoint is activated in the absence of Mst1 but with a delay in timing.

2.2.6 Loss of Mst1 leads to endogenous damage
The sensitivity of mst1 mutant cells to DNA damaging agents led me to ask
whether there was endogenous damage in the absence of Mst1. If Mst1 is necessary to
Chk1-HA
Mst1
+ + + + + +
+ + + +
- -
MMS + + + + - - - -
anti-HA
anti-PCNA
Cds1-HA
anti-HA
mst1
ts
+ + + + - - - - + -
Hrs in HU 0.25 0.5 1 2 0 0.25 0.5 1 2 0
A
B
ts ts ts ts
31

repair breaks in the presence of induced damage, I hypothesized that there must be more
damage in the absence of Mst1. To determine this I localized the homologous
recombination protein Rad22 (ScRad52). Rad22 localizes to sites of breaks within the
cell and when fluorescently tagged it marks sites of damage in vivo (MEISTER et al.
2005). We were unable to follow Rad22-YFP in living cells in mst1 mutants due to
background fluorescence. Therefore I used indirect immunofluorescence on nuclear
spreads. I observed a modest increase in Rad22 focus formation in mst1
ts
cells without
HU treatment, relative to wild type cells (figure 2.5). Rad22 focus formation increased in
mst1
ts
cells when they

were grown overnight at the semi-permissive temperature. This
suggests that the cells suffer some amount of endogenous damage in the absence of Mst1.
During acute HU treatment, ∆cds1 cells show a dramatic increase in Rad22 YFP focus
formation replication fork collapse and double strand breaks (MEISTER et al. 2005).
There is no change in the Rad22YFP foci in mst1
ts
, indicating that replication forks are
intact, this is consistent with viability assays showing mst1
ts
cells can survive an acute
exposure of HU, unlike cds1 mutants.
32

Figure 2.5 Rad22YFP foci. Rad22YFP foci were measurend in wild-type, cds1, or
mst1 cells after 2 hr in HU. Rad22YFP was detected by immunofluorescence with anti-
GFP antibody, which recognizes the YFP variant. (F) Fraction of cells with Rad22YFP
foci at 0 or 2 hr of incubation in HU. -, negative control with no Rad22YFP. Strains: wild
type (FY261), wild type with Rad22YFP (3436), mst1 Rad22YFP (3369), ∆cds1
Rad22YFP (3286). (GOMEZ et al. 2008)

2.3 Discussion
Histone acetylation is necessary for repair of DNA damage (TAMBURINI and
TYLER 2005). KAT5 enzymes, hTip60 and ScEsa1 are necessary for proper DNA damage
repair (BIRD et al. 2002; MURR et al. 2005; SQUATRITO et al. 2006). Therefore, we
hypothesized that Mst1 in S. pombe would also play a role in DNA damage repair.
Eliana Gomez and I found that Mst1 physically and genetically interacted with a
broad range of proteins and genes. This suggests that Mst1 has many different functions
within the cell. Supporting this, we found that mst1
ts
cells arrested in all stages of the cell
cycle with many different physiological phenotypes (GOMEZ et al. 2008).
32!

Figure 2.5 Rad22YFP foci. Rad22YFP foci were measurend in wild-type, cds1, or
mst1 cells after 2 hr in HU. Rad22YFP was detected by immunofluorescence with anti-
GFP antibody, which recognizes the YFP variant. (F) Fraction of cells with Rad22YFP
foci at 0 or 2 hr of incubation in HU. -, negative control with no Rad22YFP. Strains: wild
type (FY261), wild type with Rad22YFP (3436), mst1 Rad22YFP (3369), !cds1
Rad22YFP (3286). (GOMEZ et al. 2008)

2.3 Discussion
Histone acetylation is necessary for repair of DNA damage (TAMBURINI and
TYLER 2005). KAT5 enzymes, hTip60 and ScEsa1 are necessary for proper DNA damage
repair (BIRD et al. 2002; MURR et al. 2005; SQUATRITO et al. 2006). Therefore, we
hypothesized that Mst1 in S. pombe would also play a role in DNA damage repair.
Eliana Gomez and I found that Mst1 physically and genetically interacted with a
broad range of proteins and genes. This suggests that Mst1 has many different functions
within the cell. Supporting this, we found that mst1
ts
cells arrested in all stages of the cell
cycle with many different physiological phenotypes (GOMEZ et al. 2008).
33

Mst1 interacts with many different functional groups of genes and proteins. We
did not isolate any NuA4 complex members with our yeast two-hybrid experiment, which
was surprising as Mst1 is the catalytic HAT of this complex (SHEVCHENKO et al. 2008).
Given however that a yeast-two hybrid isolates proteins that directly interact, and that the
NuA4 is held together by direct and indirect interactions this result is not unexpected
(MITCHELL et al. 2008; YOUNG 1998).
Through our identified interactions, we speculate that Mst1 functions in DNA
replication and DNA damage repair, and is necessary for proper chromosome
segregation. We found that Mst1 physically interacts with Msc1, a component of the
Swr1 remodeling complex. In fission yeast, overexpression of Msc1 on a plasmid rescues
a cnp1
ts
mutants. Msc1 is also necessary for chromosome stability (AHMED et al. 2007).
In budding yeast, and more recently in S. pombe, it was shown the NuA4 and Swr1
complexes work together to acetylate and deposit the H2A.Z histone variant (SpPht1)
into the genome (KIM et al. 2009; KROGAN et al. 2004). Our inability to successfully IP
Mst1 and Msc1 was independently confirmed (KIM et al. 2009). This reflects either a
transient interaction or an interaction that occurs on the chromosome. A confirmed
physical interaction with the homologous recombination protein Rad22 (scRad52) leads
to speculation of the nature of this interaction. It could be that Mst1 acetylates Rad22
activating it after DNA damage, much like hTip60 and hATM in human cells (SUN et al.
2005). Since we found that Rad22 localized properly in the absence of Mst1 through
nuclear spreads we conclude that Mst1 is not the sole factor to localize Rad22 to double
strand breaks in vivo.
34

Mst1 mutants are sensitive to a variety of DNA damaging drugs: HU, MMS and
to a lesser extent to CPT. Given that Mst1 physically interacts with Mcm2 when
overexpressed (GOMEZ et al. 2008) and genetically interacts with many different genes
needed for replication, it comes as no surprise that mst1 mutants are HU sensitive. Mst1
homolog Hbo1 interacts with many different replication proteins in higher eukaryotes
(BURKE et al. 2001; IIZUKA et al. 2006; IIZUKA and STILLMAN 1999) showing a
conservation of MYST family replication function in S. pombe. However the role Mst1
plays during replication is unknown. In the presence of HU, mst1
ts
mutant cells did not
exhibit the same levels of Rad22 (scRad52) focus formation as mutants necessary for
replication fork protection so we speculate that the role of Mst1 is not to protect the
replication fork (MEISTER et al. 2005; NOGUCHI et al. 2003).
Histone acetylation, in general, is necessary for proper DNA damage repair
(MURR et al. 2005; TAMBURINI and TYLER 2005). ScEsa1, the budding yeast homolog to
Mst1, is necessary for double strand break repair (BIRD et al. 2002). Therefore we asked
if mst1
ts
was sensitive to drugs that produce DNA double strand breaks. We found that
mst1 mutants were indeed sensitive to these drugs, suggesting Mst1 is necessary for
either repair or recovery from DNA damage. However whether this is due to a function
independent of acetylation of flanking regions is unknown, although doubtful.
The sensitivity mst1 mutants exhibit led us to ask if Mst1 is active in either arm of
the DNA damage checkpoint response. Thus, I assayed growth of mst1
ts
and checkpoint
gene deletion mutants on different drug plates. I found that mst1
ts
∆cds1 mutants were
more sensitive to MMS than either single parent. This indicates that Mst1 functions in the
Chk1 arm of the damage response. When I assayed checkpoint activation I found that
35

Chk1 was not phosphorylated, as seen in a gel shift assay, in the absence of Mst1, even in
the presence of damage. Therefore, I conclude that Mst1 is necessary for Chk1 activation.
It is well established that the human ortholog of Mst1 hTip60 functions in activating the
DNA damage checkpoint protein ATM (SUN et al. 2005), therefore it is not unexpected
that Mst1 may also have a role in the DNA damage checkpoint.
This leads to the obvious question: Is Rad3 activated in mst1 mutant cells?
Comparing the level of sensitivity of mst1 and ∆rad3 mutant cells, I speculate that Rad3
is activated, as mst1 mutant cells are much less sensitive to drugs than ∆rad3. Previous
work showed that the downstream checkpoint protein Chk1 is activated, recruited and
retained at double strand breaks through Rad3 phosphorylation, and also independently
through the retention of Crb2 at the sites of breaks (DU et al. 2006). Crb2 gives an
interesting study on the interplay between histone modifications and damage repair. The
initial recruitment of Crb2 to breaks appears to be dependent on H2A phosphorylation,
however, it is retained at breaks by checkpoint proteins (DU et al. 2003; DU et al. 2006).
We have direct evidence that in the absence of Mst1 Chk1 is not properly phosphorylated
(Fig 2-3), more directed experiments are necessary to determine if this is due to histone
acetylation by Mst1 or by acetylation of non-histone targets such as Rad3 or Chk1 itself.
The results presented here indicate that Mst1 may function in DNA replication,
DNA damage repair and chromosome segregation. Further work will follow to dissect the
specific roles in chromosome segregation and DNA damage repair.

36

2.4 Materials and Methods:
2.4.1 Strains, media, and manipulations. Strains and plasmids used in this study are
listed in Table 2.3.

Table 2.3: Strains used in chapter 2
Strain Genotype Source
11 h- ade6-M210 our stock
261 h- ura4-D18 leu1-32 ade6-M210 can1-1 our stock
748 h- orp1-4 ura4-D18 leu1-32 ade6-M210 can1-1 our stock
786 h- cdc21-M68 ura4-D18 leu1-32 ade6-M216 (can1?) our stock
865 h- ∆cds1::ura4 ura4D-18 leu1-32 our stock
945 h- hsk1-1312 ura4-D18 leu1-32 ade6-M210 our stock
1104 h- ∆rad3::ura4 ura4 leu1-32 ade6M210(?) our stock
1109 h- pol1-1 ura4-D18 leu1-32 ade6-M 216 our stock
1754 h+/h- ∆mst1::ura4+/+ ura4-D18/ura4-D18 leu1-32/leu1-32 ade6-
M216/ade6-M210
(Gómez et al.
2005)
2056 h- ∆swi6::ura4+ leu1-32 ura4-(DS/E or D18?) ade6-M210 our stock
2180 h+ cbh1::GFP-pBSIIKS-ura4+-chh1C leu1-32 ura4-D18 our stock
2215 h- ∆clr3::kanMX6 ade6-M210 ura4-D18 leu1-32 k. ekwall
2224 h+ ∆clr4::ura4+ ade6-210 leu1-32 ura4-D18 otr1R(SphI)::ade6+ R. allshire
2449 h+ ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18 ade6-M210 this study
2339 h+ ∆mst1::ura4+ leu1::nmt-mst1L-S leu1+ ura4-D18 ade6-M216 (#7) this study
2396 h- ∆mst1::ura4+ leu1::nmt-mst1L-S leu1+ ura4-D18 ade6-M210 this study
2450 h- ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18 ade6-M210 this study
2495 h+∆taz1::ura4+ ∆mst1::kanMX6 leu1::nmt-mst1L-S leu1+ura4-D18 leu1-
32 ade6-M210
this study
2497 h- ∆rhp51::ura4+ ∆mst1::kanMX6 leu1::nmt-mst1L-S leu1+ura4-D18
leu1-32 ade6-M210
this study
2498 h- ∆rhp51::ura4+ ∆mst1::kanMX6 leu1::nmt-mst1L-S leu1+ura4-D18
leu1-32 ade6-M210
this study
2499 h+ ∆rad50::kanMX6 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ura4-D18
leu1-32 ade6-M21?
this study
2501 h+ ∆rad32::ura4+ mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18
leu1-32 ade6-M21?
this study
2505 h+ mst2::ura4+ mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18 leu1-
32 ade6-M210
this study
2506 h- mst2::ura4+ mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18 leu1-32
ade6-M210
this study
2507 h- swi6::ura4+ mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18 leu1-32
ade6-M210
this study
Table 2.3:Continued 37

2508 h+ swi6::ura4+ mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18 leu1-
32 ade6-M210
this study
2525 h- hsk1-1312 mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ leu1-32 ade6-M21? this study
2562 h+ ∆rad12::ura4+ ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ade6-M210
ura4-D18
this study
2566 h- ∆clr4::ura4+ ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ade6-M210
ura4-D18 (otrR(SphI)::ade6+) ?
this study
2568 h- orp1-4 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ ade6-M210 ura4-D18
(can1-1)?
this study
2569 h+ orp1-4 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ ade6-M210 ura4-D18
(can1-1)?
this study
2570 h+ ∆clr3::kanMX6 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ ade6-M210
ura4-D18 (can1-1)?
this study
2572 h+ mcm7-98 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ ade6-M216 ura4-
D18 (can1-1)?
this study
2574 h+ cdc19-P1 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ ade6-M210 ura4-
D18
this study
2576 h+ pol1-1 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ ade6-M210 ura4-D18 this study
2578 h+ cdc21-M68 ∆mst1::ura4+ leu1::nmt-mst1L-S-leu1+ ade6-M216 ura4-
D18 (can1-1)?
this study
2601 h+ ∆skb1::ura4+ mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18 ade6-
M210
this study
2649 h- smt0 ∆rad22::(hisG ura4+ hisG) mst1::kanMX6 leu1::nmt-mst1L-S-
leu1+ ura4-D18 ade6
this study
3286 h+ ∆cds1::ura4+ rad22YFP::KanMX6 ura4-D18 leu1-32 ade6? this study
3369 h+∆mst1::ura4+ leu1::nmt-mst1L-S leu1+ ura4-D18 ade6-M21?
rad22:YFP:kanMX4
this study
3436 h+ rad22:YFP:kanMX4 ade6-M210 ura4-D18 leu1-32 this study
2244
h- cds1-HA::ura4+ ura4-D18 his3-D1 leu1-32 ade6-M216
this study
3320
h? cds1-HA::ura4+ mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ade6-M210
this study
4487 h? chk1-HA(ep ) ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ade6-M210
ura4-D18
this study
1176 chk1-HA(ep) ade6 leu1-32 this study
2645 h+ ∆cds1::ura4+ ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ura4-D18
(ade6-M210 ?)
this study
2192
h- Δchk1::ura4+ ura4-D18 ade6-M216
this study

Strains were grown and maintained on yeast extract plus supplements (YES) or
Edinburgh minimal media (EMM) with appropriate supplements, using standard
techniques (FORSBURG and RHIND 2006). Matings were performed on synthetic
sporulation agar (SPAS) plates for 2-3 days at 25ºC. Temperature sensitive cells were
grown at 25ºC and non ts cells at 32°C. Transformations were carried out by
38

electroporation . Double mutants were constructed by standard tetrad analysis or random
spore analysis. G418 plates were YES supplemented with 100 µg/ml G418 (Sigma).

2.4.2 2 hybrid mst1+ was isolated by PCR from plasmid pEBG72 with primers HAT-3
sequence forward: AGATCTCGCCAAAAACTTGCTCAATCTTCTTCC and HAT-3
reverse: GGTACCCGACATAGACTGGCACATTACATCC and cloned into the 2-
hybrid vector pDBLeu cleaved with NcoI and NotI to create plasmid pEBG91. Budding
yeast two-hybrid strain AH109 (Clontech) with HIS3, ADE2, and lacZ reporters
downstream of heterologous GAL4-responsive promoter elements was transformed with
and an S. pombe Matchmaker cDNA library (Clontech) and screened as described
(LEVERSON et al. 2002). Positive isolates were identified by sequence and verified by
retransformation.

2.4.3 Microscopy Whole fixed cells were stained as described for DAPI and Calcofluor
(GÓMEZ and FORSBURG 2003). Cells were visualized with a Leica DMR microscope.
Objectives used were Leica 100X/1.30, PLFL, NA=1.30, and Leica 63X/1.32, PLApo,
NA=1.32. Images were captured with a Hamamatsu digital camera and Improvision
Openlab software (Improvision, Lexington, MA). Images were assembled using Canvas
(ACD/Deneba) and adjusted for contrast. Nuclear spreads were performed as in
(PANKRATZ and FORSBURG 2005) with the following modifications. Rad22yfp was
detected using Abcam 290-50 rabbit anti-gfp, 1:2000 in 5% BSA (Sigma) and secondary
donkey anti-rabbit cy3 1:500 DNA was stained with 1X Hoechst (Invitrogen). Objective
39

used was Leica 63X/1.32, PLApo, NA=1.32. Images were captured and assembled as
above.

2.4.4 Damage assays Cells were grown to A
595
=1, serially diluted five-fold and spotted
onto YES plates or YES plates containing 10 µg/ml thiabendazole (TBZ), 5 mM
hydroxyurea (HU) or 0.005%, 0.007% and 0.01% methyl methanesulfonate (MMS), and
incubated for 3-5 days at 25ºC, 29°C or 32ºC, as indicated.

2.4.5 Immunoprecipitations For co-immunoprecipitation we prepared soluble protein
lysates from fission

yeast cells in B88 buffer as in (MORENO et al. 1991). A total

of 1.0
mg protein was used per immunoprecipitation. Lysates

were precleared with sepharose A
beads (Repligen) for 1 hr.

For Cbh1-GFP and Rad22-YFP one microliter of anti-GFP
(Abcam 290), Hip1-pk and Mst1-V5 one microliter of anti-V5 (invitrogen) was left to

rotate overnight at 4°. Proteins were analyzed by 8% SDS–PAGE,

followed by
immunoblotting with anti-V5 (Invitrogen) at 1:2500

dilution, anti-GFP (living colors,
Clontech) at a 1:1000

dilution or anti-HA (16B12 Covance) at 1:1500 dilution.
Crosslinking immunoprecipitations were done as previously

described (AUGER et al.
2008). Briefly, cells were crosslinked

with 1% formaldehyde (Sigma) for 50 min on ice.
Harvested cells

were vortexed with glass beads in IP buffer (50 mM HEPES–KOH,

pH
1.6, 500 mM NaCL, 1 mM EDTA, 1% Triton X-100, 0.1% sodium

deoxycholate).
Extracts were treated with DNase I to reverse

crosslink. A total of 1.0 mg protein was
used per immunoprecipitation.

Whole-cell extracts and immunoprecipitates were
incubated with

SDS sample buffer for 1 hr at 90° before Western blot analysis.
40

2.4.6 Protein extraction and western blotting analysis. MMS damage assayed by
western blots, cells were grown at 32ºC overnight and 0.1% MMS was added for 45
minutes and protein was harvested via TCA (PANKRATZ and FORSBURG 2005). Proteins
were separated as previously described (PANKRATZ and FORSBURG 2005) and probed
with 1:1500 anti-HA (16B12 Covance) and 1:1500 PCNA for 1.5 hours room
temperature and secondary anti-mouse:HRP 1:1500 was stained for 45 minutes room
temperature. For HU damage assayed by western blots, cells were grown at 30ºC
overnight. At time zero 15mM HU was added to cultures and at indicated times 20mL of
cells were harvested for protein extraction by TCA. Proteins were separated on a 10%
SDS-PAGE gel, followed by immunoblotting wtih 1:1500 anti-HA (16B12 Covance)
overnight at 4°C and secondary anti-mouse:HRP for 45 minutes room temperature.

41

Chapter 3: Expression profiling of S. pombe acetyltransferase mutants identifies
redundant pathways of gene regulation

Reproduced from Rebecca L Nugent
1*
, Anna Johnsson
2*
, Brian Fleharty
3
, Madelaine
Gogol
3
, Yongtao Xue-Franzén
2
, Chris Seidel
3
, Anthony PH Wright
2
and Susan L
Forsburg
1
. BMC Genomics. 2010 Jan 22;11:59.

3.1 Overview: Background: Histone acetyltransferase enzymes (HATs) are implicated
in regulation of transcription. HATs from different families may overlap in target and
substrate specificity. Results: We isolated the elp3
+
gene encoding the histone
acetyltransferase subunit of the Elongator complex in fission yeast and characterized the
phenotype of an ∆elp3 mutant. We examined genetic interactions between ∆elp3 and two
other HAT mutants, ∆mst2 and ∆gcn5 and used whole genome microarray analysis to
analyze their effects on gene expression. Conclusions: Comparison of phenotypes and
expression profiles in single, double and triple mutants indicate that these HAT enzymes
have overlapping functions. Consistent with this, overlapping specificity in histone H3
acetylation is observed. However, there is no evidence for overlap with another HAT
enzyme, encoded by the essential mst1
+
gene.

3.2 Background:
Chromatin is modulated in part by the pattern of different histone modifications,
leading to the speculation that a “histone code” provides epigenetic information that
facilitates chromosome activities (JENUWEIN and ALLIS 2001; KOUZARIDES 2007). Not
42

surprisingly, the enzymes that modify chromatin have diverse roles in the cell that affect
multiple DNA-dependent events. Acetylation was the first histone modification
identified, and is associated with a variety of chromatin functions (KOUZARIDES 2007;
LEE and WORKMAN 2007). While some evidence suggests that acetylation changes
association of DNA with the underlying nucleosomes (SHOGREN-KNAAK et al. 2006), it
also creates specific binding sites for proteins involved in a variety of DNA transactions
(KOUZARIDES 2007; LEE and WORKMAN 2007). Acetylation has long been linked to
transcriptional activation, so that the histone acetyltransferase enzymes function generally
as transcriptional activators (BERGER 2002).
Histone acetyltransferases are well conserved in eukaryotes and can be separated
into multiple gene families based on primary sequence. The MYST family of histone
acetyltransferases was named for founding members identified in yeast and humans,
MOZ, YBF2/SAS3, SAS2 and TIP60 (PILLUS 2008). Most species contain multiple
members of this family. The Kat5 group, the most conserved family members, includes
SpMst1 (S. pombe), ScEsa1 (S. cerevisiae) and hTip60 (human), which acetylates
residues in the tails of histones H2A and H4 (ALLIS et al. 2007). These proteins are the
catalytic HATs for the NuA4 complex in their respective organisms (SAPOUNTZI et al.
2006; SHEVCHENKO et al. 2008). In the yeasts the Kat5 orthologues are the only MYST
family HATs that are essential for viability (CLARKE et al. 1999; GOMEZ et al. 2005).
In budding yeast there are two other MYST family members, ScSas2 and ScSas3,
which were originally isolated with defects in silencing the mating locus (EHRENHOFER-
MURRAY et al. 1997; REIFSNYDER et al. 1996). ScSas2 is the catalytic HAT for the
budding yeast SAS complex that acetylates H4K16 (CARROZZA et al. 2003). It
43

antagonizes the histone deacetylase Sir2 (SUKA et al. 2002). ScSas3 is the catalytic HAT
for the NuA3 complex in budding yeast (JOHN et al. 2000) which specifically acetylates
histone H3 (EBERHARTER et al. 1998). In S. pombe by contrast there is only one
additional MYST family member, SpMst2 (GOMEZ et al. 2005). Mst2 shows sequence
similarity to both ScSas2 and ScSas3. However, its biological function, in which it
antagonizes SpSir2 in telomere silencing, suggests that it is a functional homologue of
ScSas2 (GOMEZ et al. 2005).
Another conserved family of HATs is the Gcn5-related N-acetyltransferase
(GNAT) super-family consisting of Gcn5, Elp3, Hat1 and Hpa2, with Gcn5 (KAT2) and
Elp3 (KAT9) as the most studied members (STERNER and BERGER 2000). The
evolutionarily conserved Gcn5 is the catalytic subunit of several multi-subunit complexes
including the SAGA co-activator complex (BAKER and GRANT 2007). Gcn5 acetylates
multiple lysine residues of histones H3 and H2B and mediates both targeted and non-
targeted (global) acetylation (VOGELAUER et al. 2000). In S. cerevisiae, SAGA is
recruited to promoter regions by transcription factors like ScGal4 and ScGcn4.
Elongating RNA Pol II is associated with the Elongator complex that contains ScElp3
and has been shown to acetylate H3K14 and H4K8 in budding yeast (WINKLER et al.
2002). Elp3 is highly conserved in structure and function between human and budding
yeast (LI et al. 2005).
While neither ScGCN5 nor ScELP3 is essential in budding yeast, a double
mutation in ∆gcn5 ∆elp3 double mutant is significantly sicker than either single mutant
(WITTSCHIEBEN et al. 2000), resulting in hypoacetylation of histone H3 in gene coding
regions (KRISTJUHAN et al. 2002) and spreading of ScSir3 into sub-telomeric DNA
44

(KRISTJUHAN et al. 2003). Data from budding yeast suggest that ScGcn5 also overlaps
with ScSas3, because a double deletion ∆gcn5 ∆sas3 is lethal (HOWE et al. 2001). This
suggests that there are shared functions or targets of the NuA3, SAGA, and Elongator
complexes in budding yeast, which implies that different HAT families may perform the
same modifications. However, because the complement of HATs is somewhat different
in S. pombe, it is not clear how general this overlap may be. SpGcn5 has been previously
characterized for its effects on gene expression (HELMLINGER et al. 2008; JOHNSSON et
al. 2006) and for chromatin binding genome-wide (ROBERT et al. 2004). Surprisingly,
relatively little change in gene expression profile is observed in gcn5 mutants despite a
very high association with the chromatin. This suggests that SpGcn5 overlaps with other
HATs.
Here, we examine evidence for redundancy between HAT enzymes in S. pombe.
We report the initial characterization of fission yeast elp3
+
and examine phenotypes
associated with single, double, and triple mutations of ∆mst2, ∆gcn5 and ∆elp3. We
show that these enzymes affect expression of overlapping but non-identical sets of genes,
suggesting overlapping contributions to gene expression. Consistent with this, we
observe biochemical evidence that these proteins share common histone substrates. We
also observe that these phenotypes are distinct from the gene expression effects of a
temperature sensitive allele of mst1, and suggest that multiple histone targets regulate
gene activation in fission yeast.

45

3.3 Results
3.3.1 Characterization of ∆elp3 and interaction with other HAT mutants. In order to
compare the roles of different histone acetyltransferases on transcription in fission yeast,
we first characterized the disruption of the histone acetyltransferase gene elp3
+
, the likely
orthologue of the ScELP3 subunit of Elongator complex (WINKLER et al. 2002). We
found that S. pombe elp3
+
is a non-essential gene, as is its budding yeast orthologue
(WITTSCHIEBEN et al. 1999). However, ∆elp3 mutant cells have elongated morphology
compared to wild type, indicative of cell cycle delay (Fig3.1A). The mean length of
mononucleate cells is 6.7µm in wild type, and 10.7 µm in ∆elp3. For binucleate cells,
wild type averages 9.8 µm compared to 15.9µm in ∆elp3. Thus ∆elp3 is approximately
60% larger than wild type. Also as in budding yeast (WITTSCHIEBEN et al. 1999), fission
yeast ∆elp3 grows slowly due to a prolonged lag phase (Fig3.1B). Although the growth
rate of ∆elp3 cells once they have reached exponential phase is similar to wild type, they
appear to enter stationary phase at a lower cell density. Given the presumed role of Elp3
as part of the Elongator complex, we presume that this reflects defects in one or more
growth-associated transcription program

46

Figure 3.1: Characterization of mutant phenotypes A: ∆elp3 morphology. Wild-type
(FY368) and ∆elp3 (FY3851) cells were asynchronously grown at 32°C in YES. Cells
were fixed and stained with DAPI. The scale bar represents 10 microns. B: ∆elp3
mutants have a growth lag. Representative growth curves for wild type (triangle)
(FY368) and ∆elp3 (circle) (FY3851) cells in rich media (YES) at 30°C. The x-axis time
scale indicates hours after inoculation that stared at a cell concentration of 4x10
5
cells/ml.
The y-axis indicates number of cells/ml. C: Comparison of growth rates on YES at
different temperatures and with different levels of salt. Cells were grown to exponential
phase, serially diluted 5x and compared for growth on rich media after 2 or 3 days at
30°C.and 36°C, or onYES supplemented with indicated salt and grown for 2 to 4 days at
30°C. Strain list: wild-type (FY368), ∆elp3(FY3851), ∆mst2 (FY1890), ∆gcn5
∆mst2(Hu990), ∆gcn5 ∆elp3 (FY3847), ∆mst2 ∆elp3 (FY3850), ∆gcn5 ∆elp3 ∆mst2
(3854) D: Comparison of drug sensitivity. Exponentially growing cells were diluted 5-
fold on YES plates with the indicated drugs and grown 2-3 days at 32°C. Strain list: wild-
type (FY261), ∆swi6 (FY1584), ∆rad3 (FY1104), ∆elp3 (FY 3851), ∆gcn5 (FY2943),
∆mst2 (FY1890), ∆gcn5 ∆elp3 (FY3847), ∆gcn5 ∆mst2(FY3361), ∆mst2 ∆elp3
(FY3850), ∆gcn5 ∆elp3 ∆mst2 (3854).

47

We examined other phenotypes associated with ∆elp3, and compared them to
phenotypes associated with mutations in other non-essential histone acetyltransferases,
∆mst2 and ∆gcn5. We observed that ∆elp3 has poor growth overall compared to either
∆gcn5 or ∆mst2 (Fig3.1C). Both ∆gcn5 and ∆elp3 showed slight temperature sensitivity.
As reported previously (JOHNSSON et al. 2006), ∆gcn5 is sensitive to salts (KCl or
CaCl
2
),

but we observed no overlap in this phenotype with ∆mst2 or ∆elp3. We also
assayed the sensitivities of these HAT mutants to different DNA damaging agents
(Fig3.1D), since histone acetylation is necessary for proper repair from DNA damage
(TAMBURINI and TYLER 2005). The ∆mst2 mutants are sensitive to hydroxyurea, which
depletes nucleotides and results in replication fork stalling, and to high doses of the DNA
alkylating agent MMS, which causes DNA damage (GOMEZ et al. 2005). We observed
that ∆gcn5 and ∆mst2 show similar sensitivity to hydroxyurea. Consistent with our
previous results, ∆mst2 is modestly sensitive to low levels of MMS, but we observed no
sensitivity in ∆gcn5 or ∆elp3. We also observed no sensitivity to the topoisomerase
inhibitor camptothecin (which causes S phase specific DNA breaks) or UV irradiation.
∆mst2 is also sensitive to the microtubule poison thiabendazole (TBZ), a phenotype
typical of mutations that affect centromere function or chromosome segregation.
We next constructed double and triple mutants to see whether there was evidence
for epistasis or synthetic growth defects under these conditions. All combinations were
viable, although the triple mutant ∆gcn5 ∆elp3 ∆mst2 was very slow-growing. The slow-
growth phenotype of the triple mutant strain made it difficult to distinguish pathway
specific effects from general sickness in this strain.
48

Previously, we assigned Mst2 as the likely ScSas2 orthologue, based on the
similarity of their phenotypes, although it is also phylogenetically related to ScSas3. In
budding yeast ∆sas3 ∆gcn5 is lethal (HOWE et al. 2001), but in fission yeast ∆mst2 ∆gcn5
is viable. We assayed growth at 30° and 36° C for the single and double mutants. At
30°C, there was little effect observed. At 36°C, the ∆gcn5 ∆mst2 mutant displays a
temperature sensitivity resembling ∆gcn5, indicating that there is no overlap between
Gcn5 and Mst2 with regards to heat stress. The ∆gcn5 ∆elp3 mutant, however, shows
increased temperature sensitivity compared to the single mutant strains. The ∆mst2 ∆elp3
mutant displayed a phenotype intermediate between the parents, suggesting that the faster
growth associated with ∆mst2 in relation to wild type is also able to overcome the slow
growth associated with ∆elp3 (Fig3.1C).
We examined the salt sensitivity of the double mutants, because ∆gcn5 has been
associated with this phenotype (JOHNSSON et al. 2006). The ∆gcn5 ∆mst2 double mutant
is hypersensitive to salt compared to ∆gcn5 alone (Fig3.1C), suggesting that for this
function, these two HATs overlap. In contrast, the ∆gcn5 ∆elp3 double mutant has a
phenotype similar to ∆gcn5 alone suggesting that Elp3 does not contribute to proper salt
stress response.
Since ∆mst2 has been linked to damage sensitivity, we also examined the
response to different DNA damaging agents (Fig3.1D). ∆mst2 ∆gcn5 cells also showed
increased sensitivity to MMS and CPT treatment relative to the two single mutants,
suggesting that these two HAT enzymes make redundant contributions to replication-
specific DNA damage. Interestingly, ∆elp3 modestly suppressed the sensitivity of ∆mst2
49

to HU (Fig3.1D). All the double mutants showed some sensitivity to TBZ; however,
∆gcn5 ∆elp3 was more sensitive than the parent strains.
3.3.2 Genome wide expression studies Previous studies showed while Gcn5 is bound to
a high proportion of genes in S. pombe growing on rich media, it is requested for the
expression of only a few of its binding targets (HELMLINGER et al. 2008; JOHNSSON et al.
2006). This together with the synthetic and additive phenotypes observed here with the
different mutant combinations suggests that HAT enzymes redundantly affect common
pathways at the level of transcriptional regulation. However, it is also formally possible
that they independently affect regulation of separate pathways that overlap downstream at
the level of cellular function. To distinguish between these possibilities, we performed
genome-wide analysis of expression using microarray technology to identify target genes
that show HAT-specific changes in gene expression. We examined the effects on
transcription upon deletion of the GNAT family HATs Gcn5 and Elp3 and the MYST
HAT Mst2 both singly and in combination. We chose a very statistically rigorous cutoff
of 3.25 log2 fold change for genes that we considered differentially expressed. This
allowed us to be extremely confident that all results were biologically relevant and
eliminated most false positives.
We found that there were very few genes whose expression was significantly
changed by 3.25 log2 fold or more during asynchronous growth compared to wild-type
cells in ∆mst2, ∆gcn5 or ∆elp3 cells (Table 3.1)

50

Table 3.1: Differentially regulated genes in single HAT mutants.This table lists the down
and up-regulated genes of mutant HATs compared to wild-type cells using an Affymetrix
microarray

Down-regulated genes

∆gcn5 ∆mst2 ∆elp3
Gene
Log
change
p-
value Gene
Log
change p-value Gene
Log
change
p-
value
his3 -5.12
7.16
E-03
SPAC1
86.05c -3.77
4.00E-
07
SPAC186.
05c -4.31
1.11E-
04
SPAC186.
05c -4.09
1.26
E-07
SPBPB
2B2.06c -3.66
6.60E-
07
SPAC186.
06 -3.23
7.69E-
03
gcn5 -3.47
1.08
E-02
SPAC1
86.06 -3.52
1.94E-
06 inv1 -2.57
4.30E-
02
SPBPB2B
2.06c -3.26
3.11
E-06
SPAC1
7G8.13
c -2.76
2.03E-
02 str1 -2.50
5.79E-
03
SPAC186.
06 -3.23
5.82
E-06
SPAC1
039.02 -2.26
2.58E-
03
SPBPB2B
2.08 -2.34
3.98E-
02
SPBPB2B
2.01 -2.60
2.00
E-05
SPBPB
2B2.01 -2.23
1.12E-
04 mei2 -2.27
2.18E-
02
SPBPB2B
2.05 -2.35
1.46
E-02 ght4 -1.90
1.90E-
02
SPAC977.
14c -2.29
2.54
E-02
SPBC215.
11c -1.75
5.35E-
05
SPBPB2B
2.08 -2.22
2.01
E-02
SPAC103
9.02 -2.17
3.46
E-03
SPAC977.
05c -2.10
2.09
E-03
SPBPB10
D8.02c -2.02
1.47
E-03

Up-regulated
genes

∆gcn5 ∆mst2 ∆elp3
Gene
Log
chang
e
p-
value Gene
Log
change p-value Gene
Log
change
p-
value
spn6 2.05
4.71
E-03
SPBCP
T2R1.0
8c 2.08
3.59E-
02
SPAPB1
A11.01 1.88
1.01E-
04
spk1 2.26
4.08
E-03
SPBC3
59.06 2.29
2.33E-
02
SPCC132.
04c 2.01
6.01E-
08
SPCC794.01 2.34 3.09 SPBC2G2 2.02 2.69E-
Table 3.1: Continued 51

c E-02 .17c 05
mam2 2.45
3.38
E-03
SPBPB8B
6.03 2.05
6.89E-
04
mei2 2.57
5.66
E-03 spo6 2.05
1.63E-
04
SPCC1739.0
8c 2.94
2.22
E-02 air2 2.08
6.21E-
05
SPBC359.06 3.20
2.79
E-03
SPAC750.
04c 2.08
3.73E-
06
mfm1 3.23
4.03
E-03 spn5 2.17
9.14E-
06
mfm3 3.27
3.68
E-03 ctr4 2.22
1.49E-
03
ght3 3.87
8.30
E-03
SPAC2E1
P3.02c 2.62
5.60E-
08
SPBCPT2R1
.08c 3.89
7.73
E-04
SPAC750.
07c 3.83
2.13E-
03
matmc_1 4.18
8.90
E-03 dak2 3.86
2.68E-
02
mfm2 4.73
8.99
E-03
SPBCPT2
R1.08c 4.50
1.23E-
03
.
Of the small number of genes with increased expression, the RecQ-type DNA helicase
SPBCPT2R1.08c, located in the sub-telomere domain (tlh2
+
; (HANSEN et al. 2006;
MANDELL et al. 2005)) was the only significantly up-regulated gene in all three mutant
strains. Consistent with previously published data we found that there was an
enrichment of genes involved in mating and meiosis in ∆gcn5 cells (Table 3.2 ).
Table 3.2: GO terms differentially regulated in HAT mutants. This table lists the down
and up-regulated gene ontology (GO) terms of mutant HATs
Down-regulated GO Terms

GO annotation
Number
of
genes
Frequency
(%)
∆elp3
substrate-specific transmembrane transporter activity 2 28.6
substrate-specific transporter activity 2 28.6
transmembrane transporter activity 2 28.6

∆gcn5 ∆elp3
iron assimilation 2 9.1
Table 3.2: Continued 52

cellular di-, tri-valent inorganic cation homeostasis 3 13.6
di-, tri-valent inorganic cation homeostasis 3 13.6
iron ion transport 2 9.1
iron ion homeostasis 2 9.1
cellular iron ion homeostasis 2 9.1
di-, tri-valent inorganic cation transport 2 9.1
cellular cation homeostasis 3 13.6
cellular ion homeostasis 3 13.6
cellular chemical homeostasis 3 13.6
cation homeostasis 3 13.6
transition metal ion transport 2 9.1
ion homeostasis 3 13.6
cellular homeostasis 3 13.6
chemical homeostasis 3 13.6
ion transport 3 13.6
metal ion transport 2 9.1
cellular response to stress 6 27.3
cellular response to stimulus 6 27.3
response to oxidative stress 2 9.1
response to chemical stimulus 3 13.6
homeostatic process 3 13.6
response to stress 6 27.3

∆gcn5 ∆mst2
histone acetylation 2 5.7
amine transport 2 5.7
amino acid catabolic process 2 5.7
amino acid metabolic process 4 11.4
nitrogen compound catabolic process 2 5.7
amine catabolic process 2 5.7
positive regulation of transcription, DNA-dependent 2 5.7
positive regulation of RNA metabolic process 2 5.7
positive regulation of transcription 2 5.7
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process 2 5.7
cellular amino acid and derivative metabolic process 4 11.4
positive regulation of biosynthetic process 2 5.7
positive regulation of macromolecule biosynthetic process 2 5.7
positive regulation of gene expression 2 5.7
protein amino acid acetylation 2 5.7
cellular amine metabolic process 4 11.4
positive regulation of cellular metabolic process 2 5.7
positive regulation of metabolic process 2 5.7
cellular nitrogen compound metabolic process 4 11.4
positive regulation of macromolecule metabolic process 2 5.7
nitrogen compound metabolic process 4 11.4
protein amino acid acylation 2 5.7

∆mst2 ∆elp3
Table 3.2: Continued 53

galactose metabolic process 2 8.7
monosaccharide transport 2 8.7
disaccharide metabolic process 2 8.7
carbohydrate transport 2 8.7
cellular carbohydrate metabolic process 4 17.4
carbohydrate metabolic process 4 17.4
hexose metabolic process 2 8.7
monosaccharide metabolic process 2 8.7
cellular response to stress 6 26.1
cellular response to stimulus 6 26.1

∆gcn5 ∆elp3 ∆mst2
histone acetylation 2 6.5
positive regulation of transcription, DNA-dependent 2 6.5
positive regulation of RNA metabolic process 2 6.5
positive regulation of transcription 2 6.5
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process 2 6.5
positive regulation of biosynthetic process 2 6.5
positive regulation of macromolecule biosynthetic process 2 6.5
positive regulation of gene expression 2 6.5
protein amino acid acetylation 2 6.5
positive regulation of cellular metabolic process 2 6.5
positive regulation of metabolic process 2 6.5
positive regulation of macromolecule metabolic process 2 6.5
di-, tri-valent inorganic cation homeostasis 2 6.5
protein amino acid acylation 2 6.5

Up-regulated GO Terms

GO annotation
1
Number of genes Frequency
2
(%)
∆elp3
GO:0006812 cation transport 2 15.4
GO:0006811 ion transport 2 15.4

∆gcn5
GO:0032005 signal transduction during conjugation with cellular fusion 4 30.8
GO:0031137 regulation of conjugation with cellular fusion 4 30.8
GO:0046999 regulation of conjugation 4 30.8
GO:0043900 regulation of multi-organism process 4 30.8
GO:0019953 sexual reproduction 4 30.8
GO:0000746 conjugation 4 30.8
GO:0000747 conjugation with cellular fusion 4 30.8
GO:0051704 multi-organism process 4 30.8
GO:0000003 reproduction 5 38.5
GO:0000749 response to pheromone during conjugation with cellular
fusion 2 15.4
GO:0019236 response to pheromone 2 15.4
Table 3.2: Continued 54

GO:0007165 signal transduction 4 30.8
GO:0007154 cell communication 4 30.8
GO:0065007 biological regulation 6 46.2
GO:0050794 regulation of cellular process 5 38.5
GO:0050789 regulation of biological process 5 38.5

∆gcn5 ∆elp3
M phase of meiotic cell cycle 4 15.4
meiosis 4 15.4
meiotic cell cycle 4 15.4
amine transport 2 7.7
M phase 5 19.2
cell cycle phase 5 19.2
meiotic chromosome segregation 2 7.7

∆gcn5 ∆mst2
conjugation 13 24.1
conjugation with cellular fusion 13 24.1
sexual reproduction 13 24.1
multi-organism process 13 24.1
reproduction 15 27.8
signal transduction during conjugation with cellular fusion 5 9.3
regulation of conjugation with cellular fusion 7 13
regulation of conjugation 7 13
regulation of multi-organism process 7 13
cellular response to stress 17 31.5
cellular response to stimulus 17 31.5
monosaccharide transport 3 5.6
response to stimulus 19 35.2
response to stress 17 31.5
carbohydrate transport 3 5.6
positive regulation of meiosis 2 3.7
regulation of meiosis 3 5.6
regulation of meiotic cell cycle 3 5.6
response to pheromone during conjugation with cellular fusion 3 5.6
cell communication 9 16.7
response to pheromone 3 5.6
signal transduction 8 14.8
G-protein coupled receptor protein signaling pathway 2 3.7
MAPKKK cascade 2 3.7
protein kinase cascade 2 3.7
positive regulation of biological process 4 7.4
cell surface receptor linked signal transduction 2 3.7
regulation of cell cycle process 3 5.6
regulation of biological process 13 24.1
protein amino acid phosphorylation 4 7.4
positive regulation of cellular process 3 5.6
cellular response to nitrogen starvation 2 3.7
Table 3.2: Continued 55

cellular response to nitrogen levels 2 3.7
alcohol catabolic process 2 3.7
cellular carbohydrate metabolic process 4 7.4
regulation of cellular process 12 22.2

∆mst2 ∆elp3
DNA recombination 2 11.8
cation transport 2 11.8
ion transport 2 11.8

∆gcn5 ∆elp3 ∆mst2
iron assimilation 5 7.8
cellular di-, tri-valent inorganic cation homeostasis 7 10.9
di-, tri-valent inorganic cation homeostasis 7 10.9
iron assimilation by reduction and transport 3 4.7
signal transduction during conjugation with cellular fusion 5 7.8
iron ion homeostasis 5 7.8
cellular iron ion homeostasis 5 7.8
di-, tri-valent inorganic cation transport 5 7.8
iron ion transport 4 6.2
metal ion transport 6 9.4
transition metal ion transport 5 7.8
reproduction 11 17.2
cellular cation homeostasis 7 10.9
cellular ion homeostasis 7 10.9
cellular chemical homeostasis 7 10.9
cation homeostasis 7 10.9
ion homeostasis 7 10.9
cellular homeostasis 7 10.9
copper ion import 2 3.1
chemical homeostasis 7 10.9
conjugation 7 10.9
conjugation with cellular fusion 7 10.9
sexual reproduction 7 10.9
multi-organism process 7 10.9
regulation of conjugation with cellular fusion 5 7.8
regulation of conjugation 5 7.8
regulation of multi-organism process 5 7.8
homeostatic process 8 12.5
cation transport 6 9.4
siderophore transport 2 3.1
siderophore-iron transport 2 3.1
pheromone-dependent signal transduction during conjugation with cellular
fusion 2 3.1
transmembrane transport 4 6.2
response to pheromone during conjugation with cellular fusion 3 4.7
ion transport 6 9.4
transmembrane ion transport 3 4.7
Table 3.2: Continued 56

iron assimilation by chelation and transport 2 3.1
regulation of biological quality 9 14.1
copper ion transport 2 3.1
response to pheromone 3 4.7
G-protein coupled receptor protein signaling pathway 2 3.1
biological regulation 19 29.7
response to stimulus 16 25
cell development 3 4.7
meiotic gene conversion 2 3.1
cell surface receptor linked signal transduction 2 3.1
cellular response to stress 12 18.8
cellular response to stimulus 12 18.8
sex determination 2 3.1
mating type determination 2 3.1
reproductive developmental process 2 3.1
signal transduction 7 10.9
M phase of meiotic cell cycle 5 7.8
meiosis 5 7.8
meiotic cell cycle 5 7.8

mst1ts
cellular response to stress 50 42.2
cellular response to stimulus 50 42.4
response to stress 50 42.4
response to stimulus 52 44.1
cellular carbohydrate catabolic process 7 5.9
copper ion import 2 1.7
alcohol catabolic process 5 4.2
cellular carbohydrate metabolic process 10 8.5
iron assimilation 3 2.5
glucose catabolic process 4 3.4
hexose catabolic process 4 3.4
carbohydrate metabolic process 10 8.5
NADPH regeneration 3 2.5
pentose-phosphate shunt 3 2.5
NADP metabolic process 3 2.5
glucose 6-phosphate utilization 2 1.7
siderophore transport 2 1.7
siderophore-iron transport 2 1.7
cellular di-, tri-valent inorganic cation homeostasis 5 4.2
monosaccharide catabolic process 4 3.4
di-, tri-valent inorganic cation homeostasis 5 4.2
glucose metabolic process 4 3.4
glucose 6-phosphate metabolic process 2 1.7
pentose-phosphate shunt, oxidative branch 2 1.7
iron assimilation by chelation and transport 2 1.7
copper ion transport 2 1.7
nicotinamide metabolic process 3 2.5
Table 3.2: Continued 57

cellular iron ion homeostasis 3 2.5
iron ion homeostasis 3 2.5
di-, tri-valent inorganic cation transport 3 2.5
polyamine transport 2 1.7
hexose metabolic process 4 3.4
cation homeostasis 6 5.1
ion homeostasis 6 5.1
pyridine nucleotide metabolic process 3 2.5
metal ion transport 4 3.4
chemical homeostasis 6 5.1
disaccharide metabolic process 2 1.7
monosaccharide metabolic process 4 3.4
iron ion transport 2 1.7
transition metal ion transport 3 2.5
amine transport 3 2.5
cellular alcohol metabolic process 6 5.1
cellular cation homeostasis 5 4.2
cellular ion homeostasis 5 4.2
cellular chemical homeostasis 5 4.2
cation transport 5 4.2
.

Interestingly, of the few genes with decreased expression in ∆gcn5 and ∆mst2, most are
found within 150kb of the ends of chromosome I or II, suggesting that cells require Gcn5
and Mst2 for expression of genes localized near the sub-telomeric region (Fig3.2D).
58

Figure 3.2: Overlapping expression in different mutants A: Venn diagram of
differentially down and up-regulated genes in double HAT mutants. (Appendix A). B:
Venn diagram of differentially down and up-regulated GO terms in the double HAT
mutants using the affymetrix array. (Appendix A) C: Venn diagram of differentially
down and up-regulated GO terms of a double HAT mutant and the corresponding
single HAT mutant. (Table 3.1) D: Localization of differentially regulated genes along
chromosome 2 for the double mutant ∆gcn5 ∆mst2 (FY3361) and the corresponding
single mutants, (Tables 3.1 and fix this). Strains list: ∆gcn5 ∆elp3 (FY3847), ∆gcn5
∆mst2(FY3361), ∆mst2 ∆elp3 (FY3850), ∆gcn5 (FY2943) and ∆mst2 (FY1890).
59

The few genes that were differentially expressed in ∆elp3 and ∆gcn5 showed
significant over-representation in several functional ontology groups. In agreement with
prior reports (HELMLINGER et al. 2008) we observed that ∆gcn5 mutants de-repressed
mating and meiosis genes. Specifically we found that gene ontology (GO) terms (ASLETT
and WOOD 2006) related to mating and meiosis were found in the up-regulated genes,
indicating that Gcn5 is required for repression of these genes. In ∆elp3 mutants we found
that genes significantly enriched in GO classes associated with trans-membrane transport
were down-regulated and those associated with ion transport were up-regulated (Fig 3.2,
Table 3.2, Table 3.3).

Down-regulated genes
∆gcn5∆mst2∆elp3 ∆gcn5∆mst2∆elp3
Gene Log2 Change p-value Gene Log2 Change p-value
gcn5 -5.66 0.004193963 SPAC869.05c -2.21 0.01125063
elp3 -5.64 3.29E-13 SPAC1F12.03c -2.17 0.000970933
SPBPB10D8.01 -4.74 5.16E-06 SPAC18G6.12c -2.15 0.000137484
SPBPB10D8.02c -4.74 7.09E-06 SPBC947.04 -2.11 0.001731022
mst2 -4.41 0.01017041 SPCC622.01c -2.09 1.73E-06
SPAC57A10.06 -3.73 0.002283381 SPCC1902.02 -2.08 0.000234049
SPBPB2B2.06c -3.65 5.26E-05 SPAC589.09 -2.08 6.64E-05
SPBC26H8.11c -3.64 1.20E-08 SPBC25B2.08 -2.05 3.28E-05
SPAC1039.02 -3.40 0.001562479 SPCC1682.09c -2.04 3.76E-05
SPAC2E1P3.05c -3.17 1.71E-10 SPAC1399.04c -2.03 0.005854158
SPBPB2B2.01 -2.88 0.000283339 Msa1 -2.02 3.86E-05
SPAC186.06 -2.78 0.001161544 SPCC1223.13 -1.93 0.005773073
SPAC977.05c -2.60 0.00556226 SPBP26C9.03c -1.89 0.031834321
SPAC186.05c -2.53 0.001728652 isp4 -1.83 2.38E-05
SPAC29B12.10c -2.53 0.000532633 erg28 -1.81 1.10E-07
SPBC16A3.16 -2.39 0.002041561 SPBC21D10.07 -1.80 3.03E-07
SPAC186.03 -2.36 3.93E-05 hhf1 -1.76 1.68E-05

up-regulated genes
∆gcn5∆mst2∆elp3 ∆gcn5∆mst2∆elp3
Gene Log2 Change p-value Gene Log2 Change p-value
crp79 1.83 3.64E-06 Mam2 2.39 0.031460047
Table 3.3: Continued 60

rec24 1.83 4.67E-06 SPBC1685.13 2.39 0.009443801
SPAC6C3.07 1.79 2.44E-06 ssa1 2.41 0.009228639
meu17 1.78 2.72E-07 SPBC2G2.17c 2.42 5.92E-05
tht1 1.76 9.05E-06 SPAC922.03 2.52 1.72E-10
SPCC4G3.03 1.75 4.36E-05 SPAC1952.04c 2.53 0.00012367
caf5 1.89 0.008182728 Zym1 2.53 0.002346264
SPAC4F10.08 1.91 4.96E-07 meu14 2.67 9.57E-08
SPAC1F12.10c 1.92 0.029187088 ste6 2.67 0.002090987
SPBC1289.16c 1.92 0.009158305 SPAC1F8.08 2.67 6.91E-06
SPBC725.10 1.95 0.015549669 SPBC19C7.04c 2.68 0.002745215
SPBC1685.14c 1.96 6.09E-05 wtf20 2.72 3.34E-05
SPBC354.08c 1.97 8.65E-05 spk1 2.76 0.010948439
SPAC27D7.09c 1.98 0.007841458 mei2 2.82 0.025390591
SPCC1020.09 1.99 0.002301415 SPBC359.06 2.98 0.034921984
SPAC29A4.12c 2.02 0.000921543 fio1 3.06 0.001454197
SPCPB16A4.06c 2.02 0.000150191 SPBC947.05c 3.29 1.29E-08
SPCC74.02c 2.02 5.55E-07 mfm1 3.36 0.026192367
ste11 2.03 0.012048872 dak2 3.41 4.14E-07
rho5 2.03 0.000814839 SPBC56F2.06 3.51 0.000275571
cut2 2.04 7.84E-05 SPCC737.04 3.55 7.02E-05
spo6 2.04 2.92E-06 spn6 3.56 0.000934784
SPCC70.04c 2.06 7.02E-05 SPCC1739.08c 3.56 0.046079337
SPBC1685.05 2.07 5.19E-07 cta3 3.64 1.71E-11
SPAC14C4.01c 2.07 6.99E-05 SPBC23G7.10c 4.12 0.002206808
fip1 2.17 0.007511319 ght3 4.18 0.03579791
mcp3 2.18 3.18E-06 frp1 4.31 0.000260879
SPCC338.18 2.19 0.001391778 map2 4.47 1.54E-11
mde2 2.20 0.000144052 SPAC3G9.11c 4.62 6.82E-08
ppk33 2.22 0.003466142 matmc_1 5.33 0.016405454
SPCC1840.12 2.25 8.28E-05 mfm2 6.13 0.015267126
SPCC330.04c 2.25 2.32E-08 SPAC1F8.02c 6.36 4.47E-12
SPCC777.04 2.26 0.003985904 SPBCPT2R1.08c 6.37 0.000188046
SPAC4H3.03c 2.32 0.004334504 str3 7.18 1.76E-07
dmc1 2.33 4.79E-05
map1 2.34 0.00281451
SPAC6B12.03c 2.37 0.003999216
Table 3.3: Differentially regulated genes (3.25 fold) in the triple HAT mutant. This
table lists the down and up-regulated genes of the triple HAT mutant compared to wild-
type using an Affymetrix microarray.

Interestingly, mei2, which has been shown to be repressed by Gcn5 (HELMLINGER
et al. 2008) was down-regulated in ∆elp3 (Fig3.3). This may indicate that Gcn5 and Elp3
target the same pathway but with opposite effects. The few genes that were differentially
expressed in ∆mst2 mutants provided no over-represented GO classes.
61

Figure 3.3: Validation of microarray results by qPCR. Genes that showed
differential expression from microarray analysis were analyzed in different HAT mutants
through qualitative PCR (qPCR). The log2 fold expression ratios from microarray and
qPCR experiments for the mutants versus wild type were plotted. qPCR results are
indicated by the blue bars, microarray by the purple bars. Strain list: Strain list: ∆elp3
(FY 3851), ∆gcn5 (FY2943), ∆mst2 (FY1890), ∆gcn5 ∆elp3 (FY3847), ∆gcn5
∆mst2(FY3361), ∆mst2 ∆elp3 (FY3850), ∆gcn5 ∆elp3 ∆mst2 (3854).

62

3.3.3 Global gene expression changes in double mutants. We next asked whether the
transcription profiles of the double mutants were simply additive to the single mutants, or
whether they affected new genes not in common to the single mutant strains. We assayed
changes in gene expression in the double mutants. The number of differentially expressed
genes in the double and triple mutants was significantly increased compared to the
respective single mutants for each strain tested (Fig3.2, Table 3.3, Table 3.2), suggesting
overlapping regulation rather than an additive effect.
Only the helicase tlh2
+
and a metabolic kinase, dak1
+
were significantly up-
regulated in all mutant combinations. The double mutants ∆gcn5 ∆elp3 and ∆mst2 ∆elp3
had the most overlapping up-regulated genes (Fig3.2, Table 3.4).

Down-
regulated
∆gcn5∆elp3 ∆gcn5∆mst2 ∆mst2∆elp3
Gene Log2
Change
p-
value
Gene Log2
Chan
ge
p-
value
Gene Log2
Change
p-value
elp3 -5.81 3.53
E-15
his3 -7.51 3.17E-
04
elp3 -5.45
1.53E-
15
gcn5 -5.62 6.60
E-04
gcn5 -5.32 3.85E-
04
SPBPB2B2
.09c
-5.12
1.07E-
13
SPAC57A
10.06
-3.46 5.93
E-04
SPBPB10
D8.02c
-5.00 2.88E-
08
SPBPB2B2
.06c
-4.69
1.86E-
08
SPCC794.
04c
-3.34 1.09
E-04
SPBPB10
D8.01
-4.81 3.53E-
08
mst2 -4.37
8.06E-
04
SPBPB2B
2.08
-2.75 1.11
E-02
SPBPB2B
2.06c
-4.77 1.43E-
08
SPBPB2B2
.05
-3.73
4.40E-
04
SPBC215.
11c
-2.67 5.73
E-05
SPAC103
9.02
-4.73 8.49E-
07
SPBPB10D
8.02c
-3.70
1.98E-
06
isp5 -2.41 1.82
E-02
SPAC186.
05c
-4.59 2.32E-
08
SPBPB2B2
.10c
-3.62
2.63E-
06
Table 3.4: Continued 63

SPAC869.
05c
-2.32 1.45
E-03
mst2 -4.41 7.41E-
04
SPBPB2B2
.08
-3.40
1.02E-
03
gst2 -2.09 3.99
E-02
SPBPB2B
2.05
-4.06 1.93E-
04
SPBPB2B2
.13
-3.36
2.77E-
04
SPAC18G
6.12c
-2.08 1.37
E-05
SPAC977.
14c
-4.05 4.22E-
04
SPCC794.0
4c
-3.24
4.43E-
05
SPCC569.
03
-2.06 8.21
E-06
SPAC186.
03
-3.63 7.22E-
10
SPBPB2B2
.01
-3.02
3.01E-
06
SPAC23H
3.15c
-2.05 4.57
E-03
SPAC186.
06
-3.41 2.97E-
06
SPBC660.0
5
-2.94
1.64E-
03
srx1 -2.04 4.26
E-04
SPBPB2B
2.01
-3.30 9.24E-
07
SPAC22F8
.05
-2.58
8.09E-
05
SPCC663.
09c
-2.00 1.04
E-04
SPAC57A
10.06
-3.11 5.55E-
04
SPAC57A1
0.06
-2.58
2.76E-
03
zym1 -1.99 2.51
E-03
SPBC359.
04c
-2.98 1.81E-
09
str1 -2.44
5.05E-
05
fip1 -1.98 2.69
E-03
SPBPB21
E7.10
-2.89 1.02E-
05
SPAC869.0
5c
-2.41
3.81E-
04
SPAC29B
12.10c
-1.95 6.76
E-04
sou1 -2.87 5.39E-
09
ght5 -2.40
2.87E-
08
SPBC27.0
5
-1.93 1.65
E-05
SPBC947.
04
-2.80 1.92E-
06
SPAC23H3
.15c
-2.32
6.68E-
04
SPAC1F1
2.03c
-1.92 3.52
E-04
SPBPB2B
2.08
-2.59 8.09E-
03
SPCC569.0
3
-2.22
6.85E-
07
SPBC16A
3.16
-1.90 1.98
E-03
SPAC977.
05c
-2.38 7.28E-
04
inv1 -2.13
1.48E-
02
str1 -1.89 1.79
E-03
SPBC26H
8.11c
-2.35 4.53E-
08
SPBPB10D
8.01
-2.10
8.44E-
04
SPBPB2B
2.01
-1.88 1.61
E-03
obr1 -2.35 9.26E-
04
SPBC16A3
.16
-1.97
5.65E-
04
SPCC190
2.02
-1.80 8.76
E-05
SPCC663.
09c
-2.34 4.39E-
06
ght4 -1.89
8.80E-
03
SPAC17A
5.09c
-1.79 2.52
E-08
SPBC168
3.02
-2.31 2.23E-
06
SPCC622.0
5
-1.85
1.07E-
04
isp4 -1.76 2.08
E-06
SPAC977.
15
-2.26 3.04E-
02
isp4 -1.74
5.36E-
07
fta5 -2.17 1.44E-
06

SPBC3H7
.07c
-2.12 3.86E-
07

Table 3.4: Continued 64

SPAC23C
4.06c
-2.10 3.77E-
05

SPCC122
3.13
-2.09 1.45E-
04

SPCC569.
05c
-2.07 7.09E-
04

SPAC24B
11.14
-2.07 2.73E-
03

SPAC869.
05c
-2.05 1.65E-
03

SPBPB2B
2.18
-1.95 1.44E-
03

SPAC8C9
.05
-1.94 5.72E-
07

SPBC359.
03c
-1.91 1.26E-
11

Up-regulated genes

∆gcn5∆elp3
∆gcn
5∆ms
t2 ∆mst2∆elp3
Gene
Log2
Change p-value Gene
Log2
Chan
ge
p-
value Gene
Log2
Change
p-
valu
e
pma2 1.86
1.69E-
04
SPAC167.
06c 1.80
1.42E
-04 ctr5 1.87
4.14
E-08
SPCC7
4.02c 1.86
6.50E-
08 ste4 1.97
9.48E
-06 SPCC132.04c 1.86
9.18
E-06
SPBC1
861.06c 1.85
6.74E-
06
SPBC16E
9.16c 2.04
3.18E
-08 SPCC830.04c 1.85
1.78
E-06
SPAC4
F10.08 1.76
5.76E-
08
SPAC5H1
0.01 2.06
2.73E
-02 mug97 1.84
9.60
E-09
mpf1 1.89
4.35E-
06
SPCP31B
10.06 2.06
1.01E
-06 SPCC330.03c 1.81
1.20
E-06
SPCC8
30.04c 1.91
4.97E-
06
SPAC31G
5.07 2.07
6.02E
-09
SPAC6C3.03
c 1.92
1.73
E-06
mei4 2.00
7.97E-
06 meu10 2.09
3.59E
-07
SPAPB1A11.
01 1.97
2.41
E-07
Table 3.4: Continued 65

SPBC1
348.01 2.02
5.55E-
03
SPCC139
3.12 2.09
1.29E
-09
SPAC56F8.1
2 1.98
3.35
E-08
SPBC3
54.08c 2.03
3.56E-
06
SPBC725.
10 2.12
6.57E
-04 mde2 2.00
7.89
E-06
mam2 2.15
1.63E-
02 isp3 2.18
1.15E
-05
SPBC2G2.17
c 2.02
8.49
E-06
SPAC9
77.07c 2.16
1.03E-
07
SPBC128
9.16c 2.18
1.83E
-04 spo6 2.03
2.28
E-08
SPAC1
86.01 2.18
1.12E-
06
SPCC777.
04 2.19
2.67E
-04
SPAPB24D3.
07c 2.07
4.94
E-03
mug97 2.20
3.50E-
09
SPAC14C
4.01c 2.19
4.47E
-07 SPCC737.04 2.15
3.53
E-04
ctr4 2.20
6.91E-
07 tht1 2.23
2.19E
-09 alr2 2.16
1.83
E-09
SPAC7
50.07c 2.27
6.97E-
05
SPAC13F
5.03c 2.24
2.84E
-05
SPBC1861.06
c 2.19
1.62
E-07
mde2 2.27
6.61E-
06
SPCC70.0
4c 2.32
1.90E
-07
SPAC2E1P3.
02c 2.32
1.45
E-08
SPAC7
50.04c 2.35
3.46E-
07
SPACUN
K4.17 2.32
3.65E
-05 SPBC354.08c 2.71
1.31
E-08
SPBPB
8B6.03 2.35
1.43E-
08
SPBC146.
02 2.33
5.56E
-08 SPAC977.15 2.79
9.58
E-03
spo6 2.46
6.92E-
09
SPCC794.
04c 2.42
8.62E
-04 ctr4 2.88
2.52
E-09
SPCC7
77.04 2.48
2.27E-
04 dak2 2.56
1.74E
-07
SPBCPT2R1.
08c 2.92
7.13
E-03
spn5 2.58
4.26E-
05
SPAC4H3
.03c 2.57
7.41E
-05 dak2 4.40
3.91
E-11
mcp3 2.62
8.20E-
09
SPBPB2B
2.12c 2.63
2.11E
-02 ura4 4.44
1.44
E-02
SPAC1
952.04c 2.66
4.36E-
06 ght4 2.63
6.85E
-04
spn6 2.74
1.17E-
03
SPCC338.
18 2.63
4.83E
-06
SPAC2
E1P3.0
2c 2.76
5.64E-
09
SPBC21D
10.06c 2.64
1.15E
-12
SPBPB
8B6.02
c 2.78
2.18E-
13
SPAC1F8
.08 2.65
6.91E
-08
Table 3.4: Continued 66

grt1 2.81
1.09E-
06 map3 2.65
5.28E
-12
alr2 3.05
4.16E-
11 rho5 2.70
5.84E
-07
dak2 3.64
4.94E-
09 wtf20 2.77
3.12E
-07
SPAC9
77.05c 4.56
1.72E-
06 ran1 2.79
2.48E
-06
SPBCP
T2R1.0
8c 5.16
8.64E-
05
SPAC6B1
2.03c 2.86
2.44E
-05
ste7 2.99
3.26E
-05

SPCC737.
04 2.99
8.94E
-06
map1 3.11
4.16E
-06
ste11 3.19
7.81E
-06
ght1 3.38
1.44E
-02
ura4 3.53
4.12E
-02
ste6 3.56
2.49E
-06
agl1 3.59
1.78E
-03
fbp1 3.67
5.79E
-13

SPBC56F
2.06 3.68
2.97E
-06

SPAC3G9
.11c 3.74
8.98E
-09
shk2 3.80
2.81E
-11
spn6 3.84
1.08E
-05
ppk33 3.93
1.21E
-07
mei2 4.01
1.14E

Table 3.4: Continued 67

-04

SPCC794.
01c 4.08
6.89E
-04
rgs1 4.08
5.34E
-07
SPBC4.01 4.20
1.88E
-08

SPCC173
9.08c 4.27
1.92E
-03

SPBC359.
06 4.72
7.39E
-05
spk1 4.76
1.85E
-06
ght3 6.19
1.63E
-04
map2 6.36
9.50E
-17

SPBCPT2
R1.08c 6.70
1.71E
-06

Table 3.4: Differentially expressed genes (3.25 fold) in double HAT mutants. This file
lists the differentially changed genes in the double HAT mutants compared to wild-type
cells using an Affymetrix microarray.
These genes included metal transporters and the sporulation specific gene spo6
+
.
We found that ∆gcn5 ∆mst2 cells had a greater number of up-regulated genes related to
the mating pathway than ∆gcn5 alone, suggesting that Gcn5 and Mst2 are functionally
redundant in repressing sexual differentiation. This is also observed, although to a lesser
extent, with the ∆gcn5 ∆elp3 mutant. However changes associated with ∆mst2 ∆elp3
were not significantly enriched in gene classes associated with mating or meiosis, except
for spo6
+
, which is essential for progression of meiosis II and sporulation. When we
examined down-regulated genes in the double mutants, we again found the most overlap
between ∆gcn5 ∆elp3 and ∆mst2 ∆elp3 cells, however there were more differentially
68

expressed genes in ∆gcn5 ∆mst2. A large fraction of these genes were found to be sub-
telomeric (Fig3.2D) which suggests that Mst2 and Gcn5 but not Elp3 function
preferentially in the sub-telomeric regions. This is consistent with previous studies
suggesting that Mst2 works at the telomere (GOMEZ et al. 2005).
3.3.4 Functional redundancies between HATs. To determine whether the mutations
affected distinct functional groups, we categorized the affected gene targets by gene
ontology (GO) classification. As was apparent for the individual genes, the genes affected
by the double mutants were more significantly enriched in a larger number of GO classes
than for the single mutants. For GO classes enriched in down-regulated genes there were
23 terms for ∆gcn5 ∆elp3, 22 for ∆gcn5 ∆mst2, while ∆mst2 ∆elp3 had 10 enriched GO
terms (Fig 3.2, Table 3.2). Curiously there is almost no overlap in enriched GO terms
associated with genes down-regulated between double mutants, with the exception of
cellular response to stress and response to stimulus shared between ∆mst2 ∆elp3 and
∆gcn5 ∆elp3. Therefore we conclude that Gcn5, Mst2 and Elp3 are functionally
redundant in activating transcription. For GO categories enriched with up-regulated genes
there were 7 categories for ∆gcn5 ∆elp3, 36 for ∆gcn5 ∆mst2, and ∆mst2 ∆elp3 had 3
enriched GO terms (Fig 3.2). There are no overlapping enriched up-regulated GO
categories between double mutants. When we examined the number of genes and the GO
terms they represent in the double mutants compared to the single mutants, we conclude
that Gcn5, Mst2 and Elp3 are functionally redundant in repressing transcription because
the number of terms enriched in the double mutants cannot be explained by adding the
single mutants’ terms together. There were more significantly enriched genes in the
double mutants than in the single mutants.
69

3.3.5 Validation of microarray results. We used quantitative PCR (qPCR) to confirm
the microarray results. The ddCt method (SCHMITTGEN and LIVAK 2008) was applied to
measure relative fold differences between each strain and one wild type sample with
act1
+
used as the loading control. For each strain, we chose genes that were predicted by
the microarray to have significant changes in transcription. The fold changes of the other
two wild type samples relative to the first wild type sample was small (2-fold at the most)
across all the loci. The fold changes of the other two control genes relative to act1
+
were
also small (2-fold at the most) across all the strains. We found high degrees of
congruence in gene expression as measured by RT-PCR and microarray analysis. (Fig
3.3).
3.3.6 Salt response in ∆mst2 and ∆gcn5 mutants Since ∆mst2 and ∆gcn5 showed a
synthetic phenotype in salt sensitivity, we performed expression profiling on ∆mst2 and
∆gcn5∆mst2 double mutant under KCl treatment and compared this to our previous
results on ∆gcn5 using the same platform (JOHNSSON et al. 2006). The number of
affected genes in ∆mst2 increases during KCl induced stress but fewer genes are affected
in ∆mst2 compared to ∆gcn5, consistent with the observation that ∆mst2 alone has little
effect on salt response. To find genes that require Gcn5 or Mst2 during KCl stress we
compared the expression levels between ∆gcn5 and ∆gcn5 ∆mst2. We found 99 genes
that were significantly down-regulated and 191 genes significantly up-regulated in the
double mutant, compared to ∆gcn5 single mutant (Table 3.5). About 80% of these genes
were not significantly regulated in either of the single mutants (Fig 3.4). This suggests
that the two HAT enzymes overlap in the regulation of salt-responsive pathways,
although there was no significant overlap in particular GO pathways.
70

Figure 3.4: Salt response is redundantly regulated by multiple HAT families. Venn
diagram of differentially down and up-regulated genes after salt stress in ∆gcn5, ∆mst2
and ∆gcn5 ∆mst2 HAT mutants as determined by the Eurogenetech array platform
(Table 3.5). Strains ∆gcn5 (Hu799), ∆mst2 (1890) ∆gcn5 ∆mst2(Hu990).

Table 3.5: Genes with 2 fold change in gene expression after exposure to salt. This table
lists the down and up-regulated genes of mutant HATs using an Eurogentech microarray.

Down-
regulated
2 fold down
gcn5 KCl annotation
2 fold down
mst2 KCl annotation
SPAC977.05c conserved fungal family SPBPB2B2.19c
S. pombe specific 5Tm
protein family
SPBPB2B2.15 conserved fungal family SPAC750.05c
S. pombe specific 5Tm
protein family
SPBC1348.06c conserved fungal family SPAC977.01
S. pombe specific 5Tm
protein family
SPAC5H10.06c alcohol dehydrogenase Adh4 SPBC1348.02
S. pombe specific 5Tm
protein family
SPAC22A12.17c short chain dehydrogenase (predicted) SPBP4G3.02 acid phosphatase Pho1
SPAC3C7.14c ubiquitinated histone-like protein Uhp1 SPCC1020.10
serine/threonine protein
kinase Oca2 (predicted)
SPBC8D2.16c DUF171 family protein SPAC212.04c
S. pombe specific DUF999
family protein 1
SPBC30D10.14 dienelactone hydrolase family SPAC2H10.01
transcription factor, zf-
fungal binuclear cluster
type (predicted)
SPCC965.07c glutathione S-transferase Gst2 SPAC57A7.11 WD repeat protein Mip1
SPBC2A9.02
NAD dependent epimerase/dehydratase
family protein SPAC1786.02 phospholipase (predicted)
SPCPJ732.01 retromer complex subunit Vps5 SPCC584.16c sequence orphan
SPBC24C6.09c phosphoketolase family protein (predicted) SPBC11C11.01 RNA-binding protein
SPBC1271.08c sequence orphan SPAC1B3.16c vitamin H transporter Vth1
SPAC977.14c aldo/keto reductase, unknown biological role SPCC1840.07c
phosphoprotein
phosphatase (predicted)
SPCC16A11.15c sequence orphan SPBC651.12c sequence orphan
SPAC9E9.11 pyridoxal reductase Plr1 SPBC660.08 sequence orphan
Table 3.5: Continued 71

SPAC5H10.03 phosphoglycerate mutase family SPAC750.01 pseudogene
SPAC22H10.13 metallothionein Zym1 SPCC1235.01 sequence orphan
SPAC17G8.04c
ARP2/3 actin-organizing complex subunit
Arc5 SPBPB2B2.04
pseudo-very degraded
transporter
SPAC1039.02 phosphoprotein phosphatase (predicted) SPCC1919.13c
conserved eukaryotic
protein
SPAC4G9.12 gluconokinase SPCC132.04c
NAD-dependent glutamate
dehydrogenase (predicted)
SPCC18B5.02c cinnamoyl-CoA reductase pseudogene SPAC977.06
S. pombe specific DUF999
family protein 3
SPAC3C7.11c calnexin Cnx1 SPCC965.12
dipeptidyl peptidase
(predicted)
SPAC750.01 pseudogene SPAC2G11.02
ribosome biogenesis
protein Urb2 (predicted)
SPCC1494.03
armadillo repeat containing, Zfs1 target
number 1 SPBC19C7.04c conserved fungal protein
SPAC27E2.04c dubious SPCP1E11.03 arrestin
SPCC569.05c spermidine family transporter (predicted) SPBC409.08
spermine family
transporter (predicted)
SPAC637.03 conserved fungal protein SPAC27D7.04
4-alpha-
hydroxytetrahydrobiopterin
dehydratase (predicted)
SPBC16D10.08c heat shock protein Hsp104 (predicted) SPBC1289.14 adducin
SPAC13C5.04 amidotransferase (predicted) SPAPB8E5.07c
ribosome biogenesis
protein Rrp12
SPBC21B10.08c sequence orphan SPAPB1A10.14 F-box protein
SPAC13C5.06c sequence orphan SPAC17A2.08c sequence orphan
SPBC23G7.10c
NADH-dependent flavin oxidoreductase
(predicted) SPAC977.14c
aldo/keto reductase,
unknown biological role
SPAC16A10.01 DUF1212 family protein SPAC750.02c membrane transporter
SPBC215.11c aldo/keto reductase, unknown biological role SPBCPT2R1.01c
S. pombe specific DUF999
protein family 9
SPAC7D4.09c steroid dehydrogenase (predicted) SPAC1B3.06c
UbiE family
methyltransferase
(predicted)
SPAC513.02 phosphoglycerate mutase family SPCC24B10.19c sequence orphan
SPBC4C3.03 homoserine kinase (predicted) SPBC21C3.08c ornithine aminotransferase
SPAC27D7.09c But2 family protein SPAC1A6.08c sequence orphan
SPBC12C2.14c dubious SPAC1556.01c DNA repair protein Rad50
SPAPB1A10.05 sequence orphan SPBC146.07
U2AF large subunit
(U2AF-59)
SPCC830.07c DNAJ domain protein Psi1 SPAPB1E7.10
DNA-directed RNA
polymerase III complex
subunit Rpc17
SPCC736.05 wtf element Wtf7 SPAC18B11.05 pig-V (predicted)
SPAC1348.05 membrane transporter SPCC1919.15
ubiquitin-protein ligase E3
Brl1
SPBC21C3.08c ornithine aminotransferase SPAC6G10.12c transcription factor Ace2
SPAC2E1P3.05c fungal cellulose binding domain protein SPBC26H8.04c DEP domain protein
SPAC11D3.13 ThiJ domain protein SPAC27D7.03c
RNA-binding protein
involved in meiosis Mei2
SPAC4G9.19 DNAJ domain protein DNAJB family SPBC1685.11 RecA family ATPase Rlp1
SPAC30D11.02c sequence orphan SPCC550.12 actin-like protein Arp6
SPCC338.12
subtilisin cleaved region related protein
(predicted) SPCC1450.03
ribonucleoprotein (RNP)
complex (predicted)
SPCC1827.03c acetyl-CoA ligase (predicted) SPAC57A7.06
U3 snoRNP protein Utp14
(predicted)
SPAC2F3.05c xylose and arabinose reductase (predicted) SPAC750.07c
S. pombe specific GPI
anchored protein family 1
SPBC337.09 Erg28 protein SPBC16A3.01 septin Spn3
SPBC651.12c sequence orphan SPBC1718.02
linear element associated
protein Hop1
SPBC106.02c sulfiredoxin SPAC31G5.04
homoisocitrate
dehydrogenase
SPBC428.18 replication licensing factor Cdt1 SPCC736.03c
mitochondrial
phenylalanyl-tRNA
synthetase
Table 3.5: Continued 72

SPCC825.04c N-acetyltransferase (predicted) SPAC10F6.15
S. pombe specific
UPF0300 family protein 1
SPAC343.12 conserved fungal protein SPCC290.02
DNA-directed RNA
polymerase III complex
subunit Rpc34
SPBC1921.03c mRNA export receptor Mex67
SPBC428.04 sequence orphan
SPBC83.18c C2 domain protein Fic1
SPCC663.08c short chain dehydrogenase (predicted)
SPBC21H7.06c inositol metabolism protein Opi10 (predicted)
SPCC70.10 sequence orphan
SPAC823.15
minor serine/threonine protein phosphatase
Ppa1
SPBC3B9.18c V-type ATPase subunit F (predicted)
SPAC8E11.10 sorbose reductase (predicted)
SPBC1289.14 adducin
SPCC1223.03c glycerol-3-phosphate dehydrogenase Gut2
SPAC2H10.01
transcription factor, zf-fungal binuclear
cluster type (predicted)
SPAC6B12.07c ubiquitin-protein ligase E3 (predicted)
SPAC922.04 sequence orphan
SPCC24B10.02c NAD/NADH kinase (predicted)
SPAC24C9.08 vacuolar carboxypeptidase (predicted)
SPAC32A11.01 conserved fungal protein
SPBC3B9.06c
autophagy associated protein Apg3
(predicted)
SPBC3B9.01 Hsp70 nucleotide exchange factor (predicted)
SPAC57A7.05 conserved protein (fungal and plant)
SPBC29A10.11c
guanyl-nucleotide exchange factor Vps902
(predicted)
SPAC31A2.04c 20S proteasome component beta 4 (predicted)
SPAC977.11 CRCB domain protein
SPAC29A4.20
elongator complex, histone acetyltransferase
subunit Elp3 (predicted)
SPCC13B11.04c
glutathione-dependent formaldehyde
dehydrogenase (predicted)
SPCC663.06c short chain dehydrogenase (predicted)
SPBC1348.04 methyltransferase (predicted)
SPAC1782.04
mitochondrial mRNA processing protein
Cox24 (predicted)
SPAC890.07c
type I protein arginine N-methyltransferase
Rmt1
SPAC19D5.01 tyrosine phosphatase Pyp2
SPCC70.09c conserved fungal protein
SPAC22H12.01c sequence orphan
SPAC1F8.06
Sim4 and Mal2 associated (4 and 2
associated) protein 5
SPBC4F6.17c
mitochondrial heatshock protein Hsp78
(predicted)
SPBC20F10.10 cyclin pho85 family
SPBC725.16
MBF transcription factor complex subunit
Res1
SPAC2C4.17c MS ion channel protein 2
SPBC32F12.09 CDK inhibitor Rum1
SPAC30D11.01c alpha-glucosidase (predicted)
SPBC119.03 human COMT homolog 1
SPBC215.01 GTPase activating protein (predicted)
SPBC3H7.09 palmitoyltransferase (predicted)
SPBC3H7.02 sulfate transporter (predicted)
SPAC5H10.10 NADPH dehydrogenase (predicted)
SPBC1734.11 DNAJ domain protein Mas5 (predicted)
SPAC5D6.08c meiosis II protein Mes1
SPBC13E7.09 verprolin
SPAC1687.22c RNA-binding protein Puf3 (predicted)
SPAC977.02 S. pombe specific 5Tm protein family
SPAC19A8.02 pleckstrin homology domain protein

Table 3.5: Continued 73

2 fold down∆
gcn5 ∆mst2
KCl annotation
2 fold down∆
gcn5 ∆mst2 KCl annotation
SPAC750.05c S. pombe specific 5Tm protein family SPCC569.05c
spermidine family transporter
(predicted)
SPAC977.01 S. pombe specific 5Tm protein family SPAC11D3.02c
ELLA family acetyltransferase
(predicted)
SPBC26H8.11c conserved fungal protein SPBC12D12.07c mitochondrial thioredoxin Trx2
SPBPB2B2.19c S. pombe specific 5Tm protein family SPBC17D11.06
DNA primase large subunit
Spp2
SPBC11C11.01 RNA-binding protein SPAC56E4.07 N-acetyltransferase (predicted)
SPAC2E1P3.05c
fungal cellulose binding domain
protein SPBC1778.01c zuotin (predicted)
SPCC584.16c sequence orphan SPAC17A5.01 peroxin-6 (predicted)
SPBC1348.02 S. pombe specific 5Tm protein family SPBC16H5.10c
ATP-dependent RNA helicase
Prp43
SPAC17D4.01 peroxin-7 (predicted) SPBC24C6.09c
phosphoketolase family protein
(predicted)
SPAC57A7.11 WD repeat protein Mip1 SPBC3B9.07c
DNA-directed RNA polymerase
I complex subunit Rpa43
SPAC1039.02
phosphoprotein phosphatase
(predicted) SPAC13C5.06c sequence orphan
SPAC186.03 L-asparaginase (predicted) SPAC19B12.10 human AMSH protein homolog
SPAC22A12.06c serine hydrolase SPBC1709.07
3-keto sterol reductase
(predicted)
SPBC36.03c
spermidine family transporter
(predicted) SPBC21C3.08c ornithine aminotransferase
SPAC17C9.16c
MFS family transmembrane
transporter Mfs1 SPCC663.13c N-acetyltransferase (predicted)
SPAC20G4.01 CCR4-Not complex subunit Caf16 SPCC1259.09c
pyruvate dehydrogenase protein
x component
SPAC869.04 formamidase-like protein SPAC17G8.06c
dihydroxy-acid dehydratase
(predicted)
SPAC144.03 adenylosuccinate synthetase Ade2 SPBC215.06c human LYHRT homolog
SPBC337.09 Erg28 protein SPCC777.15
tRNA dihydrouridine synthase
Dus4 (predicted)
SPAC6F6.11c
pyridoxine-pyridoxal-pyridoxamine
kinase (predicted) SPBC2G2.05 60S ribosomal protein L13/L16
SPAC17G8.13c histone acetyltransferase Mst2 SPBC725.15
orotate
phosphoribosyltransferase Ura5
SPBC16D10.06 ZIP zinc transporter Zrt1 SPBC1709.10c copper chaperone Atx1
SPAC23C4.06c methyltransferase (predicted) SPAC6C3.09 RNase P subunit (predicted)
SPBC11B10.02c
histidinol-phosphate aminotransferase
imidazole acetol phosphate
transaminase His3 SPCC1795.05c uridylate kinase
SPBPB2B2.10c
galactose-1-phosphate
uridylyltransferase (predicted) SPAP27G11.08c sequence orphan
SPBC428.11 homocysteine synthase Met17 SPAC25G10.05c ATP phosphoribosyltransferase
SPBC3B9.18c V-type ATPase subunit F (predicted) SPAC343.05 V-type ATPase subunit A
SPAC750.02c membrane transporter SPAC2F3.11 exopolyphosphatase (predicted)
SPBC651.12c sequence orphan SPBC1271.12
oxysterol binding protein
(predicted)
SPAC1A6.10 Moeb/ThiF domain SPAC2E1P5.04c
geranylgeranyltransferase I beta
subunit Cwg2
SPBC3H7.05c sequence orphan SPBPB2B2.16c
MFS family membrane
transporter (predicted)
SPAC1786.02 phospholipase (predicted) SPAC23H3.05c Set1C complex subunit Swd1
SPBPB2B2.18 sequence orphan SPAC56F8.05c BAR domain protein (predicted)
SPBPB2B2.09c
2-dehydropantoate 2-reductase
(predicted) SPBC646.07c enoyl reductase
SPBC3H7.11
actin binding methyltransferase
(predicted) SPCC4G3.02
bis(5'-nucleosidyl)-
tetraphosphatase
SPBC24C6.04
delta-1-pyrroline-5-carboxylate
dehydrogenase SPBC577.12 endoribonuclease (predicted)
Table 3.5: Continued 74

SPBC1105.05
glucan 1,3-beta-glucosidase I/II
precursor SPBC26H8.03
phosphatidylethanolamine N-
methyltransferase Cho2
SPBC32F12.12c
Golgi membrane protein involved in
vesicle-medated transport (predicted) SPBC106.11c
phospholipase A2, PAF family
homolog
SPCC1827.03c acetyl-CoA ligase (predicted) SPAC4F10.15c WASp homolog
SPCC1840.07c
phosphoprotein phosphatase
(predicted) SPAC57A10.12c
dihydroorotate dehydrogenase
Ura3
SPBC1271.04c eIF-5A-deoxyhypusine synthase SPBC359.04c
cell surface glycoprotein
(prediected), DIPSY family
SPBC342.06c
RTT109 family histone lysine
acetyltransferase SPBC21B10.08c sequence orphan
SPBC1289.14 adducin SPBC1703.03c
armadillo repeat protein,
unknown biological role
SPAP7G5.04c
aminoadipate-semialdehyde
dehydrogenase SPBC21.01 kinetochore protein Mis17
SPBC18E5.08 N-acetyltransferase (predicted) SPBC660.12c aminotransferase (predicted)
SPAC9.02c N-acetyltransferase (predicted) SPBC1A4.07c
U3 snoRNP-associated protein
Sof1
SPCC4B3.18 phosphopantothenate-cysteine ligase SPAC56F8.10
methylenetetrahydrofolate
reductase Met9
SPAC16E8.04c chorismate mutase (predicted) SPBC18E5.05c
elongator complex subunit Iki1
(predicted)
SPBC23E6.06c
3,4-dihydroxy-2-butanone 4-phosphate
synthase (predicted) SPBC365.02c
protoheme IX
farnesyltransferase
SPCC1450.14c ER oxidoreductin Ero1b

Up-regulated
2 fold up gcn5
KCl annotation 2 fold up mst2 annotation
SPCC736.15 protein kinase inhibitor (predicted) SPAC1002.17c
uracil
phosphoribosyltransferase
(predicted)
SPAC6F12.10c
phosphoribosylformylglycinamidine
synthase Ade3 (predicted) SPAC9E9.12c ABC transporter Ybt1
SPCC13B11.01 alcohol dehydrogenase Adh1 SPCC13B11.01
alcohol dehydrogenase
Adh1
SPCC330.08 alpha-1,2-mannosyltransferase Alg11 SPBC337.16
phosphatidyl-N-
methylethanolamine N-
methyltransferase
(predicted)
SPBC530.10c
mitochondrial adenine nucleotide
carrier Anc1 SPCC191.07 cytochrome c (predicted)
SPAC3H8.06
inositol phosphorylceramide synthase
(predicted) SPAC8E11.03c
RecA family ATPase
Dmc1
SPAC644.18c
TRAPP complex subunit Bet3
(predicted) SPBC1198.14c
fructose-1,6-
bisphosphatase Fbp1
SPCC1235.02 biotin synthase SPBC646.12c
GTPase activating protein
Gap1
SPAC13D6.02c zinc finger protein Byr3 SPAC144.14 kinesin-like protein Klp8
SPAC27F1.02c tropomyosin SPBC1921.03c
mRNA export receptor
Mex67
SPAC23C11.11 serine/threonine protein kinase Cka1 SPAC3C7.14c
ubiquitinated histone-like
protein Uhp1
SPBC1347.06c serine/threonine protein kinase Cki1 SPCC1739.12
serine/threonine protein
phosphatase Ppe1
SPCC188.03 condensin, non-SMCsubunit Cnd3 SPBC119.13c
U4/U6 x U5 tri-snRNP
complex subunit Prp31
SPMIT.11 cytochrome c oxidase 2 SPAC343.12 conserved fungal protein
SPCC191.07 cytochrome c (predicted) SPCC4G3.10c
DNA repair protein
Rhp42
SPBP8B7.16c ATP-dependent RNA helicase Dbp2 SPBC14F5.05c
S-adenosylmethionine
synthetase
SPBC20F10.01
snoRNP pseudouridylase complex
protein Gar1 SPBC31F10.06c
ADP-ribosylation factor
Sar1
Table 3.5: Continued 75

SPAC140.02
nucleolar protein required for rRNA
processing SPAC1B9.02c
serine/threonine protein
kinase Sck1
SPCC736.04c alpha-1,2-galactosyltransferase Gma12 SPAC1002.18 DUF1688 family protein
SPBC354.12
glyceraldehyde 3-phosphate
dehydrogenase Gpd3 SPAC1002.19
GTP cyclohydrolase II
(predicted)
SPBC725.09c BAR adaptor protein Hob3 SPAC10F6.16
endosulphine family
protein
SPAC12G12.04
mitochondrial heat shock protein
Hsp60/Mcp60 SPAC17A5.18c
meiotic recombination
protein Rec25
SPAP8A3.04c heat shock protein Hsp9 SPAC18B11.04
related to neuronal
calcium sensor Ncs1
SPAC24H6.04 hexokinase 1 SPAC19G12.16c conserved fungal protein
SPAC11H11.04 pheromone p-factor receptor SPAC1A6.03c phospholipase (predicted)
SPAC10F6.12c
protein-S isoprenylcysteine O-
methyltransferase Mam4 SPAC22E12.06c
alpha-1,2-
galactosyltransferase
Gmh3
SPAC27D7.03c
RNA-binding protein involved in
meiosis Mei2 SPAC22G7.08
serine/threonine protein
kinase Ppk8 (predicted)
SPAC31G5.12c repressor of RNA polymerase III Maf1 SPAC23A1.14c
uncharacterised trans-
sulfuration enzyme
(predicted)
SPAC31G5.11
cAMP-independent regulatory protein
Pac2 SPAC24C9.14
ubiquitin-specific
protease (predicted)
SPAC21E11.03c transcription factor Pcr1 SPAC25A8.02 sequence orphan
SPBC14F5.04c
phosphoglycerate kinase Pgk1
(predicted) SPAC25H1.02 Jmj1 protein
SPBP22H7.05c ATPase with bromodomain protein SPAC27D7.11c But2 family protein
SPCC126.02c Ku domain protein Pku70 SPAC2F3.05c
xylose and arabinose
reductase (predicted)
SPBC365.06 SUMO SPAC31A2.12 arrestin/PY protein 1
SPAC1002.13c beta-glucosidase Psu1 (predicted) SPAC3C7.02c
protein kinase inhibitor
(predicted)
SPAC4H3.10c pyruvate kinase (predicted) SPAC3C7.13c
glucose-6-phosphate 1-
dehydrogenase
(predicted)
SPBC17G9.11c pyruvate carboxylase SPAC3G6.03c Maf-like protein
SPBC28F2.12
DNA-directed RNA polymerase II
large subunit SPAC4G8.11c
F1-F0 ATPase assembly
protein (predicted)
SPCC1020.04c
DNA-directed RNA polymerase I, II
and III subunit Rpb6 SPAC4G9.19
DNAJ domain protein
DNAJB family
SPAC22E12.13c 60S ribosomal protein L24-3 (L30) SPAC513.06c
dihydrodiol
dehydrogenase
(predicted)
SPBC29A3.04 60S ribosomal protein L7a (L8) SPAC521.03
short chain
dehydrogenase
(predicted)
SPBC119.01
19S proteasome regulatory subunit
Rpn3 SPAC57A10.09c
High-mobility group non-
histone chromatin protein
SPCC18.14c
60S acidic ribosomal protein Rpp0
(predicted) SPAC167.06c sequence orphan
SPBC14F5.05c S-adenosylmethionine synthetase SPAC630.08c
C-4 methylsterol oxidase
(predicted)
SPBC31F10.06c ADP-ribosylation factor Sar1 SPAC688.04c
glutathione S-transferase
Gst3
SPAC6G9.11 SNAP receptor, synaptobrevin family SPAC806.04c DUF89 family protein
SPAC167.03c
U4/U6 x U5 tri-snRNP complex
subunit Snu66 (predicted) SPAC869.10c
proline specific permease
(predicted)
SPAC821.10c superoxide dismutase Sod1 SPAP7G5.06
amino acid permease,
unknown 4
SPAC1002.02 nucleoporin Pom34 (predicted) SPAPB24D3.07c sequence orphan
SPAC1002.17c
uracil phosphoribosyltransferase
(predicted) SPAPB2B4.02
monothiol glutaredoxin
Grx5
SPAC1002.19 GTP cyclohydrolase II (predicted) SPAC1782.01 proteasome component
SPAC1093.05
ATP-dependent RNA helicase Hca4
(predicted) SPBC106.16
20S proteasome
component alpha 4 Pre6
SPAC10F6.16 endosulphine family protein SPBC1198.13c
transcription factor TFIIF
complex beta subunit
Table 3.5: Continued 76

Tfg2 (predicted)
SPAC11E3.07 V-type ATPase subunit E SPBC1347.11
Stress Responsive Orphan
1
SPAC11G7.03
isocitrate dehydrogenase (NAD+)
subunit 1 Idh1 SPBC14F5.10c
ubiquitin-protein ligase
E3 (predicted)
SPAC12G12.07c conserved fungal protein SPBC16E9.11c
HECT-type ubiquitin-
protein ligase Pub3
SPAC14C4.12c clr6 L associated factor 1 Laf1 SPBC19G7.06
MADS-box transcription
factor Mbx1
SPAC16.05c transcription factor Sfp1 (predicted) SPBC211.05 splicing factor 3B
SPAC16E8.06c RNA-binding protein Nop12 SPBC21D10.06c
cell surface agglutination
protein Map4
SPAC1705.03c conserved fungal family SPBC21H7.06c
inositol metabolism
protein Opi10 (predicted)
SPAC17H9.05 rRNA processing protein Ebp2 SPBC26H8.13c sequence orphan
SPAC18G6.01c calchone related protein family SPBC530.07c
phosphomethylpyrimidine
kinase (predicted)
SPAC19D5.09c retrotransposable element SPBC582.08
alanine aminotransferase
(predicted)
SPAC19G12.16c conserved fungal protein SPBC725.03 conserved fungal protein
SPAC1A6.03c phospholipase (predicted) SPBC839.16
C1-5,6,7,8-
tetrahydrofolate (THF)
synthase
SPAC1A6.04c phospholipase B homolog Plb1 SPBP19A11.02c sequence orphan
SPAC1B3.06c
UbiE family methyltransferase
(predicted) SPBP23A10.14c
RNA polymerase II
transcription elongation
factor SpELL
SPAC1F5.03c
FAD-dependent oxidoreductase
(predicted) SPCC1322.10 conserved fungal protein
SPAC227.11c
sensor for misfolded ER glycoproteins
Yos9 (predicted) SPCC16A11.04
sorting nexin Snx12
(predicted)
SPAC227.17c conserved protein (fungal and plant) SPCC16A11.15c sequence orphan
SPAC22A12.06c serine hydrolase SPCC24B10.06 sequence orphan
SPAC22A12.10
diacylglycerol
cholinephosphotranferase/
diacylglycerol
ethanolaminesphotranferase
(predicted) SPCC285.04 transthyretin (predicted)
SPAC22E12.03c
THIJ/PFPI family peptidase
(predicted) SPCC4B3.06c
NADPH-dependent FMN
reductase (predicted)
SPAC22G7.07c
mRNA (N6-adenosine)-
methyltransferase (predicted) SPCC584.11c Svf1 family protein Svf1
SPAC23A1.17 WIP homolog SPCC663.09c
short chain
dehydrogenase
(predicted)
SPAC23D3.12
inorganic phosphate transporter
(predicted) SPCC736.10c
mitochondrial ribosomal
protein subunit S8
SPAC23H4.17c
cyclin-dependent protein Srb mediator
subunit kinase Srb10 SPCC757.03c ThiJ domain protein
SPAC25B8.12c
nucleotide-sugar phosphatase
(predicted) SPCC757.11c membrane transporter
SPAC26A3.08 Sm snRNP core protein Smb1 SPCC794.15 sequence orphan
SPAC26A3.16 UBA domain protein Dph1 SPCC965.06
potassium channel
subunit (predicted)
SPAC26F1.02 pinin homologue SPCPB16A4.06c sequence orphan
SPAC27F1.06c
FKBP-type peptidyl-prolyl cis-trans
isomerase (predicted) SPCC825.03c SNARE Psy1
SPAC29A4.13 urease accessory protein UreF SPAC1250.03
ubiquitin conjugating
enzyme Ubc14
SPAC2C4.13 V-type ATPase subunit c'' SPCC330.05c
orotidine 5'-phosphate
decarboxylase Ura4
SPAC29E6.02
U4/U6 x U5 tri-snRNP complex
subunit Prp3 (predicted) SPBC649.04
UV-induced protein
Uvi15
SPAC30C2.04
cofactor for methionyl-and glutamyl-
tRNA synthetases (predicted) SPAC9E9.07c GTPase Ypt2
SPAC30D11.03 ATP-dependent RNA helicase
Table 3.5: Continued 77

Ddx27/Drs1 (predicted)
SPAC30D11.11 Haemolysin-III family protein
SPAC31G5.10 Myb family protein Eta2
SPAC323.02c
20S proteasome component alpha 5,
Pup2 (predicted)
SPAC3A12.16c
TIM23 translocase complex subunit
Tim17
SPAC4F8.06
mitochondrial ribosomal protein
subunit S12 (predicted)
SPAC513.04 sequence orphan
SPAC56F8.15 dubious
SPAC57A10.09c
High-mobility group non-histone
chromatin protein
SPAC607.06c metallopeptidase
SPAC644.08
methionine salvage haloacid
dehalogenase-like hydrolase
(predicted)
SPAC644.17c
mitochondrial ribosomal protein
subunit L9 (predicted)
SPAC683.02c zf-CCHC type zinc finger protein
SPAC6G9.08 ubiquitin C-terminal hydrolase Ubp6
SPAC732.01 V-type ATPase proteolipid subunit
SPAC806.04c DUF89 family protein
SPAC9.09 homocysteine methyltransferase
SPAC9E9.09c aldehyde dehydrogenase (predicted)
SPAP27G11.09c GTP cyclohydrolase (predicted)
SPAP7G5.06 amino acid permease, unknown 4
SPAP8A3.05
ski complex interacting GTPase
(predicted)
SPAPB1E7.07 glutamate synthase Glt1 (predicted)
SPAPB2B4.02 monothiol glutaredoxin Grx5
SPAPB2B4.07
ubiquitin family protein, human
UBTD1 homolog
SPBC106.16
20S proteasome component alpha 4
Pre6
SPBC1105.14 transcription factor Rsv2
SPBC119.09c ORMDL family protein
SPBC119.10 asparagine synthetase
SPBC1198.07c
mannan endo-1,6-alpha-mannosidase
(predicted)
SPBC1198.13c
transcription factor TFIIF complex
beta subunit Tfg2 (predicted)
SPBC11C11.05
KRE9 family cell wall biosynthesis
protein (predicted)
SPBC11G11.03 ribosome assembly protein (predicted)
SPBC1347.11 Stress Responsive Orphan 1
SPBC13E7.04 F1-ATPase delta subunit (predicted)
SPBC146.02 sequence orphan
SPBC14F5.10c ubiquitin-protein ligase E3 (predicted)
SPBC16A3.08c serpine1 related protein (predicted)
SPBC16E9.11c
HECT-type ubiquitin-protein ligase
Pub3
SPBC16H5.05c
cyclophilin family peptidyl-prolyl cis-
trans isomerase Cyp7
SPBC1703.13c
mitochondrial inorganic phosphate
transporter (predicted)
SPBC1709.15c
cleavage factor two
Cft2/polyadenylation factor CPSF-73
(predicted)
SPBC1773.01 striatin homolog
SPBC17D11.08
WD repeat protein, human WDR68
family
SPBC1E8.04 retrotransposable element: pseudo
SPBC21D10.09c ubiquitin-protein ligase E3 (predicted)
SPBC25H2.15
programmed cell death protein
homolog
SPBC29A10.06c conserved fungal protein
Table 3.5: Continued 78

SPBC29A10.09c CAF1 family ribonuclease
SPBC2A9.05c DUF846 family protein
SPBC2G2.12
mitochondrial and cytoplasmic
histidine-tRNA ligase Hrs1
SPBC2G5.05 transketolase (predicted)
SPBC30B4.08 double-strand siRNA ribonuclease
SPBC27B12.01c
Mdm10/Mdm12/Mmm1 complex
subunit Mmm1 (predicted)
SPBC359.03c amino acid permease, unknown 8
SPBC359.06 adducin
SPBC36B7.08c
nucleosome assembly protein
(predicted)
SPBC3H7.06c F-box protein Pof9
SPBC3H7.07c phosphoserine phosphatase (predicted)
SPBC543.02c
DNAJ/TPR domain protein DNAJC7
family
SPBC577.11 sequence orphan
SPBC660.05 conserved fungal protein
SPBC725.13c GINS complex subunit Psf2
SPBC776.03 homoserine dehydrogenase (predicted)
SPBC83.13
mitochondrial tricarboxylic acid
transporter
SPBC839.10 U1 snRNP-associated protein Usp107
SPBP23A10.03c ACN9 family mitochondrial protein
SPBP23A10.15c
mitochondrial processing peptidase
complex beta subunit Qcr1
SPBP23A10.16
TIM22 inner membrane protein import
complex anchor subunit Tim18
SPBP8B7.05c carbonic anhydrase (predicted)
SPBP8B7.25
cyclophilin family peptidyl-prolyl cis-
trans isomerase Cyp4
SPCC1281.06c acyl-coA desaturase (predicted)
SPCC1393.08
transcription factor, zf-GATA type
(predicted)
SPCC1393.09c RWD domain
SPCC1393.12 sequence orphan
SPCC1393.13 DUF89 family protein
SPCC1494.11c retrotransposable element: pseudo
SPCC1620.09c
transcription factor TFIIF complex
alpha subunit Tfg1 (predicted)
SPCC1682.04 centrin
SPCC16C4.08c Shk1 kinase binding protein 15
SPCC1739.09c
cytochrome c oxidase subunit VIa
(predicted)
SPCC18.05c notchless-like protein
SPCC1827.06c
aspartate semialdehyde dehydrogenase
(predicted)
SPCC191.08 DUF1715 family protein
SPCC1919.07 sequence orphan
SPCC31H12.03c RNA binding protein (predicted)
SPCC1235.01 sequence orphan
SPCC320.11c RNA-binding protein
SPCC338.10c cytochrome c oxidase subunit V
SPCC364.06 nucleosome assembly protein Nap1
SPCC417.08 translation elongation factor eEF3
SPCC550.11 karyopherin
SPCC550.15c
ribosome biogenesis protein
(predicted)
SPCC553.12c conserved fungal protein
SPCC584.11c Svf1 family protein Svf1
SPCC584.16c sequence orphan
SPCC594.04c
steroid oxidoreductase superfamily
protein
SPCC594.07c sequence orphan
SPCC11E10.01 cystathionine beta-lyase (predicted)
SPCC61.01c siderophore-iron transporter Str2
SPCC63.14 conserved fungal protein
Table 3.5: Continued 79

SPCC736.10c
mitochondrial ribosomal protein
subunit S8
SPCC737.02c
ubiquinol-cytochrome-c reductase
complex subunit 6
SPCC790.03 rhomboid family protease
SPCC794.04c membrane transporter
SPCC794.11c ENTH/VHS domain protein Ent3
SPCC970.10c ubiquitin-protein ligase E3 Brl2
SPCP1E11.05c
acyl-coA-sterol acyltransferase
(predicted)
SPCP1E11.08
ribosome biogenesis protein Nsa2
(predicted)
SPCP1E11.11 Puf family RNA-binding protein
SPCPB16A4.05c
urease accessory protein UREG
(predicted)
SPCPJ732.02c xylulose kinase (predicted)
SPBC21C3.18 serine/threonine protein kinase Spo4
SPCC188.06c
signal recognition particle subunit
Srp54
SPAC4H3.05
ATP-dependent DNA helicase, UvrD
subfamily
SPCC825.03c SNARE Psy1
SPBC776.09 ATP-dependent RNA helicase Ste13
SPAC1565.04c adaptor protein Ste4
SPCC5E4.03c
SAGA complex subunit/TATA-
binding protein associated
factor/transcription factor TFIID
complex subunit Taf5
SPAC29E6.08 TATA-binding protein (TBP)
SPAC29A4.02c
translation elongation factor EF-1
gamma subunit
SPCC1450.04
translation elongation factor EF-1 beta
subunit (eEF1B)
SPBC25H2.07 translation initiation factor eIF1A
SPBC17G9.09
translation initiation factor eIF2
gamma subunit
SPAC4D7.05 translation initiation factor eIF3i
SPBC1709.18
translation initiation factor eIF4E 4F
complex subunit
SPCC1919.09 translation initiation factor eIF6
SPCC24B10.21 triosephosphate isomerase
SPBC337.08c ubiquitin, ubi4
SPCC285.07c wtf element Wtf18
SPBC1289.17 retrotransposable element
SPBC1E8.04 retrotransposable element
SPAC13D1.01c retrotransposable element
SPAC26A3.13c retrotransposable element
SPAC167.08 retrotransposable element
SPCC1020.14 retrotransposable element
SPAPB15E9.03c retrotransposable element
SPAC27E2.08 retrotransposable element
SPAC9.04 retrotransposable element
SPBC9B6.02c retrotransposable element

2 fold up-
regulated in
∆gcn5 ∆mst2
after 60 min,,
KCL annotation
2 fold up-
regulated in
∆gcn5 ∆mst2 annotation
SPCC330.05c orotidine 5'-phosphate decarboxylase Ura4 SPAC5D6.04
auxin family transmembrane
transporter (predicted)
SPCC1739.08
c short chain dehydrogenase (predicted) SPBC800.07c
mitochondrial translation
elongation factor EF-Ts
Tsf1
Table 3.5: Continued 80

SPBC359.06 adducin SPBC18H10.05
WD repeat protein, human
WDR44 family
SPBC1198.14
c fructose-1,6-bisphosphatase Fbp1 SPBC16G5.05c MSP domain
SPAC3G9.11c pyruvate decarboxylase (predicted)
SPAPB24D3.1
0c alpha-glucosidase Agl1
SPCC794.01c
glucose-6-phosphate 1-dehydrogenase
(predicted) SPAC1327.01c
transcription factor, zf-
fungal binuclear cluster type
(predicted)
SPCC13B11.0
1 alcohol dehydrogenase Adh1
SPAPB24D3.0
7c sequence orphan
SPAC13F5.03
c
mitochondrial glycerol dehydrogenase
Gld1 SPAC19G12.08
sphingosine hydroxylase
(predicted)
SPACUNK4.1
0 hydroxyacid dehydrogenase (predicted) SPCC306.10 wtf element Wtf8, pseudo
SPAC1002.19 GTP cyclohydrolase II (predicted) SPAPB2B4.03 cyclin Cig2
SPAC22H10.1
3 metallothionein Zym1 SPBC1271.05c
zf-AN1 type zinc finger
protein
SPBC13A2.04
c PTR family peptide transporter SPCP31B10.06 C2 domain protein
SPBC19C2.05 serine/threonine protein kinase Ran1 SPAC29B12.04
pyridoxine biosynthesis
protein
SPBC1347.11 Stress Responsive Orphan 1 SPCC663.06c
short chain dehydrogenase
(predicted)
SPAC31G5.09
c MAP kinase Spk1 SPAC22F8.04
triose phosphate transporter
(predicted)
SPCC757.03c ThiJ domain protein SPCC1259.03
DNA-directed RNA
polymerase complex I
subunit Rpa12
SPAC1039.09 amino acid permease Isp5 SPCC338.18 sequence orphan
SPBC3E7.13c Splicing factor, SYF2 family SPBC646.12c
GTPase activating protein
Gap1
SPCC16A11.1
5c sequence orphan SPAC11G7.03
isocitrate dehydrogenase
(NAD+) subunit 1 Idh1
SPAC27D7.03
c
RNA-binding protein involved in meiosis
Mei2 SPAC343.12 conserved fungal protein
SPAC22F3.12
c regulator of G-protein signaling Rgs1 SPAC3G9.04
phosphoric ester hydrolase
Ssu72 (predicted)
SPAC977.16c dihydroxyacetone kinase Dak2
SPAPB24D3.0
8c
NADP-dependent
oxidoreductase (predicted)
SPAC15E1.02
c DUF1761 family protein SPBC1711.02
mating-type m-specific
polypeptide mc
SPCC1393.12 sequence orphan SPBC1683.08 hexose transporter Ght4
SPCC1020.02 kinetochore protein Spc7
SPCPB16A4.03
c
IMPcyclohydrolase/phospho
ribosylaminoimidazolecarbo
xamideformyltransferase
SPAC11H11.0
4 pheromone p-factor receptor SPAP8A3.13c Vid24 family protein
SPAC1F5.09c PAK-related kinase Shk2 SPAC2F3.10
GARP complex subunit
Vps54 (predicted)
SPCC965.06 potassium channel subunit (predicted) SPAC56F8.16
transcription factor Esc1
(predicted)
SPBC725.10
tspO homolog/ peripheral benzodiazepine
receptor homolog, involved in the
transport cytoplas/mitochondrial of haem
(predicted) SPAC26H5.08c
glucan 1,3-beta-glucosidase
Bgl2
SPBC32C12.0
2 transcription factor Ste11 SPAC1635.01
voltage-dependent anion-
selective channel
SPAC26H5.09
c GFO/IDH/MocA family oxidoreductase SPAC23D3.12
inorganic phosphate
transporter (predicted)
SPAC1A6.04c phospholipase B homolog Plb1 SPBC215.11c
aldo/keto reductase,
unknown biological role
SPAC19G12.1
6c conserved fungal protein SPBC1683.01
inorganic phosphate
transporter (predicted)
Table 3.5: Continued 81

SPAC11D3.01
c conserved fungal protein
SPAC57A10.09
c
High-mobility group non-
histone chromatin protein
SPAC19G12.0
9
NADH/NADPH dependent indole-3-
acetaldehyde reductase AKR3C2 SPBC800.10c
EPS15 repeat family actin
cortical patch component
(predicted)
SPAC26F1.14
c apoptosis-inducing factor homolog Aif1 SPAC16E8.02 DUF962 family protein
SPCC965.07c glutathione S-transferase Gst2 SPCC1919.06c wtf element
SPBC16E9.11
c HECT-type ubiquitin-protein ligase Pub3 SPAC20G8.02
mitochondrial phospholipase
(predicted)
SPCC584.11c Svf1 family protein Svf1 SPBC24C6.06 G-protein alpha subunit
SPBC19F8.07
cyclin-dependent kinase activating kinase
Crk1 SPBC1778.04
Spo4-Spo6 kinase complex
regulatory subunit Spo6
SPAC2F3.05c xylose and arabinose reductase (predicted) SPBC1711.02
mating-type m-specific
polypeptide mc
SPBC19C2.04
c ubiquitin C-terminal hydrolase Ubp11 SPAC4A8.04
vacuolar serine protease
Isp6
SPAC3C7.14c ubiquitinated histone-like protein Uhp1 SPBC3H7.02
sulfate transporter
(predicted)
SPAC8F11.10
c pyruvyltransferase Pvg1 SPAP14E8.02
homolog of S. cerevisiae
Tos4
SPBC29A10.1
4 meiotic cohesin complex subunit Rec8 SPCC1620.04c
Cdc20/Fizzy family WD
repeat protein
SPBC56F2.06 sequence orphan SPAC637.03 conserved fungal protein
SPCC737.04
S. pombe specific UPF0300 family protein
6 SPAC14C4.07 membrane transporter
SPAC21E11.0
4
L-azetidine-2-carboxylic acid
acetyltransferase SPBC2G2.17c
beta-glucosidase Psu2
(predicted)
SPCC1442.01 guanyl-nucleotide exchange factor Ste6 SPCC594.02c conserved fungal protein
SPBC1683.06
c uridine ribohydrolase (predicted) SPAC1D4.14
THO complex subunit Tho2
(predicted)
SPAC14C4.01
c DUF1770 family protein SPBP4H10.10 rhomboid family protease
SPAC4H3.03c glucan 1,4-alpha-glucosidase (predicted)
SPAC12B10.14
c
serine/threonine protein
kinase Ppk2 (predicted)
SPAC521.03 short chain dehydrogenase (predicted) SPAC9E9.03
3-isopropylmalate
dehydratase Leu2
(predicted)
SPBC19G7.06 MADS-box transcription factor Mbx1 SPCC895.08c conserved fungal protein
SPCC663.08c short chain dehydrogenase (predicted) SPAC869.10c
proline specific permease
(predicted)
SPAPB8E5.03 malic acid transport protein Mae1
SPBC29A10.03
c
chromatin remodeling
complex subunit Rlf2
(predicted)
SPCC70.08c methyltransferase (predicted)
SPAC30D11.02
c sequence orphan
SPCC548.07c hexose transporter Ght1 SPCC285.11
UBA/UAS domain protein
Ucp10
SPAC4G9.12 gluconokinase SPAC31G5.10 Myb family protein Eta2
SPBC32H8.02
c NEDD8 protease Nep2
SPAC19G12.10
c
vacuolar carboxypeptidase
Y
SPBC725.11c
CCAAT-binding factor complex subunit
Php2 SPBC119.03 human COMT homolog 1
SPBC725.03 conserved fungal protein SPAC513.02
phosphoglycerate mutase
family
SPAPB1A10.1
4 F-box protein SPCC191.01 sequence orphan
SPAC31G5.08 uroporphyrinogen-III synthase Ups1 SPBC902.05c
isocitrate dehydrogenase
(NAD+) subunit 2
SPCC306.08c malate dehydrogenase SPAC977.17
MIP water channel
(predicted)
SPAC11D3.18
c
nicotinic acid plasma membrane
transporter (predicted)
SPBC32F12.03
c glutathione peroxidase Gpx1
SPCC594.04c steroid oxidoreductase superfamily protein SPBC215.10
haloacid dehalogenase-like
hydrolase
Table 3.5: Continued 82

SPBC23G7.10
c
NADH-dependent flavin oxidoreductase
(predicted) SPAC167.05
Usp (universal stress
protein) family protein,
implicated in meiotic
chromosome segregation
SPBP23A10.1
1c conserved fungal protein SPCC1739.06c
uroporphyrin
methyltransferase
(predicted)
SPAC27D7.11
c But2 family protein SPBC8D2.18c
adenosylhomocysteinase
(predicted)
SPCC191.11 beta-fructofuranosidase SPCC16A11.04
sorting nexin Snx12
(predicted)
SPAC688.04c glutathione S-transferase Gst3 SPAC513.06c
dihydrodiol dehydrogenase
(predicted)
SPBC1921.03
c mRNA export receptor Mex67 SPAC6G9.05
coenzyme A diphosphatase
(predicted)
SPBC1773.06
c alcohol dehydrogenase (predicted) SPBC651.03c
GTPase activating protein
Gyp10
SPAC922.03
1-aminocyclopropane-1-carboxylate
deaminase (predicted) SPCC645.06c RhoGEF Rgf3
SPCC1739.01 zf-CCCH type zinc finger protein SPAC11E3.06
MADS-box transcription
factor Map1
SPAC227.13c
mitochondrial iron-sulfur cluster assembly
scaffold protein Isu1 SPBC19C2.02
DNA methyltransferase
homolog
SPAC25G10.0
9c
actin cortical patch component, with EF
hand and WH2 motif Panl (predicted) SPBC543.07 MAP kinase kinase Pek1
SPBC1718.07
c
CCCH tandem zinc finger protein, human
Tristetraprolin homolog Zfs1 SPAC4D7.02c
glycerophosphoryl diester
phosphodiesterase
(predicted)
SPCC1322.10 conserved fungal protein SPBC216.03 conserved fungal protein
SPBC25B2.03 zf-C3HC4 type zinc finger SPAC167.06c sequence orphan
SPAC806.04c DUF89 family protein SPAC19A8.12
mRNA decapping complex
subunit Dcp2
SPAC1B9.02c serine/threonine protein kinase Sck1 SPCC757.02c epimarase (predicted)
SPAC22A12.1
1 dihydroxyacetone kinase Dak1 SPBC13E7.03c
RNA hairpin binding protein
(predicted)
SPAC26F1.04
c enoyl-[acyl-carrier protein] reductase SPCC1902.01 transcription factor Gaf1
SPBPB7E8.02 PSP1 family protein SPBC337.16
phosphatidyl-N-
methylethanolamine N-
methyltransferase
(predicted)
SPBC19G7.13 DNA binding factor Trf1 SPAC5D6.13
Golgi phosphoprotein 3
family
SPBC29A10.1
6c cytochrome b5 (predicted) SPBC1718.01
F-box/WD repeat protein
Pop1
SPAC328.07c
heavy metal ion homeostasis protein
(predicted) SPCC794.07
dihydrolipoamide S-
acetyltransferase E2
(predicted)
SPAC23E2.03
c meiotic suppressor protein Ste7 SPAC20H4.11c Rho family GTPase Rho5
SPBC14F5.10
c ubiquitin-protein ligase E3 (predicted) SPCC1620.02 wtf element Wtf23
SPBC1685.05 serine protease (predicted) SPCC663.09c
short chain dehydrogenase
(predicted)
SPBC21C3.18 serine/threonine protein kinase Spo4 SPBC1D7.02c transcription factor Scr1
SPAC3H1.11 transcription factor Hsr1 SPBP4H10.12
conserved protein (fungal
and bacterial)
SPAC1F7.07c iron permease Fip1
SPAC19E9.03 cyclin Pas1

83

3.3.7 Histone acetylation levels in HAT mutants. Gcn5/SAGA is a known regulator of
H3 acetylation, as is Elp3/Elongator (WINKLER et al. 2002; YAMADA et al. 2004). The
phenotypes associated with ∆mst2 suggest it is the functional orthologue of ScSas2, but if
this is the case, there is no obvious NuA3/Sas3 homologue in S. pombe to overlap with
Gcn5 activity, as Sas3 does in S. cerevisiae. Because more genes showed changes in
expression in the double mutants than would be expected by a simple sum of those
affected in the single mutants, we examined levels of histone H3 acetylation in the
mutant strains to see whether there is evidence for overlapping specificity at the level of
global histone acetylation.
As expected, we found H3 acetylation levels on H3K9, K14 and K18 were
dramatically reduced in the ∆gcn5 mutant (Fig 3.5). In ∆elp3 and ∆mst2 as well as in the
∆mst2 ∆elp3 double mutant there is only a modest decrease in H3K9 acetylation levels
compared to wild type. In contrast, all strains lacking gcn5 show significant loss of
H3K9ac (Fig 3.5A), suggesting that Gcn5 is the major contributor to H3K9 acetylation.
Similar results were observed for H3K18ac.
For H3K14 acetylation we found significant reductions of acetylation levels for
each single mutant compared to wild-type cells. Strikingly, in the double mutant ∆gcn5
∆mst2, the signal is much more strongly reduced (Fig3.5B). None of the deletion mutants
showed any significant reduction in the overall level of histone H3 (Fig3.5D). Therefore
we conclude that Gcn5 (GNAT family) and Mst2 (MYST family) each contribute to
acetylate H3K14, which has been shown to be important for the response to salt stress
(JOHNSSON et al. 2009). Defective acetylation of H3K14 could explain the
hypersensitivity to salt stress observed in the ∆gcn5 ∆mst2 mutant.
84

Figure 3.5: Histone H3 acetylation is differentially affected by different HAT
mutants. Levels were determined by Western blots of whole cell lysates from the
indicated strains with antibodies specific to H3K9ac, H3K14ac, H3K18ac, compared to
levels of actin and total histone H3 (C-term). Strain list: wild-type (FY368), ∆gcn5
(Hu799), ∆elp3(FY3851), ∆mst2 (FY1890), ∆gcn5 ∆mst2(Hu990), ∆gcn5 ∆elp3
(FY3847), ∆mst2 ∆elp3 (FY3850), ∆gcn5 ∆elp3 ∆mst2 (3854)

3.3.8 Genes differentially expressed by the essential HAT Mst1. Finally, we examined
the essential MYST family HAT Mst1 using the temperature sensitive allele mst1
ts

(GOMEZ et al. 2008). The mst1 mutant was grown at the semi-permissive temperature
30°C overnight and RNA was isolated for microarray analysis. There were many more
differentially expressed genes in the mst1 mutant compared to any of the non-essential
HATs studied here (Table 3.6).

Down-regulated genes
mst
1ts

Gene
Log2
chan
ge p-value
SPAC1039.02 -2.66
0.000635
869
SPBC29A3.05 -2.18 5.55E-05
SPCC757.06 -2.08 1.87E-07

Table 3.6: Continued 85

Up-regulated genes
mst1
ts
mst1
ts
mst1
ts

Gene
Log 2
change p-value Gene
Log 2
change p-value Gene
Log2
change
p-
value
SPBC1348.0
9 1.89 3.69E-11 SPAC977.17 2.40
1.80E-
08 map2 3.52
2.50E-
12
SPAC22F8.0
5 1.90
0.001560
473
SPBC1348.1
4c 2.41
2.14E-
15 SPAPJ695.01c 3.52
2.00E-
09
SPAC3C7.13
c 1.92 3.23E-10
SPAC5H10.
02c 2.46
3.89E-
11 SPBC1198.01 3.55
7.19E-
16
SPBPB2B2.0
6c 1.93
0.000987
078
SPCC663.08
c 2.54
0.00980
7792 SPAC22A12.17c 3.57
1.96E-
11
SPBPB2B2.0
7c 1.93 9.41E-10 SPBC725.10 2.57
9.52E-
05 SPAPB1A11.03 3.59
1.50E-
13
nta1 1.94 3.20E-06 SPBC83.19c 2.58
3.49E-
12 SPAC1F8.04c 3.59
5.41E-
07
SPCC191.01 1.94 5.61E-06
SPCC1393.1
2 2.58
4.35E-
11 SPAC11D3.01c 3.61
1.72E-
07
SPCC70.04c 1.95 2.09E-06
SPBPB2B2.0
8 2.60
0.00786
8315 SPBPB8B6.03 3.64
2.07E-
12
meu7 1.96 2.81E-05 SPCC777.04 2.63
3.77E-
05 SPBP4G3.03 3.65
2.74E-
13
SPAC9.10 1.98 8.57E-09
SPAC26F1.0
5 2.64
1.00E-
07 SPCC663.06c 3.66
3.28E-
05
map1 1.98
0.000618
909 pma2 2.64
6.19E-
07 SPBPB21E7.04c 3.67
3.08E-
06
SPBC8E4.05
c 1.99 1.54E-08
SPAC32A11
.02c 2.65
4.69E-
09 frp1 3.69
3.37E-
05
SPAC637.03 2.03
0.000132
799
SPBC2G2.17
c 2.66
2.11E-
07 SPCC737.04 3.85
3.10E-
07
SPBC4C3.08 2.04 6.23E-08
SPAC56F8.1
5 2.68
0.00127
6426 SPBC359.06 3.91
0.0004
99938
meu10 2.05 4.69E-07
SPAPJ691.0
2 2.72
1.52E-
05 apc10 3.96
4.49E-
12
SPCC1840.1
2 2.05 4.17E-06
SPBC1773.0
6c 2.76
0.00046
9242 SPAPB8E5.10 3.98
1.31E-
12
SPBPB2B2.0
2 2.06
0.000305
555
SPBC1685.0
5 2.86
1.62E-
11 SPBC16E9.16c 4.00
6.07E-
13
SPBC19C7.0
4c 2.09
0.001283
597
SPAC4F10.1
7 2.88
6.57E-
09 SPAC29A4.12c 4.06
1.45E-
09
SPAC5H10.
04 2.10 1.33E-06
SPCC16A11.
15c 2.94
5.09E-
11 SPAC869.08 4.08
1.01E-
15
SPBC947.05
c 2.11 5.62E-08
SPCC1739.0
8c 2.96
0.02151
2753 SPBC3H7.08c 4.09
9.33E-
14
SPAC3H8.0
9c 2.11 1.77E-10
SPAC23C11.
06c 2.99
1.15E-
07 SPBCPT2R1.08c 4.16
0.0002
58571
ish1 2.11 9.95E-06
SPAC15E1.0
2c 3.00
8.68E-
09 fbp1 4.32
3.57E-
14
SPAC513.02 2.12 1.94E-06
SPBC1105.1
3c 3.02
1.10E-
07 SPBC56F2.06 4.36
2.99E-
07
SPAC4H3.0
3c 2.14
0.000486
057 grt1 3.04
7.61E-
08 mel1 4.43
2.62E-
15
SPAPB15E9.
02c 2.17 3.00E-08 SPCC338.18 3.04
7.26E-
07 SPAC139.05 4.49
1.53E-
09
SPCC794.01
c 2.18
0.042343
035
SPBPB2B2.1
8 3.05
1.46E-
05 SPCPB16A4.06c 4.53
1.21E-
11
SPAC1F8.02
c 2.18 3.57E-07
SPCC1322.0
7c 3.10
9.51E-
09 SPBC1289.14 4.61
8.12E-
16
SPBC4.01 2.20 9.35E-05
SPCC757.03
c 3.11
2.10E-
09 ght3 4.72
0.0019
73142
SPBPB8B6.0
2c 2.23 1.43E-12
SPAC4H3.0
8 3.16
4.98E-
12 zym1 4.85
1.83E-
08
SPBC36.02c 2.23
0.000135
759
SPBPB2B2.1
2c 3.16
0.00706
426 SPBC24C6.09c 4.94
1.55E-
13
SPCC1393.0
7c 2.23 4.88E-10 spk1 3.17
0.00021
6514 dak2 5.02
4.45E-
12
Table 3.6: Continued 86

SPAC513.06
c 2.24 1.52E-09 mei2 3.25
0.00088
8516 SPAC186.02c 5.11
6.43E-
15
SPCPB1C11.
02 2.25 7.04E-07
SPAC977.05
c 3.29
2.46E-
05 eno102 5.11
3.01E-
13
ste11 2.27
0.000335
259 SPAC1F8.08 3.32
2.20E-
09 SPAC3G9.11c 5.13
5.88E-
11
wtf20 2.28 4.37E-06
SPAC3G6.0
7 3.33
1.53E-
05 SPAC22G7.11c 5.22
4.34E-
14
ppk33 2.28
0.000119
009
SPACUNK4.
17 3.33
3.64E-
07 SPBC23G7.10c 5.25
4.94E-
06
SPAC1F7.06 2.33 5.44E-12
SPAC23H3.
15c 3.42
1.03E-
05 isp3 5.36
1.87E-
11
ssa1 2.34
0.000834
021 caf5 3.44
4.99E-
07 SPAC869.06c 6.61
2.79E-
13
cta3 2.36 6.88E-11 str3 3.48
2.47E-
05 SPAC869.09 6.68
2.91E-
12
agl1 2.37
0.026304
809
Table 3.6: Differentially expressed genes in mst1
ts
. This table lists the down and up-
regulated genes of mst1
ts
cells compared to wild-type cells using an Affymetrix
microarray.

There were also many more up-regulated than down-regulated genes in the mst1
mutant, suggesting that it functions in repression of gene expression. Consistent with this
there were no GO categories that were significantly enriched in the down-regulated
genes, however there were many that were enriched in the up-regulated genes (Table
3.2). These GO groups include metal and salt transporters, and other metabolic processes.
When we compared these GO categories with those observed for the other mutants, we
found that there was some overlap with the double mutant ∆gcn5 ∆mst2 and the triple
mutant ∆gcn5 ∆elp3 ∆mst2, suggesting general stress responses in these mutants are de-
regulated (Fig 3.6).
87

Figure 3.6: Venn diagram of differentially down and up-regulated GO terms of mst1
ts

mutant compared to single, double, and triple HAT mutants. (Table 3.2) Strain list:
Strain list: wild-type (FY261), mst1
ts
(FY2535) ∆elp3 (FY 3851), ∆gcn5 (FY2943),
∆mst2 (FY1890), ∆gcn5 ∆elp3 (FY3847), ∆gcn5 ∆mst2(FY3361), ∆mst2 ∆elp3
(FY3850), ∆gcn5 ∆elp3 ∆mst2 (3854).

3.4 Discussion:
Fission yeast shares several conserved histone acetyltransferases with other eukaryotes.
In the GNAT family, the Elp3 (KAT9) and Gcn5 (KAT2) enzymes are highly conserved
(ALLIS et al. 2007). In the MYST family, the Kat5 HAT Esa1/Tip60/Mst1 protein is also
highly conserved. However, the relationships between the other MYST family members
are less clear-cut. In budding yeast, two additional MYST proteins ScSas2 and ScSas3
have been characterized. ScSas2 antagonizes ScSir2 in telomere silencing as a
component of the SAS complex. ScSas3, a component of NuA3 (JOHN et al. 2000),
overlaps with Gcn5 such that a double mutant Sc∆gcn5 ∆sas3 is lethal (HOWE et al.
2001). By contrast, there is only one additional MYST protein in S. pombe, Mst2, which
88

resembles both S. cerevisiae proteins in primary sequence. Like ScSas2, SpMst2
antagonizes SpSir2 in telomere silencing (GOMEZ et al. 2005), while work from this study
suggests that like ScSas3, SpMst2 acetylates histone H3K14. This works shows that
SpMst2 functions similarly to both ScSas2 and ScSas3. To dissect out the relationship
between these potentially overlapping HAT enzymes Mst2, Elp3 and Gcn5, we compared
their phenotypic and transcriptional interactions in S. pombe.
First, we performed the initial characterization of the catalytic HAT, Elp3, which
is the likely catalytic subunit of the Elongator complex in S. pombe. The strain ∆elp3 is
viable, although it suffers defects in overall cell growth. It shows a delay in entry into the
cell cycle, and premature cell cycle exit (Fig3.1B). It should be noted that some of the
phenotypes seen in Elp3 defective strains could result from defects in other functions that
have been reported for the Elongator complex in addition to its role as a HAT (HUANG et
al. 2005; SVEJSTRUP 2007). We next investigated whether ∆elp3 shows genetic
interactions with mutations in other non-essential HAT genes encoded by gcn5
+
and
mst2
+
. Double and triple mutants are all viable, although they show increasingly severe
growth defects as more HAT genes are mutated. The viability of Sp∆mst2 ∆gcn5
contrasts with the lethality of Sc∆sas3 ∆gcn5 and suggests that Mst2 is not a simple
equivalent of ScSas3. Alternatively, there may be another enzyme in fission yeast, which
provides an additional degree of redundancy. We suggest that Mst2 fulfills many of the
functions associated with both ScSas2 and ScSas3 (see below).
Phenotypic analysis suggests distinct effects of each HAT. For example, as
shown previously ∆gcn5 mutants are de-repressed for mating and meiosis functions, and
are sensitive to certain salt-stress conditions (HELMLINGER et al. 2008; JOHNSSON et al.
89

2006). ∆mst2 mutants show modest sensitivity to DNA damaging agents such as HU and
MMS. ∆gcn5 ∆mst2 double mutants show significantly increased salt sensitivity, and a
modest increase in DNA damage sensitivity relative to single mutants. Thus, we
conclude that in response to salt stress, Gcn5 and Mst2 have a substantial functional
overlap. In contrast, ∆gcn5 ∆elp3 and ∆mst2 ∆elp3 showed less evidence for synthetic
phenotypes, with only a modest increase in TBZ sensitivity in ∆gcn5 ∆elp3 relative to the
parents (Fig3.1 C&D). In fact, Elp3 appears to be antagonistic to Mst2, because ∆elp3
suppresses ∆mst2 mutant sensitivity to high salt concentrations and HU. We speculate
this could be due to slowing down the growth of ∆mst2 cells, allowing time for the cells
to repair any damage that may have occurred. Together, these data suggest that Gcn5
affects multiple pathways, some overlapping with Elp3, and others overlapping with
Mst2. However, since the double mutants and even the triple mutants are viable, either
additional HAT enzymes play a role, or the acetylation modifications controlled by these
enzymes are not strictly essential for viability.
To determine whether the functional redundancy between HATs is at the level of
gene expression, we performed transcriptional profiling using DNA microarrays of
∆elp3, ∆gcn5, and ∆mst2. Similar to previous results with ∆gcn5 (HELMLINGER et al.
2008; JOHNSSON et al. 2006) we found that few genes were affected by deletion of any
single HAT gene under favorable growth conditions. Although HATs are presumed to be
gene activators that facilitate transcriptional initiation or elongation (BERGER 2002), we
found that gene expression was as likely to be increased as reduced in our mutant strains.
Up-regulated genes could represent indirect targets, although many Gcn5-repressed genes
are known to be bound by Gcn5 (JOHNSSON et al. 2009). This suggests that Gcn5 may
90

play a direct role in gene repression, which has been described previously (HELMLINGER
et al. 2008). It is thus possible that the other HATs studied here also play direct roles in
transcriptional repression.
When we examined the double mutants, we found that their gene expression
profiles were not simply the combination of the profiles from the two single mutants, but
affected additional genes. This supports the hypothesis that the HATs play partly
redundant roles in gene regulation, with multiple enzymes contributing to expression of
common targets. Importantly, although they may affect common genes, the regulatory
mechanisms may be distinct. In budding yeast, although ScGcn5 and ScElp3 affect
transcription of the ScHsp70 genes ScSSA3 and ScSSA4, this occurs by different
mechanisms because Gcn5 is required for transcription factor binding while Elp3 is
required for proper Pol II elongation (HAN et al. 2008). However, we have shown that in
fission yeast SpGcn5 also has a role in transcriptional elongation (JOHNSSON et al. 2009)
which could suggest a more direct mechanistic overlap for SpGcn5 and SpElp3 in this
species.
Only one gene was significantly increased in all strains: the RecQ-type DNA
helicase SPBCPT2R1.08c, located in the sub-telomere domain (Tlh2; (HANSEN et al.
2006; MANDELL et al. 2005)). We showed previously that ∆mst2 increases silencing at
the telomere and in telomere associated regions, consistent with a role for Mst2 in
antagonizing Sir2. Loss of Mst2 results in a loss of overall H4 acetylation (GOMEZ et al.
2005) and H3K9 acetylation in ∆mst2 in a very limited region adjacent to the telomere
18kb from the end. Interestingly, this region is telomere-distal to the tlh2 helicase gene
located 13kb from the end of the telomere chromosome II, which is highly up-regulated
91

in the mutant. In contrast, genes at 27.5, 29 and 31kb away from the telomere are down-
regulated in ∆mst2 (SPAC186.06, SPAC186.05 and SPBCPT2R1.02 respectively), while
at 47kb telomere distal (SPAC869.01), there is no change in expression levels. This
suggests a gradient effect on transcription of genes in these regions.
The few genes that are down-regulated in ∆gcn5 are localized near the ends of
chromosome I and II which suggest that the repression might be due to spreading of
heterochromatin by loss of H3K9ac. The combined effect of the double mutant may
indicate a combination of effects associated with loss of both histone H3K9 and H3K14
acetylation. Clearly, there are specific regions at the telomeres that are regulated by
specific HATs but more work needs to be done to fully understand the boundaries of the
telomeres and the regulation between the highly heterochromatic region and the rest of
the chromosome.
We used gene ontology (GO) classification to define the functional roles of the
few genes that were differentially expressed in single mutants. We found that those in
∆elp3 and ∆gcn5, but not ∆mst2 associated with a few distinct classes. Consistent with
previous results (HELMLINGER et al. 2008), ∆gcn5 mutants showed increased expression
of specific sexual differentiation genes as well as enrichment for GO terms (ASLETT and
WOOD 2006) related to mating and meiosis. Gcn5 represses transcription of ste11
+

(HELMLINGER et al. 2008), which is an important regulator of the mating pathway in
response to nutrient limitation. Although we find very similar functional groups that are
positively regulated in the absence of ∆gcn5, we did not see evidence for induction of
ste11 above our threshold level (Table 3.1). Consistent with prior work, our study also
found that mei2
+
was up-regulated in ∆gcn5 (HELMLINGER et al. 2008); this was also
92

seen for mst1
ts
and to a lesser extent ∆mst2 (Fig 3.3), indicating multiple inputs into this
essential regulator of sexual development. The ∆gcn5 ∆mst2 mutant increased mei2
+
and
ste11+ mRNA levels above those observed in the single mutants, suggesting these two
HATs function redundantly in repression. It is possible that they might also have non-
histone targets in common since the repression of mei2
+
expression by Gcn5 was
suggested to be mediated by a histone independent mechanism (HELMLINGER et al.
2008).
In contrast, deletion of ∆elp3 results in loss of mei2
+
transcription and in the
∆gcn5 ∆elp3 and ∆mst2 ∆elp3 double mutants there is also a reduction of mei2
+

transcription. Even the triple mutant shows lower levels of mei2
+
than the ∆gcn5 ∆mst2
double mutant, suggesting that ∆elp3 has an opposite effect on mei2
+
transcription than
∆gcn5. Interestingly transcription of SPAC1039.02, a putative phosphoesterase, shows a
similar, but opposite, regulation pattern as it is down-regulated in ∆gcn5, mst1
ts
and
∆mst2 while being up-regulated in ∆elp3. Thus, for some targets, Gcn5 and Mst2 appear
to overlap, while Elp3 appears to be antagonistic. This finding suggests that the common
model linking HAT enzymes with gene activation is to simplistic. Dissecting the
contribution of each HAT to gene expression or other effects will require future
molecular studies mapping the histone acetylation and physical binding of HATs at
different gene regions or their association with the transcription machinery.
To determine the molecular basis for the overlap of HAT targets, we examined
histone H3 acetylation. Three acetylation sites on histone H3 are associated with gene
expression: K9, K14, and K18 (POKHOLOK et al. 2005). H3K9 is acetylated in
euchromatin, but methylated in heterochromatin; consistent with other species, our data
93

indicate that Gcn5 is the primary contributor to H3K9Ac because acetylation of this
residue is strongly reduced in ∆gcn5 but relatively unperturbed by the other HAT
mutations.
H3K14 acetylation is also associated with gene expression (POKHOLOK et al.
2005). Mutations that change the H3K14 residue display hypersensitivity to KCl and
CaCl
2
induced stress in ∆gcn5 cells

(JOHNSSON et al. 2009). Little or no H3K14
acetylation is observed in the ∆gcn5 ∆mst2 double mutant. Consistent with this, we
observed that ∆gcn5 ∆mst2 is significantly more salt-sensitive than either single
mutation. We conclude that these two HATs both contribute to H3K14 acetylation in
response to stress. Importantly, this acetylation is not essential for viability in S. pombe.
Data from budding yeast also indicates an overlap between ScSas3 and ScGcn5 in H3K14
acetylation (HOWE et al. 2001). Interestingly, the budding yeast data also suggest that
∆sas3 is not lethal in combination with disruption of other SAGA subunits that are
essential for Gcn5 activity against histones, and deletion of histone N-terminal H3 tails
entirely is not lethal in budding yeast (HOWE et al. 2001). Thus, the essential redundant
function of these enzymes may not be in histone modification. It is now well-established
that HAT proteins acetylate substrates other than histones (GLOZAK et al. 2005). Perhaps
it is one such substrate that relies on Gcn5 or Sas3 in budding yeast, but on a different
enzyme in fission yeast. These results indicate that Mst2 has functions in common with
both budding yeast enzymes.
Finally, we found that as expected there was little overlap between expression
profiles in the non-essential HAT mutant strains, and cells with a temperature sensitive
mutation of the essential HAT mst1
+
. Mst1 is known to be required for DNA damage
94

response and chromosome segregation (GOMEZ et al. 2008). However, we did not see a
significant increase in GO terms related to these functions, which is consistent with data
suggesting its effects are not mediated through the transcriptional program (VAN
ATTIKUM and GASSER 2005). There was a significant overlap of regulated genes between
Mst1 and the triple mutant ∆gcn5 ∆mst2 ∆elp3, as half of the genes regulated in the triple
mutant were also regulated in mst1
ts
. When we compared the regulated GO terms from
mst1
ts
and ∆gcn5 ∆elp3 ∆mst2 we found that these mutants shared terms related to metal
and ion homeostasis, metal transports as well as regulation of meiosis. Since both strains
show severe growth defects under the conditions employed, we suggest that these
overlaps may represent the effects of general cellular stress rather than a particular
transcriptional program.

3.5 Conclusions
We isolated and characterized the putative Elongator HAT Elp3, showing ∆elp3
cells are delayed in the cell cycle relative to wild-type
cells, and then compared it to other HAT mutants. Our study suggests, through analysis
of single, double and triple mutants of MYST and GNAT family HATs, that histone
acetyltransferases play partially redundant role in gene regulation, and that their role can
be positive, or negative for the transcription of genes. We found evidence for significant
redundancy between Mst2 and Gcn5 in regulation of stress response, and response to
DNA damage. We found that different HAT families can share specificity for a common
lysine residue in histone H3, thereby contributing to the modulation of gene expression.
For example, we found that Gcn5 and Mst2 both acetylate histone H3 lysine 14. This
95

work highlights the functional redundancies of different HAT families on transcription,
salt response, and DNA damage repair. Future work will be required to investigate the
direct contributions of these HATs to individual genes, as opposed to selected regulation
of other transcriptional master regulators.

3.6 Methods:
3.6.1 Strains, media, and manipulations. Strains used in this study are listed in Table
3.3. Strains were grown and maintained on yeast extract plus supplements (YES) or
Edinburgh minimal media (EMM) with appropriate supplements, using standard
techniques (FORSBURG and RHIND 2006). Matings were performed on synthetic
sporulation agar (SPAS) plates for 2-3 days at 25ºC. Double mutants were constructed by
standard tetrad analysis or random spore analysis. G418 plates were YES supplemented
with 100 µg/ml G418 (Sigma).

Strain Genotype
FY261 h+ can1-1 leu1-32 ade6-M216 ura4-D18 SLF stock
FY368 h-, leu1-32, ura4-D18, ade6-M210 AW stock
FY1104 h- ∆rad3::ura4+ ura4 leu1-32 ade6-M210 (?) SLF stock
FY1584 h+ ∆swi6::his1+ ade6-M210 leu1-32 ura4-DS/E his1-102 R. Allshire
FY1890 h+ ∆mst2::ura4+ ura4-D18 ade6-M210 leu1-32
Gomez EB
2005
FY2535 h+ ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+ ade6-M210 ura4-D18
Gomez EB
2008
FY2943 h- ∆gcn5::kanMX ura4-D18 leu1-32 ade6-M21? his3-D1 SLF stock
FY3361 h+ ∆gcn5::Kanmx6 ∆mst2::ura4+ Ura4D18 ade6m21? leu1-32 his3D1 this work
FY3847 h+ ∆gcn5::KanMX4 ∆elp3::KanMX6 leu1-32 ura4-D18 ade6-M210 this work
Table 3.7: Continued 96

FY3850 h+ ∆elp3::KanMX6 ∆mst2::URA4+ leu1-32 ura4-D18 ade6-M216 this work
FY3851 h+ ∆elp3::KanMX6 leu1-32 ura4-D18 ade6-M21? this work
FY3854 h+ ∆gcn5::KanMX4 ∆mst2::URA4+ ∆elp3::KanMX6 leu1-32 ura4-D18 ade6-M210 this work
Hu799 h- ∆gcn5::KanMX4, leu1-32, ura4-D18, ade6-M210
Johnsson A
2006
Hu990 h- ∆gcn5::KanMX4, mst2::ura4+, leu1-32, ura4-D18, ade6-M210 this work
Table 3.7: Strains used in chapter 3. This table lists the genotypes and origins for the
strains used in this study.

3.6.2 Deletion of elp3
+
. The elp3 deletion strain was created from a diploid strain
purchased from Bioneer (www.bioneer.com). The strain (h+/h+, elp3+/elp3::KanMX6,
leu1-32/leu1-32, ura4-D18/ura4-D18, ade6-M210/ade6-M216) was haplodized by TBZ
treatment to induce mitotic instability and chromosome loss. The cells were plated on
YE media without adenine to select for red and pink colonies followed by selection for
G418 resistant clones. The isolates were checked with PCR to assure the deletion and
KanMX6 cassette was in the right place then back-crossed into a wt strain (h
-
, leu1-32,
ura4-D18, ade6-M216).

3.6.3 Growth Assays. Wild type and ∆elp3 cells were grown to stationary phase >1x10
8

cells/ml and then diluted in YES media to four different concentration 1x10
4
, 1x10
5
,
4x10
5
and 1x10
6
cells/ml respectively and grown at 30°C. Cells were counted regularly
for 48 hours generating growth curves to cover the beginning and end of the exponential
growth.

97

3.6.4 Damage assays Cells were grown to mid-log phase, serially diluted five-fold and
spotted onto YES plates or YES plates were irradiated with the indicated doses of UV
irradiation using a Stratalinker (Stratagene) or YES plates containing 10 or 12 µg/ml
thiabendazole (TBZ), 5 mM hydroxyurea (HU), 7µM camptothecin (CPT), 0.005%
methyl methanesulfonate (MMS) and incubated for 2-3 days at 32ºC. For the salt
sensitivity assays cells were plated out in five-fold dilution series on rich media (YES)
plates with or without KCl (1 M or 1.5 M) or CaCl2 (0.1 M or 0.25 M) at either 30°C or
36°C for 2 to 4 days.

3.6.5 RNA prep and Microarray protocols for Affymetrix and Eurogenetech. RNA
was isolated from three independent isolates growing at 30-32 degrees Celsius using
phenol/chloroform extraction (FORSBURG and RHIND 2006), phase lock gels (Eppendorf)
and resuspended into TE after ethanol precipitation. Biotinylated cRNA was prepared for
Affymetrix array analysis from 5 ug Total RNA using the standard Affymetrix one-cycle
target labeling protocol. Samples were assayed for gene expression using Affymetrix
GeneChip Yeast Genome 2.0 arrays consisting of probe sets representing 5,031 genes in
S. pombe based on Sanger (June 2004). Data was analyzed using the R statistical
environment. Affymetrix CEL files were processed and normalized using RMA
(IRIZARRY et al. 2003). The linear modeling package Limma (SMYTH 2004) was used to
calculate p-values and derive gene expression coefficients and to identify differentially
expressed genes. The data discussed in this publication have been deposited in NCBI's
Gene Expression Omnibus (EDGAR et al. 2002) and are accessible through GEO Series
accession numbers GSE17259 and GSE17262
98

(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=dzmlrwoyekgmypk&acc=GSE17
298). For microarrays using the Eurogenetech platform (salt sensitivity analysis), sample
collection, processing and normalization was performed as in (JOHNSSON et al. 2006).
Genes were considered differentially expressed if the mutant/wt ratio was greater than
3.25 log 2 fold, with a p-value of 0.05 or less. Appendix A lists genes differentially
expressed with a mutant/wt ratio of 1.7 log 2 fold, with a p-value of 0.05 or less.

3.6.6 qPCR: Primers for the entire S. pombe genome were created by Chris Seidel using
uPrimer. Total RNA in the amount of 2-4ug was treated with DNase (Turbo DNase
Treatment Ambion #AM1907) and 200-600ng of the treated RNA was converted to
cDNA by RT-PCR with the use of two primers. The concentration and sequence for the
primers are 2ng/uL final for the random primer pdN-15 and 20ng/uL final for the
anchored oligo-dT OdT-19N. A Corbett robot was used to load PCR reactions in 384-
well plate format for analysis on an ABI-7900. Standard curves for the 9 primer pairs
were made with 5 ten-fold dilutions of gDNA starting with 1000ng/15uL qPCR reaction
and ending with 0.1ng/15uL qPCR reaction. The qPCR experiment consisted of
measuring 9 loci in 24 samples three times each. 8ng of the cDNA was used in each
qPCR reaction without purification of the RT reaction. The final primer concentration
was 500nM each.

3.6.7 Venn diagram program, GO term analysis: Venn diagrams were made using
VENNY (Oliveros, J.C. (2007) VENNY. An interactive tool for comparing lists with
99

Venn Diagrams http://bioinfogp.cnb.csic.es/tools/venny/index.html). Gene ontology
classifications were classified at http://amigo.geneontology.org with the database filter
set as GeneDB S.pombe with a threshold of maximum p value of 0.05 and minimum
number of gene products of 2. We selected for publication only the biological process
classifications.

3.6.8 Histone acetylation. Cell lysates was obtained as described by (MATSUO et al.
2006) with the following modifications; the volume of the cell cultures were increased
2.5 times to get enough material for 10 or more gels. Briefly cells were inoculated in YES
and grown overnight (o/n) to 1x10
7
cells/ml in a total volume of 25 ml and harvested in
room temperature (RT) by centrifugation, washed once in H
2
O then resuspended in
0.75ml H
2
O and an equal volume of 0.6M NaOH, incubated 10 minutes at RT. Cells
were removed from the NaOH by centrifugation and dissolved in 175 µl of modified
SDS-sample buffer (60mMTris-HCl, pH 6.8, 4% β-mercaptethanol, 4% SDS, 0.01%
BPB, and 5% glycerol). Approximately 15 µl were used to run on precast gradient gels
(Bio-Rad, 161-1105). Transfer was performed using the iBlot
TM
Dry Blotting system
(Invitrogen). After transfer the membranes were blocked in in PBS containing 3% milk
for 30 min at RT followed by o/n incubation at 4°C with primary antibody (anti-
histones); or blocked o/n at 4°C followed by incubation with anti-actin antibody, at a 1:12
000 dilution (ms ab8224, Abcam) 1 hour at RT. For detection of histones antibodies the
following dilutions were used: H3 Cter 1:200 (ab1791, Abcam); H3K9Ac 1:500 (07-352,
Upstate); H3K14Ac 1:200 (07-353, Upstate); H3K18 Ac 1:200 (07-354, Upstate). For
detection IgG horseradish peroxidase (GE Healthcare) against mouse and rabbit
100

respectively was used along with ECL Plus (GE Healthcare) and exposed to film for 20
seconds to 3 minutes.

3.7 Author Contribution: RLN performed, designed and analyzed experiments and
wrote the manuscript. AJ performed, designed and analyzed experiments and wrote the
manuscript. BF performed and analyzed experiments. MG performed and analyzed
experiments. YXF performed and analyzed experiments. CS designed and analyzed
experiments and provided reagents. APW performed, designed and analyzed
experiments, and provided reagents. SLF designed and analyzed experiments, wrote the
manuscript and provided reagents.

3.8 External Contributions
We thank JiPing Yuan for lab support. We thank Ruben Petreaca, Sarah Sabatinos,
PaoChen Li and Lin Ding for careful reading on this manuscript. We thank Allison Peak
and Brian Fleharty for microarray analysis. We also thank Jeremy Bunch for providing
gDNA and Ariel Paulson for a custom perl script to track samples and Ct’s during qPCR
analysis. This work was supported by grants from the NIH (NIH R01 GM59321-09,
Forsburg) the DOD (W81XWH-05-1-0391 (X. Chen PI, Forsburg co-PI) and grants from
the Swedish Research Council and Swedish Cancer Society to APHW.

101

Chapter 4: The S. pombe histone acetyltransferase Mst1 is necessary for proper
centromere architecture.

4.1 Chapter 4 Abstract: Using the model organism S. pombe I focused on the KAT5
histone acetyltransferase Mst1 and found a novel role for histone acetylation in localizing
the kinetochore complex to the centromere. Genetic analysis and changes in gene
silencing show Mst1 acts specifically at the kinetochore binding region of the
centromere. Further we show that the kinetochore localization is disrupted in an mst1
mutant, although the histone variant CenpA localizes properly. I show that levels of
histone H4 acetylation are specifically changed at the kinetochore binding region of the
centromere in an mst1 mutant. Current work is being done to ask if H4 acetylation is
necessary for proper kinetochore binding.

4.2 Introduction: During chromosome segregation the centromere must be properly
shaped and structured to ensure proper dynamics. The S. pombe centromere is composed
of three regions, a central core, an inner repeat and an outer repeat (Clarke and Baum
1990). The outer repeat is highly heterochromatic, mediated through histone H3 lysine 9
methylation and RNAi, and is necessary for proper chromosome segregation (rev in
(Allshire and Karpen 2008)). There is an inner repeat containing two tRNA genes
necessary for preventing the dense heterochromatin from the outer repeat from spreading
into the central core (PARTRIDGE et al. 2000). The central core contains the histone H3
variant, CenpA (SpCnp1), which replaces histone H3 in the histone H3/4 tetramer at the
centromere (PALMER et al. 1991). Out of the 27 predicted nucleosomes at the central core
102

3 are thought to contain CenpA. These CenpA containing nucleosomes are essential for
kinetochore binding at this region (JOGLEKAR et al. 2008; SONG et al. 2008).
The kinetochore is a large protein complex that connects the microtubules to the
centromeres during chromosome segregation (rev in (WESTERMANN et al. 2007)). The
kinetochore is composed of an inner region that interacts with the centromere, containing
the NDC80 complex and Mis6 (Sim4 complex) and Mis12 (ASAKAWA et al. 2005;
MELLONE and ALLSHIRE 2003). Mis6 has a specific role at maintaining proper central
core structure, (PARTRIDGE et al. 2000). The outer kinetochore interacts with the
microtubule.
Swi6 regulates the highly heterochromatic otr region. The heterochromatic
structure is necessary for proper chromosome segregation as mutants that disrupt the
heterochromatin formation display improper segregation (rev in (ALLSHIRE and KARPEN
2008)). The heterochromatin is mediated through histone H3K9 methylation by the
methylase clr4 (BANNISTER et al. 2001). This histone modification recruits Swi6, which
in turn recruits cohesin and in a feedback loop the methylase Clr4 (NONAKA et al. 2002).
KAT5-family histone acetyltransferases are the catalytic subunits of a large
complex called NuA4 (SHEVCHENKO et al. 2008). S. pombe Mst1 is an essential KAT5-
family member that has roles in DNA damage repair and chromosome segregation
(GOMEZ et al. 2005; GOMEZ et al. 2008), as well as assembly of Swi6 (Xhemalce and
Kouzarides 2010).
Here evidence is shown for Mst1 in promoting proper centromere architecture. I
show that Mst1 acts specifically in maintaining proper centromere silencing at the central
103

core. Kinetochore localization is disrupted in mst1 mutant cells. I examined histone H4
acetylation as a possible mechanism for kinetochore localization.

4.3 Results: It was previously observed that mst1 mutants have negative synthetic
genetic interactions with clr3 (encoding a histone deacetylase; HDAC), clr4 ( a histone
methyltransferase, HMT), and swi6 (heterochromatin protein 1, HP1) including reduced
rates of growth (GOMEZ et al. 2008). These mutants show evidence for chromosome mis-
segregation, consistent with a disruption in centromere function (Figure 4.1)
104

Figure 4.1 mst1 mutants cells show evidence for chromosome segregation defects A.
mst1 mutants show chromosome mis-segregation. Cells were grown overnight at 25° or
32° in YES media. Asynchronous exponentially growing cells were harvested, fixed and
stained with Dapi. Scale bar indicated 10 microns. B. Quantification of mst1 mutant cells.
Cells were scored as mononucleates, binucleates or abnormal. The x-axis of the chart
indicates the sample and the y-axis is the percentage of cells with abnormal nuclei. C.
mst1 double mutants are hypersensitive to TBZ. Exponentially growing cells mst1 double
mutants were grown at 25° and then serially diluted three fold on YES or YES plus the
indicated amount of TBZ at 25° or 32° and grown 4-6 days. Strain list: WT (261) mst1
ts

(2535) ∆clr3 (2215), mst1
ts
∆clr3 (2570), ∆clr4 (2224), mst1
ts
∆clr4 (2566), ∆swi6 (2056),
mst1
ts
∆swi6 (2508).
5
10
15
20
25
30
Wild-type
mst1
ts
clr3
mst1
ts
clr3
clr4
mst1
ts
clr4
swi6
mst1
ts
swi6
Wild-type
mst1
ts
clr3
mst1
ts
clr3
clr4
mst1
ts
clr4
swi6
mst1
ts
swi6
25° 32°
% of cells with
abnormal segregation
0
B A
Wild-type
25° 32°
clr3
mst1
ts
clr3
clr4
6µg/mL
YES
6µg/mL
25°C
32°C
WT
mst1
ts
mst1
ts
clr3
mst1
ts
clr4
mst1
ts
swi6
swi6
clr4
clr3
WT
mst1
ts
mst1
ts
clr3
mst1
ts
clr4
mst1
ts
swi6
swi6
clr4
clr3
TBZ
YES 7µg/mL
swi6
25° 32°
25° 32°
25° 32°
mst1
ts
clr4
mst1
ts
swi6
mst1
ts
C
105

Clr3, Clr4, and Swi6 are necessary for creating and maintaining heterochromatin at the
outer repeat region of the centromere (rev in (Allshire and Karpen 2008)). I found that the
mst1 double mutants were hypersensitive to the spindle poison thiabendazole. Sensitivity
to thiabendazole is a general measure of proper chromosome segregation. The more
severe phenotypes in the double mutants suggest that Mst1 contributes to centromere
function in a pathway complementary to Clr3, Cl4, and Swi6. One way this could occur
is by affecting regions outside of the Swi6-dependent heterochromatin domain.
To assess Mst1 region-specific roles at the centromere I assayed gene silencing of
a ura4
+
transgene integrated in the outer repeat (otr::ura4
+
) or the central core
(cnt::ura4
+
) of the centromere. Cells that successfully silence ura4
+
are resistant to the
toxic compound 5-fluoro-orotic acid (5’FOA). I found that mst1 mutants at the
permissive temperature were competent for silencing at the outer repeat and central core
regions. However, at the semi-permissive temperature, I found a significant reduction in
silencing at the central core in mst1 cells (Fig 4.2).

106

Figure 4.2 mst1
ts
shows a selective defect in gene silencing at the central core.
Silencing assay of the centromere. Exponentially growing cells were diluted fivefold on
YES or PMG containing 5’FOA at the indicated temperatures and grown for 3-5 days.
Wild-type ura- (261) cen:ura4+ (1587) otr::ura4+ (1590), ∆swi6 otr::ura4+ (2228),
mst1 otr::ura4+ (3553), mst1 cen::ura4+ (4672).

The central core is characterized by assembly of the kinetochore that assembles at
the central core and attaches to the spindle through the microtubules (rev in
(WESTERMANN et al. 2007)). Using chromatin immunoprecipitation, I observed that the
kinetochore constituent Ndc80-GFP is disrupted in a mst1
ts
mutant (Fig 4.3 A&B). As
seen in figure 4.3 Ndc80-GFP localization is significantly disrupted when mst1
ts
cells are
grown at the non-permissive temperature 36°C for two cells cycles. This indicated that
Mst1 is necessary for proper kinetochore localization. Kinetochore assembly depends on
the histone variant CenpA, which replaces canonical H3 in the centromere domain (rev in
(Allshire and Karpen 2008)). There was no effect of mst1
ts
on Cenp A localization. The
CenpA loading factor Mis18, a putative histone deacetylase (HAYASHI et al. 2004), was
normal in the absence of Mst1 (Fig 4.3 C&D). I conclude that the decrease in
kinetochore localization in mst1 mutants was due to a CenpA-independent pathway.
ura-
cen::ura4+
otr::ura4+
Wild-type
swi6 otr::ura4+
mst1ts
otr::ura4+
otr::ura4+
cen::ura4+
cen::ura4+
YES PMG5'FOA YES PMG5'FOA
25°C 32°C
107

Figure 4.3 The kinetochore does not localize to the centromere in the absence of
Mst1. A. Ndc80-GFP localization at the central core using chromatin
immunoprecipitation (ChIP). Ndc80-GFP was pulled down using anti-GFP antibody.
Cells were shifted from 25° to either 25° or 36° for 8hrs. Primers specific for the central
core on chromosome 3 and actin were used to probe Ndc80-GFP localization and
products were run on a 2% agarose gel. Wild-type no tag (261), Wild-type Ndc80-GFP
(1649), mst1
ts
Ndc80-GFP (4876) mock IPs were performed on Wild-type Ndc80-GFP
cells (1649). B. Quantification of Ndc80-GFP ChIP. Immunoprecipitated DNA (IP) of
the central core signal over the IP actin signal ratio was divided by the input DNA signal
of the central core over actin. Band densities were measured using an FX scanner and
read by Quantity One software (Bio-Rad). The double asterisks indicates significant
change between wild-type and mst1 cells at 36° measured by a p-value less than 0.05 C.
CenpA (SpCnp1) and Mis18 localization at the central core of the centromere using ChIP.
Cnp1-GFP and Mis18-GFP were pulled down and analyzed as in A. Wild-type no tag
(261), Wild-type Cnp1-GFP (3946), mst1
ts
Cnp1-GFP (4140), Wild-type Mis18-GFP
(4157), mst1
ts
Mis18-GFP (4353) mock was performed on Wild-type Cnp1-GFP cells. D.
Quantification of Cnp1-GFP ChIP, measurements were performed as in B. E.
Quantification of Mis18-GFP ChIP, measurements were performed as in B.
No Tag
Wild-Type
mst1
ts
Wild-Type
mst1
ts
Mock
25°C 36°C
No Tag
Wild-Type
mst1
ts
Wild-Type
mst1
ts
Mock
25°C 36°C
Cnp1-GFP
A
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
No Tag Wild-Type mst1
ts
Wild-Type mst1
ts
Mock
25°C 36°C
Cnp1-GFP Mis18-GFP
Wild-Type mst1
ts
Wild-Type mst1
ts
Cnp1-GFP Mis18-GFP
Input
IP
Input
IP
Input
IP
Input
IP
cnt3
Actin
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
No Tag Wild-Type mst1ts Wild-Type mst1ts Mock
25°C 36°C
1
0
2
3
4
5
6
7
8
Ndc80-GFP at the central core (cnt)
No Tag
Wild-Type
mst1ts
Wild-Type
mst1ts
Mock
25°C 36°C
cnt3
Actin
0
5
10
15
20
25
30
Mis18-GFP
10
12
14
16
18
0
2
4
6
8
B
C
D E
**
IP/Input
IP/Input
IP/Input
108

Mst1 acetylates histone H4 (GOMEZ et al. 2008), and members of this KAT5 family have
been specifically linked to acetylation of residues H4K5, K8, and K12 (Kimura and
Horikoshi 1998). The HDACs Clr6 and Mis18 HDACs are implicated in deacetylation of
H4 particularly at the centromere (GREWAL et al. 1998; HAYASHI et al. 2004). I
examined global levels of H4K5, K8 and K12 acetylation in mst1, clr6 and mis18 single
and double mutants, and observed a reduction particularly of H4K8Ac and K12Ac in
mst1ts (Fig 4.4)

Figure 4.4 Histone H4 acetylation is differentially affected by Mst1 and Clr6. Levels
were determined by Western blots of whole cell lysates from the indicated strains with
antibodies specific to H4K5Ac, H4K8Ac, H4K12Ac, compared to levels of tubulin. WT
(261), mst1
ts
(2535), mis18
ts
(4469), mst1
ts
mis18
ts
(4470), clr6
ts
(4468), mst1
ts
clr6
ts
(4478).

H4K5Ac and H4K12Ac were undetectable in mst1 mis18 double mutants. In contrast
both H4K5Ac and H4K12Ac modifications were enhanced in clr6 single and double
mutants: that is loss of Clr6 rescues the defect observed with mst1ts. This is consistent
!tubulin
!H4K5Ac
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
25°C 36°C
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
25°C 36°C
25°C 36°C
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
!tubulin
wild-type
mst1
ts
mis18
ts
mst1
ts
msi18
ts
clr6
ts
mst1
ts
clr6
ts
!tubulin
!H4K8Ac
!H4K12Ac
109

with previous reports that Clr6 antagonizes the NuA4 complex in global histone H4
acetylation (MINODA et al. 2005). I found no strong genetic interactions between Mst1
with Mis18 or Clr6, although there was a slight increase in sensitivity of mst1
ts
mis18
ts
to
TBZ (Fig 4.5).

Figure 4.5. mst1
ts
does not exhibit genetic interactions with central core specific
histone deacetylases. Exponentially growing cells were diluted 5 fold on YES or YES
containing TBZ and grown at the indicated temperatures. WT (261), mst1
ts
(2535),
mis18
ts
(4469), mst1
ts
mis18
ts
(4470), clr6
ts
(4468), mst1
ts
clr6
ts
(4478).

The substantial change in global histone modification is consistent with data indicating
that mst1ts de-regulates a large number of genes (NUGENT et al. 2010)
In order to assess the effect of Mst1 on acetylation on the centromere, I performed
chromatin immunoprecipitation. Instead of comparing these to an endogenous sequence,
which could undergo global changes in modification, each experiment included a
common reference sample of a wild type strain with a unique DNA sequence not found in
S. pombe. By adding a constant concentration of reference cells while crosslinking
proteins to DNA, this allowed an unchanging reference between samples.
Using antibodies specific for acetylated histone H4 lysine 5, 8 and K12 I observed
there was a significant reduction of H4 acetylation in mst1 mutant cells at 25°C at the
central core, consistent with the reduction in the global signal. In contrast, I found a
WT
mst1ts
mis18ts
mis18ts mst1ts
clr6ts
clr6ts mst1ts
YES 8µg/mLTBZ YES 10µg/mLTBZ
32° 25°
110

significant increase of H4 lysine 5 acetylation in mis18 and clr6 mutant cells at 25°C
confirming their roles as histone deacetylases in this region. Similar to observations with
global levels of histone acetylation, we observed that mst1
ts
mis18
ts
mutant cells had
reduced levels of lysine 5 acetylation, similar to levels found in mst1
ts
cells, while mst1
ts

clr6
ts
mutants had elevated level acetylation levels like clr6
ts
cells.
At the non-permissive temperature of 36°C there was a significant reduction of
H4 acetylation even in our wild-type sample. There was little change in the mutant lines.
Similar to the trends observed at 25°C, I found that mis18
ts
, clr6
ts
, and mst1
ts
clr6
ts
all had
elevated levels of histone H4 lysine 5 acetylation (Fig 4.6). Similar trends existed for H4
lysine 8 and 12 levels.
111

Figure 4.6 Histone H4 acetylation patterns at the central core. A. Histone H4 K5Ac is
significantly regulated by Mst1 at the central core as measured by chromatin
immunoprecipitation. Histone H4 acetylated lysine 5 was pulled down using an anti-
H4K5Ac antibody (Epitomics). Cells were shifted from 25° to 25° or 36° for 4 hrs. Cell
at a concentration of 5e7 containing the GFP sequence were added to the 50 mL during
crosslinking. Primers specific for the central coreand gfp were used to probe H4k5Ac and
PCR products were run on a 2% agarose gel. Bands were quantified as in 4.3B. The
double asterisk indicates a significant change in value, as compared to wild-type at the
equivalent temperature B. Histone H4K8Ac is significantly regulated by Mst1 at the
central core. H4K8Ac was immunoprecipitated using an anti-H4K8Ac antibody (Cell
Signaling). Samples were analyzed using the PCR primers and techniques as in A. C.
Histone H4K12Ac is not significantly regulated by Mst1 at the central core. H4K12Ac
was immunoprecipitated using an anti-H4K12Ac antibody (Millipore). Samples were
analyzed using the PCR primers and techniques as in A. WT (261), mst1
ts
(2535), mis18
ts
(4469), mst1
ts
mis18
ts
(4470), clr6
ts
(4468), mst1
ts
clr6
ts
(4478).
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
25°C
wild-type
mst1
ts
mst1
ts
mis18
ts
mst1
ts
clr6
ts
36°C
mis18
ts
clr6
ts
mst1
ts
clr6
ts
mis18
ts
mst1
ts
clr6
ts
mst1
ts
mis18
ts
wild-type
mst1
ts
clr6
ts
mis18
ts
mst1
ts
clr6
ts
mst1
ts
mis18
ts
wild-type
25°C
36°C
**
**
**
**
**
**
**
0.1
0.2
0.3
0.4
0.5
H4 K5Ac
mst1
ts
clr6
ts
mis18
ts
mst1
ts
clr6
ts
mst1
ts
mis18
ts
wild-type
mst1
ts
clr6
ts
mis18
ts
mst1
ts
clr6
ts
mst1
ts
mis18
ts
wild-type
25°C
36°C
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
25°C
wild-type
mst1
ts
mst1
ts
mis18
ts
mst1
ts
clr6
ts
36°C
mis18
ts
clr6
ts
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
cnt
gfp
0.1
0.2
0.3
0.4
H4 K8Ac
** **
**
**
cnt
gfp
wild-type
mst1
ts
mis18
ts
mst1
ts
mis18
ts
clr6
ts
mst1
ts
clr6
ts
25°C
wild-type
mst1
ts
mst1
ts
mis18
ts
mst1
ts
clr6
ts
36°C
mis18
ts
clr6
ts
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
Input
IP
mst1
ts
clr6
ts
mis18
ts
mst1
ts
clr6
ts
mst1
ts
mis18
ts
wild-type
mst1
ts
clr6
ts
mis18
ts
mst1
ts
clr6
ts
mst1
ts
mis18
ts
wild-type
25°C
36°C
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
cnt
gfp
H4 K12Ac
**
**
**
**
H4 K12Ac
H4 K8Ac
H4 K5Ac
A
B
C
IP/Input
IP/Input
IP/Input
112

In order to assess if histone acetylation impacted kinetochore binding at the
centromere I measured Ndc80 localization in a strain that had only one copy of histone
H4, h4.2, with the remaining H4 lysine 8 was mutated to alanine. Fission yeast has three
copies of the histone H4 gene: h4.1, h4.2 and h4.3. Previous work showed deletion of
h4.1/4.2 and h4.2/4.3 resulted in increased TBZ sensitivity, but had no silencing defects
at the outer repeat region of the centromere. A deletion of histone h4.1/4.3 resulted in no
changes in TBZ sensitivity, although a H4.2K8A strain in the ∆h4.1/4.3 genetic
background was TBZ sensitive (MELLONE et al. 2003). I found kinetochore localization
decreased in all strains containing only one copy of histone H4, h4.2, regardless of
histone H4 K8Ac (Figure 4.7).

Figure 4.7 Kinetochore localization in mutants with only one copy of histone H4.
Ndc80-GFP localization was assayed using chromatin immunoprecipitation as in 4.3A.
Bands were quantified as in 4.3B. Strains: ∆h4.1/∆h4.3 Ndc80GFP (4785) ∆h4.1/∆h4.3
H4.2K8A Ndc80GFP (4786), ∆h4.1/∆h4.3 H4.2K8A (4286), Ndc80GFP (1649).

This data indicates that the amount of histone H4 is important for proper kinetochore
binding.

hhf1 hhf3
Ndc80GFP Mock
hhf1 hhf3
hhf2-K8A
Ndc80-GFP Ndc80-GFP
Input
IP
Input
IP
Input
IP
Input
IP
cnt
actin
Mock hhf1 hhf3
Ndc80GFP
hhf1 hhf3
hhf2-K8A
Ndc80-GFP
Ndc80-GFP
0.5
1.5
1.0
2.0
2.5
3.0
3.5
4.0
Ndc80-GFP at the central core
IP/Input
*
*
113

4.4 Discussion:
In this report I show that the histone acetyltransferase Mst1 is necessary for
maintaining proper centromere architecture at the central core. I show in the absence of
Mst1 the kinetochore mislocalizes, and this may be due to a lack of acetylation of histone
H4 lysines 5, 8 and 12 at the centromere.
The S. pombe centromere is composed of three distinct regions (PARTRIDGE et al.
2000). The central core region is where the kinetochore, a large protein complex,
interacts with the chromosome during cytokinesis. Kinetochore localization depends on
the histone H3 variant CenpA (rev in (WESTERMANN et al. 2007)). Data suggests that an
alternate pathway to kinetochore localization exists, mediated by histone H4.
In mst1 mutants kinetochore binding is modestly, yet significantly, reduced at the
central core. However, CenpA localization does not change at this region (Figure 4.3).
Mst1 operates within a large protein complex called the NuA4. Previously a mutant
member of this complex, alp5
ts
, was shown to disrupt central core silencing. A
nucleosome mapping technique, MNase digestion, showed that the central core had no
changes in overall structure in this mutant (MINODA et al. 2005). Consistent with the data
presented here the researchers found CenpA and CenpA loading factors localized
properly in the alp5 mutant (MINODA et al. 2005).
Assuming that the role of Mst1 at the centromere is associated with the NuA4
complex then we expect no disruption in centromere structure in mst1 mutant cells. This
leads to the question of how does Mst1 regulate kinetochore binding? Data suggests that
this is most likely due to histone H4 acetylation, however the phenomenon seen here may
114

just be a coincidental effect. Experiments presented here do not distinguish between
histone H4 acetylation between H4/H3 versus H4/CenpA tetramers at the central core.
Mst1 does not regulate gene expression of any of the three histone H4 genes (NUGENT et
al. 2010), but it is unclear if histone H4 deposition changes selectively at the central core
in a mst1 mutant. This seems very unlikely given the normal nucleosome structure in the
Nua4 complex mutant Alp5 (MINODA et al. 2005).
Mst1 is known to acetylate the histone H2A variant H2Az (SpPht1) in fission
yeast (KIM et al. 2009). Pht1 is necessary for proper chromosome segregation and pht1
cells that cannot be acetylated by Mst1 show chromosomal entanglements but
kinetochore localization is not disrupted (AHMED et al. 2007; KIM et al. 2009). This
indicates that the role of Mst1 in kinetochore binding is not mediated through acetylation
of Pht1.
Mst1 is necessary for proper assembly of heterochromatin formation genes at the
outer repeat region of the centromere. Mst1 acetylates histone H3 lysine 4 and in H3K4R
mutants there is a 2 fold reduction in Chp2 binding and a modest reduction of Swi6 and
Clr3 at the outer repeat region (XHEMALCE and KOUZARIDES 2010). Researchers found
Mst1 specifically binds at the outer repeat region of the centromere using ChIP, however
it is unclear if they localized Mst1 to any other region of the centromere. Attempts to
localize Mst1 to the centromere in my work failed. The discrepancies in Mst1 localization
are presumably due to differences in experimental methods. Mst1 was only found to bind
the centromere in very gentle lysis and sonication conditions (personal communication).
Also the increased number of abnormal nuclei and TBZ sensitivity of mst1 mutants
115

lacking Swi6, Clr3, or Clr4 (Figure 4.1) indicates that the disruption of kinetochore
binding is not solely due to changes in the outer repeat.
Future work will elucidate the mechanism of histone H4 in kinetochore binding.

4.5 Materials and Methods:
4.5.1 Strains, media, and manipulations:
Strains used in this study are listed in Table 4.1.
Table 4.1 Strains used in this study
261 h- ura4-D18 leu1-32 ade6-M210 can1-1 our stock
2056 h- ∆swi6::ura4+ leu1-32 ura4-(DS/E or D18?)
ade6-M210
our stock
2215 h- ∆clr3::kanMX6 ade6-M210 ura4-D18 leu1-
32
k. ekwall
2224 h+ ∆clr4::ura4+ ade6-210 leu1-32 ura4-D18
otr1R(SphI)::ade6+
R. allshire
2535 h- ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+
ura4-D18 ade6-M210
this study
2508 h+ swi6::ura4+ mst1::kanMX6 leu1::nmt-
mst1L-S-leu1+ ura4-D18 leu1-32 ade6-M210
this study
2566 h- ∆clr4::ura4+ ∆mst1::kanMX6 leu1::nmt-
mst1L-S-leu1+ ade6-M210 ura4-D18
(otrR(SphI)::ade6+) ?
this study
2570 h+ ∆clr3::kanMX6 ∆mst1::ura4+ leu1::nmt-
mst1L-S-leu1+ ade6-M210 ura4-D18 (can1-1)?
this study
2228
h- ∆swi6::his1+ otr1L(dh/HindIII)::ura4+ ade6-
M210 leu1-32 ura4-DS/E his1-102 our stock
Table 4.1: Continued
116

1590
h- otr1L(dh/HindIII)::ura4+ ade6-M210 leu1-32
ura4-DS/E his1-102 our stock
1587
h- tm1(NcoI)::ura4+ ade6-M210 leu1-32 ura4-
DS/E his1-102
Robin
Allshire
3553
h? ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+
otr1L(dh/HindIII)::ura4+ leu1-32 ura4∆S/E
ade6∆N/N [ch16 M23::LEU2+ tel::ade6+] Gomez 2008
4672
h? ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1
tm1(NcoI)::ura4+ ade6-M210 leu1-32 ura4-
DS/E his? this study
4469 h? mis18-262 leu1-32 Ura4D18 this study
4468 h? clr6-1 leu1-32 this study
4470
h? ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+
mis18-262 Ura4-D18 this study
4478
h? ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+
clr6-1 this study
1649
h- ndc80GFP::kanmx6 bub1-HA::ura4+ ade6
leu1 ura4-
john
kilmartin
3946 h- leu1 ura4 Native promoter-cnp1-GFP[lys1+] this study
4157 h- leu1(-32?) mis18-GFP-LEU2
yeast genetic
research
counsil
4353
h? mis18-GFP-LEU2 ∆mst1::kanMX6
leu1::nmt-mst1L-S-leu1 ade?ura4? this study
4140
h? ∆mst1::kanMX6 leu1::nmt-mst1L-S-leu1+
Native promoter-cnp1-GFP[lys1+] ura4- leu1- this study
4784
h? ndc80GFP::kanmx6 ∆mst1::kanMX6 leu1::nmt-
mst1L-S-leu1+ ade6 ura4-D18
4785
h? ndc80GFP::kanmx6 H3.1/H4.1::his3+
H3.3/H4.3::arg3+ leu1-32 ura4-D18 his3-
D1 arg3-D4 ade6-
Table 4.1: Continued
117

4876
h? ndc80GFP::kanmx6 H4.2K8A
H3.1/H4.1::his3+ H3.3/H4.3::arg3+ leu1-32
ura4-D18 his3-D1

Gene
Primer
number sequence source
cnt-
340 1279 AGTTAAGCGGTATTATCACG
Gen Dev (2002) 16:
1766-1778.
1280 GAATTGACATATACTCTGTC
Gen Dev (2002) 16:
1766-1778.
actin 1315
GAG TCC AAG ACG ATA CCA
GTG
Science (2008)
319:94-97
1316
GGC ATC ACA CTT TCT ACA
ACG
Science (2008)
319:94-97
dg 1041 TTTTCAGCGAGACATGTACC our stock
1042 TCATAAAGCAACACTGGGTG our stock
gfp 1305 gat gac gg aac tac aag aca our stock
1306 ttg ttt gtc tgc cat gat gta our stock
Table 4.2 Primers used in this study
Strains were

grown and maintained on yeast extract plus supplements (YES)

or
Edinburgh minimal media with appropriate supplements, using

standard techniques
(FORSBURG and RHIND 2006). Matings were

performed on synthetic sporulation agar
plates for 2–3

days at 25°. Temperature-sensitive (ts) cells were grown

at 25° and non-ts
cells at 32°. Transformations were

carried out by electroporation. Double mutants were
constructed

by standard tetrad analysis or random spore analysis. G418 plates

were YES
supplemented with 100 µg/ml G418 (Sigma, St.

Louis).
Microscopy:

118

Whole fixed cells were stained as described for DAPI (GOMEZ and FORSBURG 2004).
Cells were visualized with

a Leica DMR microscope. Objectives used were Leica
100X/1.30,

PLFL, NA = 1.30, and Leica 63X/1.32, PLApo, NA = 1.32. Images

were
captured with a Hamamatsu digital camera and Improvision

Openlab software
(Improvision, Lexington, MA). Images were assembled

using Canvas (ACD/Deneba) and
adjusted for contrast.
Damage Assay: Cells were grown to mid-exponential phase, serially diluted threefold,
and

spotted onto YES plates or YES plates containing 8 or 10 µg/ml

thiabendazole (TBZ)
(and incubated for 5 days at 25° or 32°,

as indicated.
Silencing assay: Cells were grown to mid-exponential phase, serially diluted fivefold,
and

spotted onto YES plates or PMG +5’FOA (Zymo Research) and incubated for 5 days
at 25° or 32°,

as indicated.
Chromatin Immunoprecipitation (ChIP): Cells were grown at either 25°C or 32°C
overnight to early exponential phase and then were shifted to 36° for 8 hrs. ChIP assays
were performed as described previously (GOMEZ et al. 2005). Anti-GFP antibody (abcam
290) was used to precipitate GFP tagged proteins. Immunoprecipitated DNA was
analyzed by PCR using SybrGreen (Invitrogen) using primers specific for cnt-340 and
actin. Band intensity was measured by Quantity One (Bio-Rad) Data was graphed as the
ratio of IP signal of (cnt/actin) over input of (cnt/actin).
Histone Chromatin Immunoprecipitation: Cells were grown at 25°C overnight and
then shifted to 36°C for 4 hours. ChIP assay was performed as described previously, with

119

the addition of approx 5E7 cells containing an integrated GFP sequence (4157) to the
cultures immediately preceding crosslinking (GOMEZ et al. 2005). Anti-H4K5Ac
(Epitomics), Anti-H4K8Ac (Cell signaling) or Anti-H4K12Ac (Millipore) was used to
precipitate histones. Immunoprecipitated DNA was analyzed by PCR using SybrGreen
using primers specific for cnt-340 and gfp. Band intensity was measured by Quantity One
(Bio-Rad) Data was graphed as the ratio of IP signal of (cnt/gfp) over input of (cnt/gfp).
Histone acetylation western blots: Extracts were prepared as in (MATSUO et al. 2006).
10 microliters of proteins were analyzed using a 15% SDS-PAGE gel. A 1:1000 Anti-
H4K5Ac (Epitomics), 1:500 Anti-H4K8Ac (Cell signaling) 1:1000Anti-H4K12Ac
(Millipore) or 1:1000 Anti-tubulin 4A1 (our stock) antibody dilution was left to incubate
overnight at 4°C.

Bibliography

120

AHMED, S., B. DUL, X. QIU and N. C. WALWORTH, 2007 Msc1 acts through histone
H2A.Z to promote chromosome stability in Schizosaccharomyces pombe.
Genetics 177: 1487-1497.
AHMED, S., C. PALERMO, S. WAN and N. C. WALWORTH, 2004 A novel protein with
similarities to Rb binding protein 2 compensates for loss of Chk1 function and
affects histone modification in fission yeast. Mol Cell Biol 24: 3660-3669.
AHN, S. H., W. L. CHEUNG, J. Y. HSU, R. L. DIAZ, M. M. SMITH et al., 2005 Sterile 20
kinase phosphorylates histone H2B at serine 10 during hydrogen peroxide-
induced apoptosis in S. cerevisiae. Cell 120: 25-36.
AKHTAR, A., and P. B. BECKER, 2000 Activation of transcription through histone H4
acetylation by MOF, an acetyltransferase essential for dosage compensation in
Drosophila. Mol Cell 5: 367-375.
ALLARD, S., R. T. UTLEY, J. SAVARD, A. CLARKE, P. GRANT et al., 1999 NuA4, an
essential transcription adaptor/histone H4 acetyltransferase complex containing
Esa1p and the ATM-related cofactor Tra1p. EMBO J 18: 5108-5119.
ALLFREY, V. G., R. FAULKNER and A. E. MIRSKY, 1964 Acetylation and Methylation of
Histones and Their Possible Role in the Regulation of Rna Synthesis. Proc Natl
Acad Sci U S A 51: 786-794.
ALLIS, C. D., S. L. BERGER, J. COTE, S. DENT, T. JENUWIEN et al., 2007 New
nomenclature for chromatin-modifying enzymes. Cell 131: 633-636.
ALLSHIRE, R. C., and G. H. KARPEN, 2008 Epigenetic regulation of centromeric
chromatin: old dogs, new tricks? Nat Rev Genet 9: 923-937.
ASAKAWA, H., A. HAYASHI, T. HARAGUCHI and Y. HIRAOKA, 2005 Dissociation of the
Nuf2-Ndc80 complex releases centromeres from the spindle-pole body during
meiotic prophase in fission yeast. Mol Biol Cell 16: 2325-2338.

121

ASLETT, M., and V. WOOD, 2006 Gene Ontology annotation status of the fission yeast
genome: preliminary coverage approaches 100%. Yeast 23: 913-919.
ATANASSOV, B. S., Y. A. EVRARD, A. S. MULTANI, Z. ZHANG, L. TORA et al., 2009 Gcn5
and SAGA regulate shelterin protein turnover and telomere maintenance. Mol
Cell 35: 352-364.
AUGER, A., L. GALARNEAU, M. ALTAF, A. NOURANI, Y. DOYON et al., 2008 Eaf1 is the
platform for NuA4 molecular assembly that evolutionarily links chromatin
acetylation to ATP-dependent exchange of histone H2A variants. Mol Cell Biol
28: 2257-2270.
BAKER, S. P., and P. A. GRANT, 2007 The SAGA continues: expanding the cellular role of
a transcriptional co-activator complex. Oncogene 26: 5329-5340.
BANNISTER, A. J., P. ZEGERMAN, J. F. PARTRIDGE, E. A. MISKA, J. O. THOMAS et al., 2001
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo
domain. Nature 410: 120-124.
BAO, S., Y. QYANG, P. YANG, H. KIM, H. DU et al., 2001 The highly conserved protein
methyltransferase, Skb1, is a mediator of hyperosmotic stress response in the
fission yeast Schizosaccharomyces pombe. J Biol Chem 276: 14549-14552.
BARBER, C. M., F. B. TURNER, Y. WANG, K. HAGSTROM, S. D. TAVERNA et al., 2004 The
enhancement of histone H4 and H2A serine 1 phosphorylation during mitosis and
S-phase is evolutionarily conserved. Chromosoma 112: 360-371.
BAUM, M., and L. CLARKE, 2000 Fission yeast homologs of human CENP-B have
redundant functions affecting cell growth and chromosome segregation. Mol Cell
Biol 20: 2852-2864.
BERGER, S. L., 2002 Histone modifications in transcriptional regulation. Curr Opin Genet
Dev 12: 142-148.

122

BERGER, S. L., B. PINA, N. SILVERMAN, G. A. MARCUS, J. AGAPITE et al., 1992 Genetic
isolation of ADA2: a potential transcriptional adaptor required for function of
certain acidic activation domains. Cell 70: 251-265.
BERNDSEN, C. E., W. SELLECK, S. J. MCBRYANT, J. C. HANSEN, S. TAN et al., 2007
Nucleosome recognition by the Piccolo NuA4 histone acetyltransferase complex.
Biochemistry 46: 2091-2099.
BIRD, A. W., D. Y. YU, M. G. PRAY-GRANT, Q. QIU, K. E. HARMON et al., 2002
Acetylation of histone H4 by Esa1 is required for DNA double-strand break
repair. Nature 419: 411-415.
BLACKWELL, C., K. A. MARTIN, A. GREENALL, A. PIDOUX, R. C. ALLSHIRE et al., 2004
The Schizosaccharomyces pombe HIRA-like protein Hip1 is required for the
periodic expression of histone genes and contributes to the function of complex
centromeres. Mol Cell Biol 24: 4309-4320.
BORROW, J., V. P. STANTON, JR., J. M. ANDRESEN, R. BECHER, F. G. BEHM et al., 1996
The translocation t(8;16)(p11;p13) of acute myeloid leukaemia fuses a putative
acetyltransferase to the CREB-binding protein. Nat Genet 14: 33-41.
BOUDREAULT, A. A., D. CRONIER, W. SELLECK, N. LACOSTE, R. T. UTLEY et al., 2003
Yeast enhancer of polycomb defines global Esa1-dependent acetylation of
chromatin. Genes Dev 17: 1415-1428.
BRAND, M., J. G. MOGGS, M. OULAD-ABDELGHANI, F. LEJEUNE, F. J. DILWORTH et al.,
2001 UV-damaged DNA-binding protein in the TFTC complex links DNA
damage recognition to nucleosome acetylation. EMBO J 20: 3187-3196.
BROWNELL, J. E., J. ZHOU, T. RANALLI, R. KOBAYASHI, D. G. EDMONDSON et al., 1996
Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking
histone acetylation to gene activation. Cell 84: 843-851.

123

BUCHANAN, L., M. DURAND-DUBIEF, A. ROGUEV, C. SAKALAR, B. WILHELM et al., 2009
The Schizosaccharomyces pombe JmjC-protein, Msc1, prevents H2A.Z
localization in centromeric and subtelomeric chromatin domains. PLoS Genet 5:
e1000726.
BURKE, T. W., J. G. COOK, M. ASANO and J. R. NEVINS, 2001 Replication factors MCM2
and ORC1 interact with the histone acetyltransferase HBO1. J Biol Chem 276:
15397-15408.
CAMPOREALE, G., A. M. OOMMEN, J. B. GRIFFIN, G. SARATH and J. ZEMPLENI, 2007 K12-
biotinylated histone H4 marks heterochromatin in human lymphoblastoma cells. J
Nutr Biochem 18: 760-768.
CARRE, C., D. SZYMCZAK, J. PIDOUX and C. ANTONIEWSKI, 2005 The histone H3
acetylase dGcn5 is a key player in Drosophila melanogaster metamorphosis. Mol
Cell Biol 25: 8228-8238.
CARROZZA, M. J., R. T. UTLEY, J. L. WORKMAN and J. COTE, 2003 The diverse functions
of histone acetyltransferase complexes. Trends Genet 19: 321-329.
CHADWICK, B. P., and H. F. WILLARD, 2001 A novel chromatin protein, distantly related
to histone H2A, is largely excluded from the inactive X chromosome. J Cell Biol
152: 375-384.
CHOY, J. S., and S. J. KRON, 2002 NuA4 subunit Yng2 function in intra-S-phase DNA
damage response. Mol Cell Biol 22: 8215-8225.
CHOY, J. S., B. T. TOBE, J. H. HUH and S. J. KRON, 2001 Yng2p-dependent NuA4 histone
H4 acetylation activity is required for mitotic and meiotic progression. J Biol
Chem 276: 43653-43662.
CLARKE, A. S., J. E. LOWELL, S. J. JACOBSON and L. PILLUS, 1999 Esa1p is an essential
histone acetyltransferase required for cell cycle progression. Mol Cell Biol 19:
2515-2526.

124

CLARKE, A. S., E. SAMAL and L. PILLUS, 2006 Distinct roles for the essential MYST
family HAT Esa1p in transcriptional silencing. Mol Biol Cell 17: 1744-1757.
CLARKE, L., and M. P. BAUM, 1990 Functional analysis of a centromere from fission
yeast: a role for centromere-specific repeated DNA sequences. Mol Cell Biol 10:
1863-1872.
COOKE, C. A., R. L. BERNAT and W. C. EARNSHAW, 1990 CENP-B: a major human
centromere protein located beneath the kinetochore. J Cell Biol 110: 1475-1488.
COTE, J., and S. RICHARD, 2005 Tudor domains bind symmetrical dimethylated arginines.
J Biol Chem 280: 28476-28483.
DECKER, P. V., D. Y. YU, M. IIZUKA, Q. QIU and M. M. SMITH, 2008 Catalytic-site
mutations in the MYST family histone Acetyltransferase Esa1. Genetics 178:
1209-1220.
DOWNS, J. A., S. ALLARD, O. JOBIN-ROBITAILLE, A. JAVAHERI, A. AUGER et al., 2004
Binding of chromatin-modifying activities to phosphorylated histone H2A at
DNA damage sites. Mol Cell 16: 979-990.
DOYON, Y., C. CAYROU, M. ULLAH, A. J. LANDRY, V. COTE et al., 2006 ING tumor
suppressor proteins are critical regulators of chromatin acetylation required for
genome expression and perpetuation. Mol Cell 21: 51-64.
DOYON, Y., and J. COTE, 2004 The highly conserved and multifunctional NuA4 HAT
complex. Curr Opin Genet Dev 14: 147-154.
DOYON, Y., W. SELLECK, W. S. LANE, S. TAN and J. COTE, 2004 Structural and functional
conservation of the NuA4 histone acetyltransferase complex from yeast to
humans. Mol Cell Biol 24: 1884-1896.
DU, L. L., T. M. NAKAMURA, B. A. MOSER and P. RUSSELL, 2003 Retention but not
recruitment of Crb2 at double-strand breaks requires Rad1 and Rad3 complexes.
Mol Cell Biol 23: 6150-6158.

125

DU, L. L., T. M. NAKAMURA and P. RUSSELL, 2006 Histone modification-dependent and -
independent pathways for recruitment of checkpoint protein Crb2 to double-
strand breaks. Genes Dev 20: 1583-1596.
DUL, B. E., and N. C. WALWORTH, 2007 The plant homeodomain fingers of fission yeast
Msc1 exhibit E3 ubiquitin ligase activity. J Biol Chem 282: 18397-18406.
EBERHARTER, A., S. JOHN, P. A. GRANT, R. T. UTLEY and J. L. WORKMAN, 1998
Identification and analysis of yeast nucleosomal histone acetyltransferase
complexes. Methods 15: 315-321.
EDGAR, R., M. DOMRACHEV and A. E. LASH, 2002 Gene Expression Omnibus: NCBI
gene expression and hybridization array data repository. Nucleic Acids Res 30:
207-210.
EHRENHOFER-MURRAY, A. E., D. H. RIVIER and J. RINE, 1997 The role of Sas2, an
acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC
function. Genetics 145: 923-934.
ELGIN, S. C., and S. I. GREWAL, 2003 Heterochromatin: silence is golden. Curr Biol 13:
R895-898.
FERNANDEZ-CAPETILLO, O., A. LEE, M. NUSSENZWEIG and A. NUSSENZWEIG, 2004
H2AX: the histone guardian of the genome. DNA Repair (Amst) 3: 959-967.
FORSBURG, S. L., and N. RHIND, 2006 Basic methods for fission yeast. Yeast 23: 173-
183.
FRANCESCONI, S., M. GRENON, D. BOUVIER and G. BALDACCI, 1997 p56(chk1) protein
kinase is required for the DNA replication checkpoint at 37 degrees C in fission
yeast. EMBO J 16: 1332-1341.
FREEMAN-COOK, L. L., E. B. GOMEZ, E. J. SPEDALE, J. MARLETT, S. L. FORSBURG et al.,
2005 Conserved locus-specific silencing functions of Schizosaccharomyces
pombe sir2+. Genetics 169: 1243-1260.

126

GALARNEAU, L., A. NOURANI, A. A. BOUDREAULT, Y. ZHANG, L. HELIOT et al., 2000
Multiple links between the NuA4 histone acetyltransferase complex and
epigenetic control of transcription. Mol Cell 5: 927-937.
GALLINARI, P., S. DI MARCO, P. JONES, M. PALLAORO and C. STEINKUHLER, 2007
HDACs, histone deacetylation and gene transcription: from molecular biology to
cancer therapeutics. Cell Res 17: 195-211.
GAME, J. C., and S. B. CHERNIKOVA, 2009 The role of RAD6 in recombinational repair,
checkpoints and meiosis via histone modification. DNA Repair (Amst) 8: 470-
482.
GEORGAKOPOULOS, T., and G. THIREOS, 1992 Two distinct yeast transcriptional
activators require the function of the GCN5 protein to promote normal levels of
transcription. EMBO J 11: 4145-4152.
GILBRETH, M., P. YANG, D. WANG, J. FROST, A. POLVERINO et al., 1996 The highly
conserved skb1 gene encodes a protein that interacts with Shk1, a fission yeast
Ste20/PAK homolog. Proc Natl Acad Sci U S A 93: 13802-13807.
GLOZAK, M. A., N. SENGUPTA, X. ZHANG and E. SETO, 2005 Acetylation and
deacetylation of non-histone proteins. Gene 363: 15-23.
GLYNN, J. M., R. J. LUSTIG, A. BERLIN and F. CHANG, 2001 Role of bud6p and tea1p in
the interaction between actin and microtubules for the establishment of cell
polarity in fission yeast. Curr Biol 11: 836-845.
GOLDKNOPF, I. L., C. W. TAYLOR, R. M. BAUM, L. C. YEOMAN, M. O. OLSON et al., 1975
Isolation and characterization of protein A24, a "histone-like" non-histone
chromosomal protein. J Biol Chem 250: 7182-7187.
GOMEZ, E. B., J. M. ESPINOSA and S. L. FORSBURG, 2005 Schizosaccharomyces pombe
mst2+ encodes a MYST family histone acetyltransferase that negatively regulates
telomere silencing. Mol Cell Biol 25: 8887-8903.

127

GOMEZ, E. B., and S. L. FORSBURG, 2004 Analysis of the fission yeast
Schizosaccharomyces pombe cell cycle. Methods Mol Biol 241: 93-111.
GOMEZ, E. B., R. L. NUGENT, S. LARIA and S. L. FORSBURG, 2008 Schizosaccharomyces
pombe histone acetyltransferase Mst1 (KAT5) is an essential protein required for
damage response and chromosome segregation. Genetics 179: 757-771.
GÓMEZ, E. G., and S. L. FORSBURG, 2003 Analysis of Schizosaccharomyces pombe cell
cycle., pp. 93-111 in Cell cycle checkpoint protocols., edited by H. G.
LIEBERMAN. Humana Press, Tatawa, NJ.
GORRINI, C., M. SQUATRITO, C. LUISE, N. SYED, D. PERNA et al., 2007 Tip60 is a haplo-
insufficient tumour suppressor required for an oncogene-induced DNA damage
response. Nature 448: 1063-1067.
GRANT, P. A., L. DUGGAN, J. COTE, S. M. ROBERTS, J. E. BROWNELL et al., 1997 Yeast
Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones:
characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes
Dev 11: 1640-1650.
GRANT, P. A., D. SCHIELTZ, M. G. PRAY-GRANT, D. J. STEGER, J. C. REESE et al., 1998 A
subset of TAF(II)s are integral components of the SAGA complex required for
nucleosome acetylation and transcriptional stimulation. Cell 94: 45-53.
GREWAL, S. I., M. J. BONADUCE and A. J. KLAR, 1998 Histone deacetylase homologs
regulate epigenetic inheritance of transcriptional silencing and chromosome
segregation in fission yeast. Genetics 150: 563-576.
HALDAR, D., and R. T. KAMAKAKA, 2006 tRNA genes as chromatin barriers. Nat Struct
Mol Biol 13: 192-193.
HAN, Q., J. LU, J. DUAN, D. SU, X. HOU et al., 2008 Gcn5- and Elp3-induced histone H3
acetylation regulates hsp70 gene transcription in yeast. Biochem J 409: 779-788.

128

HANSEN, K. R., P. T. IBARRA and G. THON, 2006 Evolutionary-conserved telomere-linked
helicase genes of fission yeast are repressed by silencing factors, RNAi
components and the telomere-binding protein Taz1. Nucleic Acids Res 34: 78-88.
HAYASHI, T., Y. FUJITA, O. IWASAKI, Y. ADACHI, K. TAKAHASHI et al., 2004 Mis16 and
Mis18 are required for CENP-A loading and histone deacetylation at centromeres.
Cell 118: 715-729.
HELMLINGER, D., S. MARGUERAT, J. VILLEN, S. P. GYGI, J. BAHLER et al., 2008 The S.
pombe SAGA complex controls the switch from proliferation to sexual
differentiation through the opposing roles of its subunits Gcn5 and Spt8. Genes
Dev 22: 3184-3195.
HENIKOFF, S., and K. AHMAD, 2005 Assembly of variant histones into chromatin. Annu
Rev Cell Dev Biol 21: 133-153.
HOU, H., Y. WANG, S. P. KALLGREN, J. THOMPSON, J. R. YATES, 3RD et al., Histone
variant H2A.Z regulates centromere silencing and chromosome segregation in
fission yeast. J Biol Chem 285: 1909-1918.
HOWE, L., D. AUSTON, P. GRANT, S. JOHN, R. G. COOK et al., 2001 Histone H3 specific
acetyltransferases are essential for cell cycle progression. Genes Dev 15: 3144-
3154.
HUANG, B., M. J. JOHANSSON and A. S. BYSTROM, 2005 An early step in wobble uridine
tRNA modification requires the Elongator complex. RNA 11: 424-436.
IIZUKA, M., T. MATSUI, H. TAKISAWA and M. M. SMITH, 2006 Regulation of replication
licensing by acetyltransferase Hbo1. Mol Cell Biol 26: 1098-1108.
IIZUKA, M., and B. STILLMAN, 1999 Histone acetyltransferase HBO1 interacts with the
ORC1 subunit of the human initiator protein. J Biol Chem 274: 23027-23034.

129

IKURA, T., V. V. OGRYZKO, M. GRIGORIEV, R. GROISMAN, J. WANG et al., 2000
Involvement of the TIP60 histone acetylase complex in DNA repair and
apoptosis. Cell 102: 463-473.
IRIZARRY, R. A., B. HOBBS, F. COLLIN, Y. D. BEAZER-BARCLAY, K. J. ANTONELLIS et al.,
2003 Exploration, normalization, and summaries of high density oligonucleotide
array probe level data. Biostatistics 4: 249-264.
JACOBS, S. A., S. D. TAVERNA, Y. ZHANG, S. D. BRIGGS, J. LI et al., 2001 Specificity of
the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J
20: 5232-5241.
JENUWEIN, T., and C. D. ALLIS, 2001 Translating the histone code. Science 293: 1074-
1080.
JOGLEKAR, A. P., D. BOUCK, K. FINLEY, X. LIU, Y. WAN et al., 2008 Molecular
architecture of the kinetochore-microtubule attachment site is conserved between
point and regional centromeres. J Cell Biol 181: 587-594.
JOHN, S., L. HOWE, S. T. TAFROV, P. A. GRANT, R. STERNGLANZ et al., 2000 The
something about silencing protein, Sas3, is the catalytic subunit of NuA3, a
yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the
yeast CP (Cdc68/Pob3)-FACT complex. Genes Dev 14: 1196-1208.
JOHNSSON, A., M. DURAND-DUBIEF, Y. XUE-FRANZÉN, M. RÖNNERBLAD, K. EKWALL et
al., 2009 HAT-HDAC interplay modulates global histone H3K14 acetylation in
gene coding regions during stress. Embo Reports in press.
JOHNSSON, A., Y. XUE-FRANZEN, M. LUNDIN and A. P. WRIGHT, 2006 Stress-specific role
of fission yeast Gcn5 histone acetyltransferase in programming a subset of stress
response genes. Eukaryot Cell 5: 1337-1346.

130

KAMINE, J., B. ELANGOVAN, T. SUBRAMANIAN, D. COLEMAN and G. CHINNADURAI, 1996
Identification of a cellular protein that specifically interacts with the essential
cysteine region of the HIV-1 Tat transactivator. Virology 216: 357-366.
KIM, D. U., J. HAYLES, D. KIM, V. WOOD, H. O. PARK et al., 2010 Analysis of a genome-
wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat
Biotechnol 28: 617-623.
KIM, H. S., V. VANOOSTHUYSE, J. FILLINGHAM, A. ROGUEV, S. WATT et al., 2009 An
acetylated form of histone H2A.Z regulates chromosome architecture in
Schizosaccharomyces pombe. Nat Struct Mol Biol 16: 1286-1293.
KIMURA, A., and M. HORIKOSHI, 1998 Tip60 acetylates six lysines of a specific class in
core histones in vitro. Genes Cells 3: 789-800.
KLOC, A., M. ZARATIEGUI, E. NORA and R. MARTIENSSEN, 2008 RNA interference guides
histone modification during the S phase of chromosomal replication. Curr Biol
18: 490-495.
KOUZARIDES, T., 2007 Chromatin modifications and their function. Cell 128: 693-705.
KRISTJUHAN, A., J. WALKER, N. SUKA, M. GRUNSTEIN, D. ROBERTS et al., 2002
Transcriptional inhibition of genes with severe histone h3 hypoacetylation in the
coding region. Mol Cell 10: 925-933.
KRISTJUHAN, A., B. O. WITTSCHIEBEN, J. WALKER, D. ROBERTS, B. R. CAIRNS et al.,
2003 Spreading of Sir3 protein in cells with severe histone H3 hypoacetylation.
Proc Natl Acad Sci U S A 100: 7551-7556.
KROGAN, N. J., K. BAETZ, M. C. KEOGH, N. DATTA, C. SAWA et al., 2004 Regulation of
chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin
remodeling complex, and the histone acetyltransferase NuA4. Proc Natl Acad Sci
U S A 101: 13513-13518.

131

KROGAN, N. J., M. C. KEOGH, N. DATTA, C. SAWA, O. W. RYAN et al., 2003 A Snf2
family ATPase complex required for recruitment of the histone H2A variant Htz1.
Mol Cell 12: 1565-1576.
KURDISTANI, S. K., S. TAVAZOIE and M. GRUNSTEIN, 2004 Mapping global histone
acetylation patterns to gene expression. Cell 117: 721-733.
LATHAM, J. A., and S. Y. DENT, 2007 Cross-regulation of histone modifications. Nat
Struct Mol Biol 14: 1017-1024.
LEE, K. K., and J. L. WORKMAN, 2007 Histone acetyltransferase complexes: one size
doesn't fit all. Nat Rev Mol Cell Biol 8: 284-295.
LEVERSON, J. D., H. K. HUANG, S. L. FORSBURG and T. HUNTER, 2002 The
Schizosaccharomyces pombe aurora-related kinase Ark1 interacts with the inner
centromere protein Pic1 and mediates chromosome segregation and cytokinesis.
Mol Biol Cell 13: 1132-1143.
LI, F., J. LU, Q. HAN, G. ZHANG and B. HUANG, 2005 The Elp3 subunit of human
Elongator complex is functionally similar to its counterpart in yeast. Mol Genet
Genomics 273: 264-272.
LIN, Y. Y., J. Y. LU, J. ZHANG, W. WALTER, W. DANG et al., 2009 Protein acetylation
microarray reveals that NuA4 controls key metabolic target regulating
gluconeogenesis. Cell 136: 1073-1084.
LINDSAY, H. D., D. J. GRIFFITHS, R. J. EDWARDS, P. U. CHRISTENSEN, J. M. MURRAY et
al., 1998 S-phase-specific activation of Cds1 kinase defines a subpathway of the
checkpoint response in Schizosaccharomyces pombe. Genes Dev 12: 382-395.
LOTTERSBERGER, F., A. PANZA, G. LUCCHINI and M. P. LONGHESE, 2007 Functional and
physical interactions between yeast 14-3-3 proteins, acetyltransferases, and
deacetylases in response to DNA replication perturbations. Mol Cell Biol 27:
3266-3281.

132

MANDELL, J. G., K. J. GOODRICH, J. BAHLER and T. R. CECH, 2005 Expression of a RecQ
helicase homolog affects progression through crisis in fission yeast lacking
telomerase. J Biol Chem 280: 5249-5257.
MATSUO, Y., K. ASAKAWA, T. TODA and S. KATAYAMA, 2006 A rapid method for protein
extraction from fission yeast. Biosci Biotechnol Biochem 70: 1992-1994.
MEISTER, P., A. TADDEI, L. VERNIS, M. POIDEVIN, S. M. GASSER et al., 2005 Temporal
separation of replication and recombination requires the intra-S checkpoint. J Cell
Biol 168: 537-544.
MELLONE, B. G., and R. C. ALLSHIRE, 2003 Stretching it: putting the CEN(P-A) in
centromere. Curr Opin Genet Dev 13: 191-198.
MELLONE, B. G., L. BALL, N. SUKA, M. R. GRUNSTEIN, J. F. PARTRIDGE et al., 2003
Centromere silencing and function in fission yeast is governed by the amino
terminus of histone H3. Curr Biol 13: 1748-1757.
MENEGHINI, M. D., M. WU and H. D. MADHANI, 2003 Conserved histone variant H2A.Z
protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112:
725-736.
MILLAR, C. B., and M. GRUNSTEIN, 2006 Genome-wide patterns of histone modifications
in yeast. Nat Rev Mol Cell Biol 7: 657-666.
MINODA, A., S. SAITOH, K. TAKAHASHI and T. TODA, 2005 BAF53/Arp4 homolog Alp5
in fission yeast is required for histone H4 acetylation, kinetochore-spindle
attachment, and gene silencing at centromere. Mol Biol Cell 16: 316-327.
MIOTTO, B., and K. STRUHL, HBO1 histone acetylase activity is essential for DNA
replication licensing and inhibited by Geminin. Mol Cell 37: 57-66.

133

MITCHELL, L., J. P. LAMBERT, M. GERDES, A. S. AL-MADHOUN, I. S. SKERJANC et al.,
2008 Functional dissection of the NuA4 histone acetyltransferase reveals its role
as a genetic hub and that Eaf1 is essential for complex integrity. Mol Cell Biol 28:
2244-2256.
MIYAMOTO, M., K. TANAKA and H. OKAYAMA, 1994 res2+, a new member of the
cdc10+/SWI4 family, controls the 'start' of mitotic and meiotic cycles in fission
yeast. EMBO J 13: 1873-1880.
MORENO, S., A. KLAR and P. NURSE, 1991 Molecular genetic analysis of fission yeast
Schizosaccharomyces pombe. Methods Enzymol 194: 795-823.
MUJTABA, S., L. ZENG and M. M. ZHOU, 2007 Structure and acetyl-lysine recognition of
the bromodomain. Oncogene 26: 5521-5527.
MURR, R., J. I. LOIZOU, Y. G. YANG, C. CUENIN, H. LI et al., 2005 Histone acetylation by
Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-
strand breaks. Nat Cell Biol.
NAKAGAWA, H., J. K. LEE, J. HURWITZ, R. C. ALLSHIRE, J. NAKAYAMA et al., 2002
Fission yeast CENP-B homologs nucleate centromeric heterochromatin by
promoting heterochromatin-specific histone tail modifications. Genes Dev 16:
1766-1778.
NAKAMURA, T. M., L. L. DU, C. REDON and P. RUSSELL, 2004 Histone H2A
phosphorylation controls Crb2 recruitment at DNA breaks, maintains checkpoint
arrest, and influences DNA repair in fission yeast. Mol Cell Biol 24: 6215-6230.
NAKAMURA, T. M., B. A. MOSER, L. L. DU and P. RUSSELL, 2005 Cooperative control of
Crb2 by ATM family and Cdc2 kinases is essential for the DNA damage
checkpoint in fission yeast. Mol Cell Biol 25: 10721-10730.

134

NAKASHIMA, K., T. HAGIWARA and M. YAMADA, 2002 Nuclear localization of
peptidylarginine deiminase V and histone deimination in granulocytes. J Biol
Chem 277: 49562-49568.
NAKAYAMA, J., J. C. RICE, B. D. STRAHL, C. D. ALLIS and S. I. GREWAL, 2001 Role of
histone H3 lysine 9 methylation in epigenetic control of heterochromatin
assembly. Science 292: 110-113.
NATHAN, D., K. INGVARSDOTTIR, D. E. STERNER, G. R. BYLEBYL, M. DOKMANOVIC et al.,
2006 Histone sumoylation is a negative regulator in Saccharomyces cerevisiae
and shows dynamic interplay with positive-acting histone modifications. Genes
Dev 20: 966-976.
NELSON, C. J., H. SANTOS-ROSA and T. KOUZARIDES, 2006 Proline isomerization of
histone H3 regulates lysine methylation and gene expression. Cell 126: 905-916.
NOGUCHI, E., C. NOGUCHI, L. L. DU and P. RUSSELL, 2003 Swi1 prevents replication fork
collapse and controls checkpoint kinase Cds1. Mol Cell Biol 23: 7861-7874.
NONAKA, N., T. KITAJIMA, S. YOKOBAYASHI, G. XIAO, M. YAMAMOTO et al., 2002
Recruitment of cohesin to heterochromatic regions by Swi6/HP1 in fission yeast.
Nat Cell Biol 4: 89-93.
NUGENT, R. L., A. JOHNSSON, B. FLEHARTY, M. GOGOL, Y. XUE-FRANZEN et al., 2010
Expression profiling of S. pombe acetyltransferase mutants identifies redundant
pathways of gene regulation. BMC Genomics 11: 59.
OSTERMANN, K., A. LORENTZ and H. SCHMIDT, 1993 The fission yeast rad22 gene,
having a function in mating-type switching and repair of DNA damages, encodes
a protein homolog to Rad52 of Saccharomyces cerevisiae. Nucleic Acids Res 21:
5940-5944.

135

OTERO, G., J. FELLOWS, Y. LI, T. DE BIZEMONT, A. M. DIRAC et al., 1999 Elongator, a
multisubunit component of a novel RNA polymerase II holoenzyme for
transcriptional elongation. Mol Cell 3: 109-118.
OUDET, P., M. GROSS-BELLARD and P. CHAMBON, 1975 Electron microscopic and
biochemical evidence that chromatin structure is a repeating unit. Cell 4: 281-300.
PALMER, D. K., K. O'DAY, H. L. TRONG, H. CHARBONNEAU and R. L. MARGOLIS, 1991
Purification of the centromere-specific protein CENP-A and demonstration that it
is a distinctive histone. Proc Natl Acad Sci U S A 88: 3734-3738.
PANKRATZ, D. G., and S. L. FORSBURG, 2005 Meiotic S-phase damage activates
recombination without checkpoint arrest. Mol Biol Cell 16: 1651-1660.
PARTRIDGE, J. F., B. BORGSTROM and R. C. ALLSHIRE, 2000 Distinct protein interaction
domains and protein spreading in a complex centromere. Genes Dev 14: 783-791.
PASSARGE, E., 1979 Emil Heitz and the concept of heterochromatin: longitudinal
chromosome differentiation was recognized fifty years ago. Am J Hum Genet 31:
106-115.
PILLUS, L., 2008 MYSTs mark chromatin for chromosomal functions. Curr Opin Cell
Biol 20: 326-333.
POKHOLOK, D. K., C. T. HARBISON, S. LEVINE, M. COLE, N. M. HANNETT et al., 2005
Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122:
517-527.
QIN, S., and M. R. PARTHUN, 2002 Histone H3 and the histone acetyltransferase Hat1p
contribute to DNA double-strand break repair. Mol Cell Biol 22: 8353-8365.
RAISNER, R. M., P. D. HARTLEY, M. D. MENEGHINI, M. Z. BAO, C. L. LIU et al., 2005
Histone variant H2A.Z marks the 5' ends of both active and inactive genes in
euchromatin. Cell 123: 233-248.

136

REDON, C., D. PILCH, E. ROGAKOU, O. SEDELNIKOVA, K. NEWROCK et al., 2002 Histone
H2A variants H2AX and H2AZ. Curr Opin Genet Dev 12: 162-169.
REIFSNYDER, C., J. LOWELL, A. CLARKE and L. PILLUS, 1996 Yeast SAS silencing genes
and human genes associated with AML and HIV-1 Tat interactions are
homologous with acetyltransferases. Nat Genet 14: 42-49.
RICE, J. C., S. D. BRIGGS, B. UEBERHEIDE, C. M. BARBER, J. SHABANOWITZ et al., 2003
Histone methyltransferases direct different degrees of methylation to define
distinct chromatin domains. Mol Cell 12: 1591-1598.
ROBERT, F., D. K. POKHOLOK, N. M. HANNETT, N. J. RINALDI, M. CHANDY et al., 2004
Global position and recruitment of HATs and HDACs in the yeast genome. Mol
Cell 16: 199-209.
SAPOUNTZI, V., I. R. LOGAN and C. N. ROBSON, 2006 Cellular functions of TIP60. Int J
Biochem Cell Biol 38: 1496-1509.
SCHMITTGEN, T. D., and K. J. LIVAK, 2008 Analyzing real-time PCR data by the
comparative C(T) method. Nat Protoc 3: 1101-1108.
SCHONES, D. E., K. CUI, S. CUDDAPAH, T. Y. ROH, A. BARSKI et al., 2008 Dynamic
regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
SELLECK, W., I. FORTIN, D. SERMWITTAYAWONG, J. COTE and S. TAN, 2005 The
Saccharomyces cerevisiae Piccolo NuA4 histone acetyltransferase complex
requires the Enhancer of Polycomb A domain and chromodomain to acetylate
nucleosomes. Mol Cell Biol 25: 5535-5542.
SHEVCHENKO, A., A. ROGUEV, D. SCHAFT, L. BUCHANAN, B. HABERMANN et al., 2008
Chromatin Central: towards the comparative proteome by accurate mapping of the
yeast proteomic environment. Genome Biol 9: R167.

137

SHOGREN-KNAAK, M., H. ISHII, J. M. SUN, M. J. PAZIN, J. R. DAVIE et al., 2006 Histone
H4-K16 acetylation controls chromatin structure and protein interactions. Science
311: 844-847.
SMITH, E. R., A. EISEN, W. GU, M. SATTAH, A. PANNUTI et al., 1998 ESA1 is a histone
acetyltransferase that is essential for growth in yeast. Proc Natl Acad Sci U S A
95: 3561-3565.
SMITH, M. M., 2002 Centromeres and variant histones: what, where, when and why? Curr
Opin Cell Biol 14: 279-285.
SMYTH, G. K., 2004 Linear models and empirical bayes methods for assessing differential
expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
SONG, J. S., X. LIU, X. S. LIU and X. HE, 2008 A high-resolution map of nucleosome
positioning on a fission yeast centromere. Genome Res 18: 1064-1072.
SQUATRITO, M., C. GORRINI and B. AMATI, 2006 Tip60 in DNA damage response and
growth control: many tricks in one HAT. Trends Cell Biol.
STERNER, D. E., and S. L. BERGER, 2000 Acetylation of histones and transcription-related
factors. Microbiol Mol Biol Rev 64: 435-459.
SUKA, N., K. LUO and M. GRUNSTEIN, 2002 Sir2p and Sas2p opposingly regulate
acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat
Genet 32: 378-383.
SUN, Y., X. JIANG, S. CHEN, N. FERNANDES and B. D. PRICE, 2005 A role for the Tip60
histone acetyltransferase in the acetylation and activation of ATM. Proc Natl
Acad Sci U S A 102: 13182-13187.
SVEJSTRUP, J. Q., 2007 Elongator complex: how many roles does it play? Curr Opin Cell
Biol 19: 331-336.

138

SYKES, S. M., H. S. MELLERT, M. A. HOLBERT, K. LI, R. MARMORSTEIN et al., 2006
Acetylation of the p53 DNA-binding domain regulates apoptosis induction. Mol
Cell 24: 841-851.
TADDEI, A., F. HEDIGER, F. R. NEUMANN and S. M. GASSER, 2004 The function of
nuclear architecture: a genetic approach. Annu Rev Genet 38: 305-345.
TAMBURINI, B. A., and J. K. TYLER, 2005 Localized histone acetylation and deacetylation
triggered by the homologous recombination pathway of double-strand DNA
repair. Mol Cell Biol 25: 4903-4913.
TANG, Y., J. LUO, W. ZHANG and W. GU, 2006 Tip60-dependent acetylation of p53
modulates the decision between cell-cycle arrest and apoptosis. Mol Cell 24: 827-
839.
THATCHER, T. H., and M. A. GOROVSKY, 1994 Phylogenetic analysis of the core histones
H2A, H2B, H3, and H4. Nucleic Acids Res 22: 174-179.
UENO, M., R. KUROKAWA, H. RENAULD, K. WATANABE, T. USHIMARU et al., 2001
Schizosaccharomyces pombe taf1+ is required for nitrogen starvation-induced
sexual development and for entering the dormant GO state. Curr Genet 38: 307-
313.
UTLEY, R. T., and J. COTE, 2003 The MYST family of histone acetyltransferases. Curr
Top Microbiol Immunol 274: 203-236.
VAN ATTIKUM, H., and S. M. GASSER, 2005 The histone code at DNA breaks: a guide to
repair? Nat Rev Mol Cell Biol 6: 757-765.
VAN ATTIKUM, H., and S. M. GASSER, 2009 Crosstalk between histone modifications
during the DNA damage response. Trends Cell Biol 19: 207-217.
VOGELAUER, M., J. WU, N. SUKA and M. GRUNSTEIN, 2000 Global histone acetylation
and deacetylation in yeast. Nature 408: 495-498.

139

WANG, L., C. MIZZEN, C. YING, R. CANDAU, N. BARLEV et al., 1997 Histone
acetyltransferase activity is conserved between yeast and human GCN5 and is
required for complementation of growth and transcriptional activation. Mol Cell
Biol 17: 519-527.
WANG, Y., M. LI, S. STADLER, S. CORRELL, P. LI et al., 2009 Histone hypercitrullination
mediates chromatin decondensation and neutrophil extracellular trap formation. J
Cell Biol 184: 205-213.
WEAKE, V. M., and J. L. WORKMAN, 2008 Histone ubiquitination: triggering gene
activity. Mol Cell 29: 653-663.
WEGEL, E., and P. SHAW, 2005 Gene activation and deactivation related changes in the
three-dimensional structure of chromatin. Chromosoma 114: 331-337.
WESTERMANN, S., D. G. DRUBIN and G. BARNES, 2007 Structures and functions of yeast
kinetochore complexes. Annu Rev Biochem 76: 563-591.
WHITE, E. M., D. L. SHAPIRO, C. D. ALLIS and M. A. GOROVSKY, 1988 Sequence and
properties of the message encoding Tetrahymena hv1, a highly evolutionarily
conserved histone H2A variant that is associated with active genes. Nucleic Acids
Res 16: 179-198.
WINKLER, G. S., A. KRISTJUHAN, H. ERDJUMENT-BROMAGE, P. TEMPST and J. Q.
SVEJSTRUP, 2002 Elongator is a histone H3 and H4 acetyltransferase important for
normal histone acetylation levels in vivo. Proc Natl Acad Sci U S A 99: 3517-
3522.
WINSTON, F., D. T. CHALEFF, B. VALENT and G. R. FINK, 1984 Mutations affecting Ty-
mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics
107: 179-197.

140

WIREN, M., R. A. SILVERSTEIN, I. SINHA, J. WALFRIDSSON, H. M. LEE et al., 2005
Genomewide analysis of nucleosome density histone acetylation and HDAC
function in fission yeast. EMBO J 24: 2906-2918.
WITTSCHIEBEN, B. O., J. FELLOWS, W. DU, D. J. STILLMAN and J. Q. SVEJSTRUP, 2000
Overlapping roles for the histone acetyltransferase activities of SAGA and
elongator in vivo. EMBO J 19: 3060-3068.
WITTSCHIEBEN, B. O., G. OTERO, T. DE BIZEMONT, J. FELLOWS, H. ERDJUMENT-
BROMAGE et al., 1999 A novel histone acetyltransferase is an integral subunit of
elongating RNA polymerase II holoenzyme. Mol Cell 4: 123-128.
WU, Z. Q., and X. LIU, 2008 Role for Plk1 phosphorylation of Hbo1 in regulation of
replication licensing. Proc Natl Acad Sci U S A 105: 1919-1924.
WYSOCKA, J., T. SWIGUT, T. A. MILNE, Y. DOU, X. ZHANG et al., 2005 WDR5 associates
with histone H3 methylated at K4 and is essential for H3 K4 methylation and
vertebrate development. Cell 121: 859-872.
XHEMALCE, B., and T. KOUZARIDES, 2010 A chromodomain switch mediated by histone
H3 Lys 4 acetylation regulates heterochromatin assembly. Genes Dev 24: 647-
652.
XU, W., D. G. EDMONDSON, Y. A. EVRARD, M. WAKAMIYA, R. R. BEHRINGER et al., 2000
Loss of Gcn5l2 leads to increased apoptosis and mesodermal defects during
mouse development. Nat Genet 26: 229-232.
XU, W., D. G. EDMONDSON and S. Y. ROTH, 1998 Mammalian GCN5 and P/CAF
acetyltransferases have homologous amino-terminal domains important for
recognition of nucleosomal substrates. Mol Cell Biol 18: 5659-5669.
YAMADA, T., K. MIZUNO, K. HIROTA, N. KON, W. P. WAHLS et al., 2004 Roles of histone
acetylation and chromatin remodeling factor in a meiotic recombination hotspot.
EMBO J 23: 1792-1803.

141

YAMAGUCHI, Y., T. NARITA, N. INUKAI, T. WADA and H. HANDA, 2001 SPT genes: key
players in the regulation of transcription, chromatin structure and other cellular
processes. J Biochem 129: 185-191.
YAMAMOTO, T., and M. HORIKOSHI, 1997 Novel substrate specificity of the histone
acetyltransferase activity of HIV-1-Tat interactive protein Tip60. J Biol Chem
272: 30595-30598.
YAN, Y., N. A. BARLEV, R. H. HALEY, S. L. BERGER and R. MARMORSTEIN, 2000 Crystal
structure of yeast Esa1 suggests a unified mechanism for catalysis and substrate
binding by histone acetyltransferases. Mol Cell 6: 1195-1205.
YOUNG, K. H., 1998 Yeast two-hybrid: so many interactions, (in) so little time. Biol
Reprod 58: 302-311.
YU, Y., Y. TENG, H. LIU, S. H. REED and R. WATERS, 2005 UV irradiation stimulates
histone acetylation and chromatin remodeling at a repressed yeast locus. Proc Natl
Acad Sci U S A 102: 8650-8655.
ZHANG, W., H. DENG, X. BAO, S. LERACH, J. GIRTON et al., 2006 The JIL-1 histone
H3S10 kinase regulates dimethyl H3K9 modifications and heterochromatic
spreading in Drosophila. Development 133: 229-235.
ZHAO, S., W. XU, W. JIANG, W. YU, Y. LIN et al., 2010 Regulation of cellular metabolism
by protein lysine acetylation. Science 327: 1000-1004.
ZOFALL, M., T. FISCHER, K. ZHANG, M. ZHOU, B. CUI et al., 2009 Histone H2A.Z
cooperates with RNAi and heterochromatin factors to suppress antisense RNAs.
Nature 461: 419-422.

142

Appendix A: Differentially expressed genes (1.7 fold) in HAT mutants

Table A.1 Differentially expressed genes (1.7 fold) in HAT mutants

Down
regula
ted
∆elp3 ∆gcn5 ∆mst2
Gene
Log2
Chan
ge
pvalu
e Gene
Log2
Change pvalue Gene
Log2
Change pvalue
SPAC29
A4.20 -4.98
7.31E
-15
SPBC11B1
0.02c -5.12
7.16E-
03
SPAC186.0
5c -3.77
4.00E-
07
SPAC18
6.05c -4.31
6.03E
-08
SPAC186.0
5c -4.09
1.26E-
07
SPBPB2B2
.06c -3.66
6.60E-
07
SPAC18
6.06 -3.23
5.87E
-06
SPAC1952.
05 -3.47
1.08E-
02
SPAC186.0
6 -3.52
1.94E-
06
SPCC79
4.04c -3.13
6.59E
-05
SPBPB2B2
.06c -3.26
3.11E-
06
SPAC17G8
.13c -2.76
2.03E-
02
SPCC19
1.11 -2.57
4.45E
-03
SPAC186.0
6 -3.23
5.82E-
06
SPAC1039.
02 -2.26
2.58E-
03
SPBC4F
6.09 -2.50
3.77E
-05
SPBPB2B2
.01 -2.60
2.00E-
05
SPBPB2B2
.01 -2.23
1.12E-
04
SPBPB2
B2.08 -2.34
1.48E
-02
SPBPB2B2
.05 -2.35
1.46E-
02
SPAC977.0
5c -1.70
9.42E-
03
SPAC27
D7.03c -2.27
1.22E
-02
SPBPB2B2
.08 -2.22
2.01E-
02
SPAC1F8.
06 -1.57
7.11E-
05
SPCC12
35.14 -2.22
8.76E
-08
SPAC977.1
4c -2.21
2.84E-
02
SPBC29B5
.02c -1.36
1.32E-
05
SPCC56
9.03 -2.18
9.22E
-07
SPAC1039.
02 -2.17
3.46E-
03
SPCC285.0
5 -1.28
6.43E-
03
SPAC23
H3.15c -2.16
1.25E
-03
SPAC977.0
5c -2.10
2.09E-
03
SPBPB2B2
.18 -1.25
2.65E-
02
SPBC66
0.05 -2.08
1.75E
-02
SPBPB10D
8.02c -2.02
1.47E-
03
SPBC947.0
4 -1.24
6.60E-
03
SPBC35
4.12 -2.06
5.60E
-08
SPAC23H3
.15c -1.82
4.83E-
03
SPCC1393.
10 -1.22
2.17E-
04
SPAC86
9.05c -2.00
1.97E
-03
SPAC57A1
0.06 -1.69
3.58E-
02
SPCC584.1
6c -1.20
1.05E-
02
Table
A.1:
Continued
143

SPBC16
83.08 -1.90
8.55E
-03
SPCC569.0
5c -1.57
6.36E-
03
SPCPB1C1
1.01 -1.18
2.27E-
03
SPAC57
A10.06 -1.87
2.15E
-02
SPAC3C7.
14c -1.54
1.83E-
02
SPAC8E11
.10 -1.15
6.06E-
04
SPBC21
5.11c -1.75
1.23E
-03
SPAC24B1
1.14 -1.48
2.34E-
02
SPBCPT2R
1.02 -1.11
4.33E-
04
SPBP4H
10.10 -1.64
7.21E
-03
SPBPB2B2
.18 -1.28
2.35E-
02
SPCC1682.
09c -1.10
6.11E-
04
SPBC16
A3.16 -1.62
2.87E
-03
SPBPB10D
8.01 -1.20
3.42E-
02
SPAC1002.
17c -1.08
3.88E-
02
SPAC97
7.05c -1.56
1.59E
-02
SPBC106.0
2c -1.17
1.30E-
02
SPCC965.1
4c -1.06
2.34E-
02
SPCC19
02.02 -1.55
1.30E
-04
SPBC947.0
4 -1.14
1.13E-
02
SPAC1B3.
16c -1.05
2.17E-
04
SPAC27
D7.11c -1.53
8.73E
-04
SPBCPT2R
1.02 -1.09
5.27E-
04
SPAC1399.
02 -1.05
7.38E-
06
SPAC16
7.06c -1.51
7.97E
-04
SPAC11D3
.03c -1.06
2.67E-
03
SPCC965.1
2 -1.03
5.83E-
04
SPCC19
1.01 -1.51
1.11E
-04
SPAC23C4
.06c -1.02
1.68E-
02
SPBC317.0
1 -1.03
1.23E-
03
SPAC18
G6.12c -1.49
1.70E
-04
SPAC1F8.
06 -0.99
4.64E-
03
SPAC869.1
0c -1.03
1.38E-
02
SPAC3F
10.15c -1.49
9.46E
-04
SPBC29B5
.02c -0.98
4.53E-
04
SPAC1399.
04c -0.99
4.40E-
02
SPAC17
A5.09c -1.46
1.02E
-07
SPCC663.0
9c -0.94
1.75E-
02
SPAC1002.
19 -0.98
2.31E-
02
SPBC26
H8.11c -1.46
2.72E
-05
SPCC1682.
08c -0.90
1.17E-
02
SPCC576.0
2 -0.97
2.90E-
04
SPBC29
B5.02c -1.42
8.03E
-06
SPAC869.0
9 -0.88
4.42E-
02
SPAC24H6
.13 -0.96
1.58E-
03
SPAC26
F1.04c -1.41
4.05E
-06
SPBC1683.
02 -0.87
1.97E-
02
SPCC1223.
13 -0.95
4.28E-
02
SPBC16
D10.06 -1.33
5.84E
-07
SPCC965.1
2 -0.85
3.09E-
03
SPCC1682.
08c -0.94
9.14E-
03
SPAC27
D7.09c -1.32
2.41E
-02
SPAC869.0
6c -0.84
2.68E-
02
SPBC3H7.
09 -0.93
3.24E-
03
SPBC8
D2.09c -1.29
5.60E
-03
SPCC965.1
1c -0.92
5.10E-
03
SPCC32
0.06 -1.28
1.85E
-05
SPBC36.01
c -0.91
3.53E-
03
Table
A.1:
Continued
144

SPAC22
H10.13 -1.26
2.24E
-02
SPBC30B4
.01c -0.89
2.83E-
02
SPAPY
UG7.04c -1.26
9.16E
-04
SPBC25H2
.04c -0.84
4.97E-
04
SPAC58
9.09 -1.26
3.20E
-04
SPAC869.0
6c -0.82
2.99E-
02
SPBC3E
7.02c -1.26
1.67E
-02
SPAC4G9.
20c -0.81
4.41E-
03
SPBPB2
1E7.04c -1.25
3.58E
-02
SPBC359.0
4c -0.80
7.80E-
03
SPBC10
6.02c -1.23
9.24E
-03
SPBC725.1
2 -0.80
4.37E-
02
SPCC33
8.18 -1.23
7.79E
-03
SPBPB7
E8.02 -1.21
6.51E
-03
SPBC33
7.16 -1.21
5.42E
-06
SPAC20
G4.03c -1.20
2.45E
-03
SPAC22
F8.05 -1.20
3.03E
-02
SPCC23
B6.05c -1.19
8.61E
-04
SPBP22
H7.03 -1.17
5.35E
-05
SPAC8
C9.16c -1.17
2.29E
-04
SPAC19
G12.09 -1.17
1.89E
-04
SPAC1F
12.03c -1.17
7.84E
-03
SPAC29
B12.11c -1.16
1.24E
-04
SPAC16
87.14c -1.16
7.79E
-04
SPAC11
E3.06 -1.16
2.61E
-02
SPBPB2
B2.06c -1.16
2.98E
-02
Table
A.1:
Continued
145

SPBC36
5.01 -1.15
1.02E
-05
SPAC22
F3.05c -1.15
8.55E
-03
SPAC18
G6.01c -1.14
1.62E
-02
SPCC33
8.12 -1.12
1.07E
-03
SPAC2F
3.05c -1.12
1.46E
-04
SPBC72
5.03 -1.09
1.43E
-02
SPAC1F
7.07c -1.08
4.80E
-02
SPBC3B
8.10c -1.08
1.68E
-03
SPAC18
34.03c -1.07
9.71E
-05
SPCC66
3.09c -1.05
9.10E
-03
SPAC18
B11.04 -1.05
2.05E
-04
SPAC15
65.04c -1.05
4.55E
-03
SPAC31
G5.21 -1.05
7.46E
-03
SPBC6B
1.02 -1.04
4.82E
-06
SPAC23
A1.09 -1.04
1.65E
-04
SPAC63
7.03 -1.04
2.36E
-02
SPAC17
G6.02c -1.04
2.58E
-05
SPCC16
20.01c -1.03
4.29E
-05
SPBP8B
7.08c -1.03
5.77E
-04
SPBC24
C6.06 -1.03
5.47E
-04
Table
A.1:
Continued
146

SPAC9E
9.14 -1.03
2.89E
-04
SPAC45
8.06 -1.02
1.77E
-05
SPBC36
.03c -1.02
1.89E
-04
SPAC25
B8.01 -1.01
4.41E
-03
SPBC21
C3.04c -0.98
5.78E
-04
SPCC12
23.13 -0.97
3.85E
-02
SPBC27
.05 -0.97
4.18E
-03
SPBC25
B2.10 -0.97
1.16E
-04
SPCC18
B5.09c -0.97
4.67E
-05
SPBC20
F10.06 -0.96
7.36E
-03
SPBC80
0.14c -0.95
1.16E
-03
SPBC2F
12.15c -0.95
2.78E
-04
SPAC17
86.01c -0.95
1.68E
-04
SPAP32
A8.02 -0.95
1.26E
-04
SPBC12
71.05c -0.95
2.85E
-03
SPBC16
E9.16c -0.94
4.50E
-04
SPBC36
5.20c -0.93
9.54E
-04
SPAC29
A4.12c -0.93
1.84E
-02
SPBP19
A11.01 -0.93
8.52E
-07
SPCC63
.03 -0.93
3.31E
-02
Table
A.1:
Continued
147

SPAC24
H6.05 -0.93
7.03E
-05
SPAC86
9.09 -0.92
3.59E
-02
SPCC12
59.15c -0.92
5.18E
-07
SPAC27
D7.04 -0.92
3.36E
-06
SPAC12
B10.10 -0.91
3.95E
-02
SPBC35
4.12 -0.91
1.66E
-06
SPCC12
23.12c -0.90
3.36E
-03
SPBC14
6.04 -0.89
4.44E
-03
SPBC21
C3.16c -0.89
1.18E
-05
SPBC57
7.08c -0.89
1.39E
-05
SPAC68
8.03c -0.88
8.76E
-04
SPCC19
19.04 -0.88
9.77E
-04
SPAC3
A12.14 -0.88
1.79E
-07
SPBC21
1.01 -0.88
1.18E
-04
SPBC11
98.13c -0.88
5.20E
-06
SPAC12
B10.06c -0.87
1.57E
-02
SPBC17
73.02c -0.87
3.76E
-03
SPAC6
G10.12c -0.87
2.71E
-02
SPCC18
8.02 -0.87
1.73E
-08
SPAC15
A10.05c -0.87
1.67E
-02
Table
A.1:
Continued
148

SPAC1
B3.10c -0.87
3.86E
-02
SPAC23
A1.02c -0.86
8.86E
-03
SPAC4
G9.13c -0.86
3.94E
-03
SPACU
NK4.16c -0.85
6.56E
-03
SPAC1
B3.20 -0.85
1.93E
-02
SPBC3
H7.13 -0.85
1.99E
-04
SPCC16
72.08c -0.85
3.90E
-07
SPBC11
9.06 -0.85
2.16E
-04
SPAC23
A1.05 -0.84
1.14E
-03
SPCC19
1.03c -0.84
2.87E
-03
SPAC14
4.17c -0.84
2.86E
-05
SPAC57
A10.08c -0.84
7.06E
-05
SPAC6F
12.02 -0.83
1.75E
-05
SPBC21
H7.06c -0.83
1.70E
-02
SPCC11
E10.02c -0.83
6.38E
-07
SPBC17
09.18 -0.83
2.02E
-07
SPAC4
A8.02c -0.82
3.94E
-04
SPAC13
D6.05 -0.82
9.99E
-07
SPCC73
6.10c -0.82
4.83E
-04
SPAC31
A2.08 -0.82
1.10E
-02
Table
A.1:
Continued
149

SPAC25
G10.01 -0.82
5.24E
-03
SPAC17
G6.09 -0.82
2.27E
-05
SPCC11
83.09c -0.82
3.40E
-03
SPBC3B
9.01 -0.82
2.16E
-02
SPAP8A
3.02c -0.81
3.77E
-02
SPAC25
B8.18 -0.81
7.38E
-04
SPAC11
D3.15 -0.81
2.09E
-02
SPAC51
3.07 -0.81
3.57E
-02
SPBC16
04.20c -0.80
4.51E
-02
SPCC62
2.02 -0.80
5.30E
-04
SPBC19
F8.05 -0.80
3.61E
-03
SPAPB2
B4.03 -0.80
1.46E
-02
SPBC66
0.14 -0.80
2.04E
-02
SPBC40
5.04c -0.80
2.75E
-04

∆gcn5 ∆elp3 ∆gcn5 ∆mst2 ∆mst2 ∆elp3
Gene
Log2
Chan
ge pvalue Gene
Log2
Chang
e pvalue Gene
Log2
Change pvalue
SPAC29
A4.20 -5.81
3.53E-
15
SPBC11
B10.02c -7.51
3.17E-
04
SPAC29A4.
20 -5.45 1.53E-15
SPAC19
52.05 -5.62
6.60E-
04
SPAC19
52.05 -5.32
3.85E-
04
SPBPB2B2.
09c -5.12 1.07E-13
SPAC57
-3.46
5.93E-

SPBPB1
-5.00
2.88E-

SPBPB2B2.
-4.69 1.86E-08
Table
A.1:
Continued
150

A10.06 04 0D8.02c 08 06c
SPCC79
4.04c -3.34
1.09E-
04
SPBPB1
0D8.01 -4.81
3.53E-
08
SPAC17G8.
13c -4.37 8.06E-04
SPBPB2
B2.08 -2.75
1.11E-
02
SPBPB2
B2.06c -4.77
1.43E-
08
SPBPB2B2.
05 -3.73 4.40E-04
SPBC21
5.11c -2.67
5.73E-
05
SPAC10
39.02 -4.73
8.49E-
07
SPBPB10D8
.02c -3.70 1.98E-06
SPAC10
39.09 -2.41
1.82E-
02
SPAC18
6.05c -4.59
2.32E-
08
SPBPB2B2.
10c -3.62 2.63E-06
SPAC86
9.05c -2.32
1.45E-
03
SPAC17
G8.13c -4.41
7.41E-
04
SPBPB2B2.
08 -3.40 1.02E-03
SPCC96
5.07c -2.09
3.99E-
02
SPBPB2
B2.05 -4.06
1.93E-
04
SPBPB2B2.
13 -3.36 2.77E-04
SPAC18
G6.12c -2.08
1.37E-
05
SPAC97
7.14c -4.03
3.87E-
04
SPCC794.04
c -3.24 4.43E-05
SPCC56
9.03 -2.06
8.21E-
06
SPAC18
6.03 -3.63
7.22E-
10
SPBPB2B2.
01 -3.02 3.01E-06
SPAC23
H3.15c -2.05
4.57E-
03
SPAC18
6.06 -3.41
2.97E-
06 SPBC660.05 -2.94 1.64E-03
SPBC10
6.02c -2.04
4.26E-
04
SPBPB2
B2.01 -3.30
9.24E-
07
SPAC22F8.0
5 -2.58 8.09E-05
SPCC66
3.09c -2.00
1.04E-
04
SPAC57
A10.06 -3.11
5.55E-
04
SPAC57A10
.06 -2.58 2.76E-03
SPAC22
H10.13 -1.99
2.51E-
03
SPBC35
9.04c -2.98
1.81E-
09 SPBC4F6.09 -2.44 5.05E-05
SPAC1F
7.07c -1.98
2.69E-
03
SPBPB2
1E7.10 -2.89
1.02E-
05
SPAC869.05
c -2.41 3.81E-04
SPAC29
B12.10c -1.95
6.76E-
04
SPAC8E
11.10 -2.87
5.39E-
09
SPCC1235.1
4 -2.40 2.87E-08
SPBC27
.05 -1.93
1.65E-
05
SPBC94
7.04 -2.80
1.92E-
06
SPAC23H3.
15c -2.32 6.68E-04
SPAC1F
12.03c -1.92
3.52E-
04
SPBPB2
B2.08 -2.59
8.09E-
03 SPCC569.03 -2.22 6.85E-07
SPBC16
A3.16 -1.90
1.98E-
03
SPAC97
7.05c -2.38
7.28E-
04 SPCC191.11 -2.13 1.48E-02
SPBC4F
6.09 -1.89
1.79E-
03
SPBC26
H8.11c -2.35
4.53E-
08
SPBPB10D8
.01 -2.10 8.44E-04
SPBPB2
B2.01 -1.88
1.61E-
03
SPAC3C
7.14c -2.35
9.26E-
04
SPBC16A3.
16 -1.97 5.65E-04
Table
A.1:
Continued
151

SPBC23
G7.13c -1.83
1.88E-
02
SPCC66
3.09c -2.34
4.39E-
06
SPBC1683.0
8 -1.89 8.80E-03
SPBPB2
B2.06c -1.82
3.75E-
03
SPBC16
83.02 -2.31
2.23E-
06 SPCC622.05 -1.85 1.07E-04
SPCC19
02.02 -1.80
8.76E-
05
SPAC97
7.15 -2.26
3.04E-
02
SPAP8A3.0
4c -1.79 1.88E-03
SPAC17
A5.09c -1.79
2.52E-
08
SPAC1F
8.06 -2.17
1.44E-
06
SPBC29B5.
02c -1.74 5.36E-07
SPBC29
B5.02c -1.76
2.08E-
06
SPCC96
5.14c -2.14
9.02E-
05
SPBC21C3.
19 -1.67 4.47E-02
SPBC8
D2.09c -1.58
2.92E-
03
SPBC3H
7.07c -2.12
3.86E-
07
SPCC1902.0
2 -1.66 6.45E-05
SPBC2
A9.02 -1.56
1.55E-
02
SPAC23
C4.06c -2.10
3.77E-
05
SPBPB2B2.
02 -1.64 2.22E-03
SPBC65
1.04 -1.55
4.97E-
05
SPCC12
23.13 -2.09
1.45E-
04
SPAC27D7.
11c -1.64 4.70E-04
SPAPY
UG7.04c -1.55
3.96E-
04
SPCC56
9.05c -2.07
7.09E-
04 SPMIT.05 -1.62 5.03E-03
SPBPB1
0D8.02c -1.54
1.95E-
02
SPAC24
B11.14 -2.07
2.73E-
03
SPAC977.05
c -1.58 1.46E-02
SPAC26
F1.04c -1.53
6.29E-
06
SPAC86
9.05c -2.05
1.65E-
03
SPAC18G6.
12c -1.54 1.16E-04
SPBC66
0.14 -1.51
4.12E-
04
SPBPB2
B2.18 -1.95
1.44E-
03
SPAC1B3.2
0 -1.52 2.25E-04
SPAC29
B12.11c -1.51
2.30E-
05
SPAC8C
9.05 -1.94
5.72E-
07 SPCC320.06 -1.52 2.31E-06
SPBC26
H8.11c -1.51
6.60E-
05
SPBC35
9.03c -1.91
1.26E-
11
SPAC22H10
.13 -1.48 9.21E-03
SPCC33
8.18 -1.48
4.62E-
03
SPAC29
B12.10c -1.87
3.53E-
04
SPAC1782.1
2c -1.46 6.28E-04
SPAC58
9.09 -1.47
2.20E-
04
SPBC12
71.08c -1.83
3.88E-
03
SPAC18G6.
01c -1.39 4.68E-03
SPCC96
5.06 -1.46
3.05E-
04
SPBC10
6.02c -1.80
4.98E-
04
SPBC21H7.
06c -1.39 3.69E-04
SPBC12
71.08c -1.44
3.17E-
02
SPAC86
9.02c -1.76
1.16E-
04
SPAC1834.0
3c -1.38 4.61E-06
SPAC3F
10.15c -1.43
3.20E-
03
SPAC17
C9.16c -1.76
5.57E-
08
SPAC2F3.05
c -1.37 1.51E-05
SPBC12
71.05c -1.42
2.03E-
04
SPBC2A
9.02 -1.74
3.71E-
03
SPBC106.02
c -1.36 4.92E-03
Table
A.1:
Continued
152

SPBC36
5.01 -1.41
3.33E-
06
SPBPB2
1E7.07 -1.72
2.78E-
04
SPAC15A10
.05c -1.34 7.05E-04
SPAC6
G10.12c -1.38
3.12E-
03
SPAC2E
1P3.05c -1.70
1.36E-
08
SPACUNK4
.17 -1.34 5.69E-03
SPCC32
0.06 -1.36
3.41E-
05
SPCC16
82.09c -1.69
5.46E-
06
SPAC24C9.
16c -1.33 6.37E-04
SPAC1F
7.08 -1.36
4.91E-
02
SPAC5H
10.03 -1.67
6.49E-
07
SPAPYUG7.
04c -1.33 5.75E-04
SPBC21
C3.04c -1.35
7.30E-
05
SPBP4H
10.20 -1.57
6.02E-
10
SPBP4H10.1
0 -1.32 2.56E-02
SPAC13
C5.04 -1.34
1.36E-
03
SPAC23
H3.13c -1.55
7.95E-
07
SPBC215.11
c -1.30 1.06E-02
SPBC10
6.17c -1.33
6.19E-
04
SPBC12
D12.07c -1.54
7.64E-
05
SPCC757.07
c -1.26 1.13E-02
SPCC28
5.04 -1.32
2.97E-
04
SPBC33
7.09 -1.52
8.40E-
09
SPAC22A12
.17c -1.23 7.99E-05
SPBP26
C9.02c -1.29
8.88E-
06
SPAC68
8.02c -1.51
3.12E-
05
SPAC167.06
c -1.21 4.54E-03
SPBC19
F8.05 -1.29
1.43E-
04
SPBC18
61.01c -1.51
4.17E-
03
SPAC23C11
.10 -1.20 1.62E-03
SPCC16
20.01c -1.27
1.34E-
05
SPBC16
A3.16 -1.50
5.00E-
03
SPCC191.03
c -1.20 1.09E-04
SPAC9E
9.11 -1.27
8.38E-
03
SPBC36
5.11 -1.45
1.39E-
03
SPCC1739.0
6c -1.19 7.81E-05
SPBC3
H7.07c -1.27
5.96E-
04
SPBC10
6.17c -1.45
8.85E-
05
SPAC26F1.0
4c -1.19 3.30E-05
SPAC19
G12.09 -1.27
2.62E-
04
SPAC51
3.07 -1.43
7.98E-
04 SPAC343.12 -1.18 1.67E-02
SPAC31
G5.21 -1.26
4.38E-
03
SPBC21
5.11c -1.42
6.12E-
03 SPAC869.09 -1.17 9.62E-03
SPAC18
B11.04 -1.25
1.10E-
04
SPAC11
D3.17 -1.41
4.98E-
03
SPAC25B8.
01 -1.16 1.56E-03
SPAC17
86.01c -1.25
2.77E-
05
SPBC25
B2.08 -1.40
4.91E-
05
SPAC29B12
.10c -1.15 1.44E-02
SPCC18
B5.09c -1.24
9.61E-
06
SPBP8B
7.31 -1.39
2.00E-
04
SPBC20F10.
06 -1.14 2.02E-03
SPAC18
34.03c -1.22
7.83E-
05
SPAPB2
4D3.08c -1.38
1.34E-
02
SPAC31G5.
21 -1.11 4.91E-03
SPAC2F
3.05c -1.21
2.09E-
04
SPBC31
F10.17c -1.37
1.72E-
02 SPBC887.17 -1.11 5.51E-05
Table
A.1:
Continued
153

SPAC16
87.14c -1.21
1.46E-
03
SPBC17
D1.06 -1.36
1.01E-
03
SPBC8D2.0
9c -1.10 1.47E-02
SPBC56
F2.14 -1.21
2.27E-
02
SPAC97
7.09c -1.35
1.27E-
04 SPAC589.09 -1.10 1.11E-03
SPAC17
A2.10c -1.19
1.19E-
02
SPAC58
9.09 -1.35
1.68E-
04 SPBC725.03 -1.10 1.32E-02
SPCC16
82.08c -1.19
3.92E-
03
SPBC16
D10.01c -1.34
5.78E-
04
SPBC16E9.1
6c -1.10 9.95E-05
SPAC23
A1.09 -1.18
1.43E-
04
SPAC13
99.02 -1.34
2.92E-
07
SPAC17A5.
09c -1.09 5.42E-06
SPAC17
A5.10 -1.17
7.85E-
04
SPCC62
2.01c -1.33
7.03E-
06
SPAC869.10
c -1.09 9.65E-03
SPAC11
G7.01 -1.17
1.15E-
02
SPBC36
5.04c -1.32
1.16E-
03
SPAC23H3.
12c -1.09 3.46E-04
SPBC2F
12.15c -1.17
1.04E-
04
SPBPB2
B2.02 -1.31
1.06E-
02 SPCC63.03 -1.09 1.47E-02
SPAC6
C3.04 -1.17
1.60E-
08
SPCC28
5.05 -1.30
5.61E-
03
SPCC663.09
c -1.08 7.79E-03
SPAP8A
3.02c -1.17
1.00E-
02
SPAC9E
9.11 -1.29
3.45E-
03
SPAC1F12.0
3c -1.07 1.38E-02
SPAC45
8.06 -1.16
1.50E-
05
SPBC2G
2.05 -1.27
2.31E-
07
SPBC4B4.0
8 -1.06 9.99E-05
SPBC20
F10.06 -1.15
4.60E-
03
SPBC17
18.03 -1.27
7.62E-
04
SPCC1494.0
9c -1.06 3.51E-05
SPAPB1
E7.04c -1.14
4.38E-
03
SPBC11
98.02 -1.25
8.82E-
04 SPAC637.03 -1.06 2.16E-02
SPBC3E
7.02c -1.14
4.65E-
02
SPAC19
G12.05 -1.25
2.52E-
05
SPAC27D7.
04 -1.05 5.14E-07
SPBC88
7.17 -1.14
1.30E-
04
SPAC75
0.07c -1.25
5.33E-
03
SPAC29A4.
17c -1.05 4.32E-03
SPCC19
1.03c -1.14
5.33E-
04
SPBCPT
2R1.02 -1.25
1.38E-
04
SPAC26F1.1
4c -1.05 7.37E-03
SPBC3B
8.10c -1.13
2.81E-
03
SPBPB1
0D8.07c -1.24
2.06E-
04
SPAC23C4.
11 -1.04 2.85E-03
SPBC83
.04 -1.13
3.97E-
03
SPCC4B
3.18 -1.24
5.28E-
05
SPAC23A1.
09 -1.04 1.69E-04
SPCC12
23.09 -1.13
5.71E-
04
SPBC21
6.04c -1.24
1.46E-
03
SPBC20F10.
03 -1.04 2.94E-03
SPAC15
A10.05c -1.11
7.50E-
03
SPBC4B
4.11 -1.23
5.28E-
04
SPAC1A6.0
8c -1.03 1.34E-02
Table
A.1:
Continued
154

SPAC10
93.01 -1.10
2.86E-
05
SPCC12
59.02c -1.23
1.19E-
08
SPBP8B7.08
c -1.03 5.97E-04
SPCC24
B10.20 -1.10
1.08E-
02
SPBC2G
2.15c -1.22
7.76E-
08 SPBC354.12 -1.02 3.41E-04
SPBP23
A10.12 -1.10
2.05E-
04
SPAC16
A10.05c -1.20
4.87E-
02
SPAC19A8.
09 -1.02 1.72E-03
SPCC16
82.09c -1.09
1.71E-
03
SPCC13
93.10 -1.20
2.55E-
04
SPAC3H8.0
7c -1.02 1.90E-03
SPCC62
2.02 -1.09
7.34E-
05
SPAC12
50.04c -1.19
1.55E-
03
SPAC2F3.17
c -1.01 1.32E-02
SPBC6B
1.02 -1.09
1.13E-
05
SPBP8B
7.28c -1.18
3.12E-
03
SPAC29B12
.11c -1.00 5.31E-04
SPBC17
73.02c -1.09
1.61E-
03
SPBC2G
2.01c -1.17
3.95E-
05
SPBC25B2.
08 -1.00 1.35E-03
SPBP22
H7.03 -1.08
4.10E-
04
SPACU
NK4.09 -1.17
6.96E-
05
SPAP32A8.
02 -0.99 7.50E-05
SPCC63
.03 -1.07
2.83E-
02
SPBP16
F5.05c -1.17
1.47E-
03
SPAC23A1.
02c -0.99 3.30E-03
SPAC18
05.16c -1.07
7.00E-
06
SPBC16
83.05 -1.16
7.95E-
05 SPAC139.05 -0.99 2.34E-02
SPAC5
H10.05c -1.07
2.17E-
03
SPBC83.
15 -1.16
2.27E-
04
SPBC56F2.1
4 -0.99 3.49E-02
SPBC19
F8.07 -1.06
8.84E-
04
SPAC31
G5.08 -1.15
1.42E-
07 SPCC338.12 -0.99 3.09E-03
SPBC26
H8.13c -1.06
2.65E-
03
SPAC12
G12.02 -1.15
6.67E-
04
SPBC1677.0
2 -0.98 2.30E-03
SPAC1
B3.10c -1.06
2.54E-
02
SPBC17
03.08c -1.14
5.27E-
03 SPBC337.16 -0.98 6.34E-05
SPBC57
7.08c -1.05
6.60E-
06
SPAC1F
12.03c -1.14
8.97E-
03
SPBC25B2.
10 -0.98 1.07E-04
SPBC71
3.08 -1.05
7.90E-
04
SPAC10
F6.10 -1.14
4.44E-
03 SPBC887.01 -0.97 7.00E-03
SPBC16
85.03 -1.05
6.02E-
05
SPAC10
39.04 -1.13
1.30E-
04
SPAC3G6.0
2 -0.97 6.00E-04
SPBC21
1.01 -1.05
5.62E-
05
SPAC4H
3.01 -1.13
2.06E-
04
SPAC7D4.0
5 -0.97 1.34E-03
SPAC24
H6.05 -1.04
6.62E-
05
SPCC18
B5.01c -1.12
1.26E-
03
SPBC365.12
c -0.95 1.37E-02
SPBC15
D4.08c -1.04
4.43E-
02
SPBC18
61.02 -1.12
2.57E-
02
SPAC22F3.0
5c -0.95 2.57E-02
Table
A.1:
Continued
155

SPAC1
B3.20 -1.03
1.20E-
02
SPBC12
71.07c -1.11
1.35E-
05
SPBC21C3.
16c -0.94 6.03E-06
SPAC86
9.09 -1.03
3.49E-
02
SPCC4B
3.10c -1.11
1.33E-
03
SPBC11G11
.04 -0.94 1.07E-03
SPAC5
D6.09c -1.03
7.34E-
04
SPAC56
F8.10 -1.11
4.38E-
08 SPBC685.05 -0.94 5.44E-03
SPBC4F
6.08c -1.03
1.58E-
02
SPAC97
7.10 -1.10
1.15E-
07
SPBC19F8.0
5 -0.94 1.04E-03
SPBC27
B12.11c -1.02
1.97E-
04
SPBC17
34.14c -1.10
1.07E-
03
SPBC1711.0
9c -0.94 1.93E-05
SPAC12
B10.10 -1.02
4.04E-
02
SPAC92
6.05c -1.10
2.28E-
03 SPCC191.01 -0.93 6.80E-03
SPBC27
.04 -1.02
2.52E-
02
SPBC4F
6.09 -1.10
2.85E-
02 SPBC119.06 -0.93 8.38E-05
SPAC27
D7.04 -1.01
3.94E-
06
SPAC20
H4.08 -1.10
5.12E-
03
SPCC1620.0
1c -0.92 1.46E-04
SPCC23
B6.05c -1.01
7.31E-
03
SPAC1D
4.01 -1.10
8.07E-
03
SPCC23B6.
05c -0.92 6.54E-03
SPBC21
C3.16c -1.01
1.07E-
05
SPCC33
8.11c -1.09
2.18E-
03
SPBC365.20
c -0.92 1.11E-03
SPBC42
8.13c -1.01
5.78E-
03
SPAC11
D3.02c -1.09
2.08E-
04
SPBC3B8.1
0c -0.91 5.90E-03
SPCC62
2.01c -1.00
5.11E-
04
SPBC2A
9.12 -1.09
1.92E-
02 SPCC338.18 -0.91 3.85E-02
SPBC12
D12.07c -1.00
8.08E-
03
SPAC11
E3.03 -1.09
1.59E-
02
SPAC3H5.0
5c -0.91 1.61E-05
SPBC11
9.06 -1.00
1.24E-
04
SPBC11
G11.05 -1.09
3.88E-
03 SPCC188.02 -0.91 8.51E-09
SPAC27
D7.07c -1.00
1.34E-
03
SPBC21
D10.07 -1.08
2.92E-
06 SPBP8B7.13 -0.91 1.03E-05
SPAC86
9.10c -0.99
2.97E-
02
SPBC23
E6.06c -1.08
3.80E-
06 SPAC458.06 -0.91 6.88E-05
SPAC32
8.10c -0.99
2.09E-
04
SPCC4G
3.17 -1.08
2.94E-
05
SPAC869.06
c -0.90 1.90E-02
SPBC17
D11.03c -0.99
2.20E-
05
SPAC22
7.16c -1.08
6.91E-
05
SPBC13E7.1
1 -0.89 1.21E-05
SPBC42
8.18 -0.98
3.35E-
03
SPBC21
5.06c -1.07
3.81E-
02
SPAC3H8.0
3 -0.89 6.49E-04
SPBC11
G11.06c -0.98
1.01E-
03
SPAC20
G4.01 -1.07
2.70E-
08
SPBC6B1.0
2 -0.88 3.57E-05
Table
A.1:
Continued
156

SPBC21
6.04c -0.98
1.58E-
02
SPCC66
3.13c -1.06
1.12E-
02
SPBC800.12
c -0.88 1.52E-04
SPBC10
6.15 -0.98
2.02E-
05
SPBC17
11.05 -1.05
4.59E-
04
SPAC15E1.
08 -0.88 1.30E-03
SPCC18
8.02 -0.98
1.58E-
08
SPBC65
1.04 -1.05
8.32E-
04
SPAC12B10
.10 -0.88 4.65E-02
SPBC30
D10.14 -0.97
5.51E-
04
SPAC13
99.04c -1.04
3.65E-
02 SPCC622.02 -0.88 2.19E-04
SPAC25
B8.01 -0.96
1.27E-
02
SPBC3B
8.06 -1.04
7.05E-
06
SPBC20F10.
10 -0.88 1.77E-02
SPCC18
.01c -0.96
1.69E-
03
SPCC12
6.03 -1.03
1.90E-
03
SPAC9E9.1
4 -0.87 1.26E-03
SPBP4H
10.11c -0.96
2.11E-
03
SPAC58
9.03c -1.03
1.43E-
03
SPAC869.07
c -0.87 1.20E-04
SPAC11
0.01 -0.95
1.04E-
05
SPBC3H
7.14 -1.03
8.78E-
04
SPBC3H7.0
2 -0.87 4.00E-05
SPBC20
F10.10 -0.94
2.23E-
02
SPBC35
9.05 -1.03
6.28E-
03
SPAC4F10.2
0 -0.87 1.47E-03
SPAC8
C9.16c -0.94
4.09E-
03
SPCC16
A11.07 -1.02
2.53E-
03
SPBC11G11
.06c -0.87 1.14E-03
SPAC23
A1.02c -0.94
1.05E-
02
SPAC4G
9.10 -1.02
1.04E-
05
SPAC16A10
.06c -0.87 7.44E-03
SPAC86
9.06c -0.94
2.73E-
02
SPAC11
D3.03c -1.01
3.65E-
03
SPBC31F10.
15c -0.86 3.93E-03
SPBC72
5.12 -0.93
3.69E-
02
SPCC24
B10.20 -1.01
9.41E-
03
SPAC222.03
c -0.86 1.48E-02
SPBC11
9.05c -0.93
3.95E-
03
SPAC22
7.05 -1.01
2.81E-
02
SPBC23E6.0
3c -0.86 8.65E-03
SPBC14
C8.10 -0.93
5.93E-
04
SPAC27
D7.07c -1.00
4.73E-
04
SPBC4F6.08
c -0.86 2.30E-02
SPBC65
1.06 -0.93
1.42E-
02
SPBC3B
9.07c -0.99
9.59E-
04
SPBC4B4.0
5 -0.86 2.59E-02
SPBC17
G9.12c -0.92
3.17E-
02
SPAC32
8.09 -0.99
2.26E-
03
SPCC622.01
c -0.86 7.95E-04
SPAC17
G6.02c -0.92
2.92E-
04
SPBC25
H2.04c -0.99
9.46E-
05
SPAC15A10
.07 -0.85 3.57E-03
SPAC9E
9.14 -0.92
1.99E-
03
SPAC14
0.03 -0.99
1.23E-
03
SPBC21C3.
04c -0.85 1.99E-03
SPAC17
G6.09 -0.92
2.04E-
05
SPCC33
0.03c -0.99
1.07E-
03
SPAC1786.0
1c -0.85 5.15E-04
Table
A.1:
Continued
157

SPAC82
3.06 -0.92
1.82E-
02
SPAC29
A4.14c -0.98
1.32E-
04 SPMIT.11 -0.85 4.84E-03
SPAC13
D6.05 -0.92
9.52E-
07
SPAC23
C11.13c -0.98
3.36E-
05
SPBC359.04
c -0.84 5.58E-03
SPAC3
A12.14 -0.92
4.37E-
07
SPAC20
G4.04c -0.98
5.35E-
03
SPAC8C9.1
6c -0.84 4.07E-03
SPCC19
1.01 -0.92
1.49E-
02
SPBC23
G7.07c -0.97
3.19E-
02
SPAC1834.0
5 -0.84 3.29E-06
SPAC20
G4.03c -0.92
2.71E-
02
SPBC15
39.10 -0.97
1.50E-
02 SPBC211.01 -0.83 1.99E-04
SPAC22
7.08c -0.91
1.61E-
03
SPAC19
B12.12c -0.97
1.74E-
04
SPAC25G10
.02 -0.83 8.43E-03
SPBC33
7.16 -0.91
4.23E-
04
SPAC5H
10.06c -0.97
6.81E-
04
SPCC18B5.
09c -0.83 2.39E-04
SPBC16
C6.03c -0.91
3.96E-
05
SPBC32
H8.08c -0.97
1.96E-
05
SPAC11D3.
10 -0.83 9.40E-06
SPBC17
09.18 -0.91
2.52E-
07
SPBP35
G2.13c -0.96
2.00E-
03 SPCC330.10 -0.82 9.31E-04
SPBC32
H8.02c -0.91
1.68E-
02
SPAC14
86.08 -0.96
3.15E-
02
SPBC2D10.
09 -0.82 1.97E-05
SPBC68
5.05 -0.90
1.41E-
02
SPAPB1
E7.10 -0.96
1.08E-
02
SPCC1672.0
4c -0.82 1.05E-02
SPAC58
9.03c -0.90
8.87E-
03
SPAC14
C4.12c -0.96
6.10E-
03
SPBC800.14
c -0.82 3.93E-03
SPBC25
B2.11 -0.90
8.61E-
04
SPCC19
19.13c -0.95
8.78E-
04
SPAC589.03
c -0.82 8.19E-03
SPBC88
7.01 -0.90
2.19E-
02
SPAC6B
12.09 -0.95
4.34E-
03
SPAC12B10
.06c -0.81 2.29E-02
SPAC14
4.08 -0.90
1.55E-
04
SPAC19
52.06c -0.95
9.74E-
06
SPAC23C4.
09c -0.81 1.84E-02
SPBC3
H7.13 -0.89
3.56E-
04
SPCC18
40.07c -0.95
1.58E-
05
SPAC1610.0
1 -0.81 1.17E-03
SPBC1
D7.03 -0.89
9.54E-
03
SPBC19
C7.07c -0.94
9.43E-
04
SPAC25B8.
18 -0.81 8.09E-04
SPAC23
A1.05 -0.89
1.80E-
03
SPAC25
B8.02 -0.94
6.63E-
06
SPAC15A10
.12c -0.80 2.04E-02
SPAC17
A2.05 -0.89
1.83E-
02
SPCC62
2.02 -0.94
1.10E-
04
SPAC11D3.
15 -0.80 2.23E-02
SPAC10
F6.07c -0.89
1.62E-
03
SPBC16
D10.02 -0.94
3.25E-
04
SPBC16D10
.06 -0.80 2.43E-04
Table
A.1:
Continued
158

SPAC24
H6.08 -0.89
1.44E-
04
SPCC17
39.05 -0.94
3.01E-
03
SPAC11H11
.02c -0.80 4.63E-03
SPBC17
03.09 -0.89
3.06E-
03
SPCC12
81.07c -0.93
1.01E-
02
SPBPB2B2.
11 -0.80 4.15E-03
SPCC16
A11.07 -0.88
1.43E-
02
SPAC17
A2.14 -0.93
2.07E-
07
SPBC2D10.
03c -0.80 3.63E-04
SPAC11
D3.16c -0.88
2.27E-
03
SPAC16
C9.02c -0.93
3.32E-
05
SPBC26H8.
11c -0.80 6.76E-03
SPBC21
D10.07 -0.88
1.26E-
04
SPAC3H
1.07 -0.92
9.62E-
04
SPAC19D5.
02c -0.80 1.24E-04
SPBC64
6.08c -0.88
1.26E-
04
SPBC72
5.16 -0.92
1.42E-
03
SPAC3
H1.11 -0.88
4.33E-
03
SPAC23
H3.14 -0.92
7.28E-
07
SPBC36
5.20c -0.87
4.02E-
03
SPBC2G
2.08 -0.92
5.20E-
03
SPCC14
42.16c -0.87
8.93E-
05
SPBC19
G7.04 -0.92
1.06E-
02
SPAC51
3.07 -0.87
4.12E-
02
SPCC16
82.08c -0.91
1.08E-
02
SPBC16
E9.01c -0.87
1.03E-
03
SPAC3G
6.05 -0.91
1.94E-
05
SPBC14
C8.07c -0.87
1.46E-
02
SPBP23
A10.12 -0.91
4.61E-
04
SPCC12
35.14 -0.87
7.60E-
03
SPAC18
34.07 -0.90
8.70E-
05
SPCC19
19.04 -0.86
2.74E-
03
SPAC56
F8.09 -0.90
5.09E-
03
SPBC11
G11.04 -0.86
5.20E-
03
SPBC30
D10.15 -0.90
2.02E-
03
SPAC66
4.13 -0.86
4.73E-
04
SPBC12
D12.02c -0.90
2.97E-
03
SPAC23
C4.11 -0.86
2.06E-
02
SPBC19
C2.03 -0.89
3.24E-
03
SPCC16
72.08c -0.85
1.63E-
06
SPAC5H
10.12c -0.89
6.27E-
04
SPCC73
6.10c -0.85
9.25E-
04
SPAC24
H6.11c -0.89
3.09E-
04
SPAC12
B10.06c -0.85
3.17E-
02
SPAC8C
9.10c -0.89
9.33E-
03
Table
A.1:
Continued
159

SPCC12
59.15c -0.85
6.07E-
06
SPAC19
52.03 -0.88
9.83E-
03
SPAC6F
12.06 -0.85
4.20E-
05
SPBP26
C9.02c -0.88
1.94E-
04
SPAC22
F8.02c -0.85
4.59E-
04
SPBC57
7.04 -0.88
1.93E-
03
SPCC17
95.04c -0.84
1.69E-
05
SPAC11
G7.01 -0.88
3.01E-
02
SPBP19
A11.01 -0.84
1.25E-
05
SPBC21.
03c -0.87
2.81E-
03
SPBC19
F5.03 -0.84
2.18E-
04
SPCC73
7.06c -0.87
1.05E-
04
SPBP8B
7.08c -0.84
7.08E-
03
SPBC25
B2.05 -0.87
2.10E-
02
SPCC62
2.12c -0.84
2.46E-
06
SPAC13
G7.09c -0.87
1.54E-
02
SPBC42
8.04 -0.84
1.45E-
03
SPAC5H
10.05c -0.87
4.45E-
03
SPAC22
7.16c -0.84
2.21E-
03
SPAC56
E4.07 -0.86
5.28E-
05
SPAC31
G5.18c -0.84
3.07E-
05
SPAC1B
3.16c -0.86
1.43E-
03
SPCC24
B10.05 -0.83
7.87E-
03
SPCC18.
12c -0.86
2.27E-
02
SPBC24
C6.06 -0.83
7.28E-
03
SPBC2D
10.15c -0.86
4.18E-
04
SPAC6
G9.11 -0.83
7.63E-
04
SPAC23
G3.05c -0.86
3.53E-
03
SPAC3
H1.14 -0.83
1.83E-
02
SPBC83
9.03c -0.86
5.61E-
05
SPAC24
C9.16c -0.83
3.48E-
02
SPAC17
G8.05 -0.86
4.74E-
04
SPAC16
E8.13 -0.82
1.35E-
05
SPAC60
7.04 -0.86
3.40E-
03
SPAPB1
A11.02 -0.82
1.30E-
02
SPAC82
1.09 -0.85
2.22E-
02
SPBC14
6.04 -0.82
1.61E-
02
SPBC88
7.01 -0.85
1.62E-
02
SPAPB1
A10.10c -0.82
5.45E-
04
SPBC34
2.06c -0.85
7.29E-
03
Table
A.1:
Continued
160

SPBC54
3.08 -0.82
1.90E-
03
SPAC2C
4.08 -0.85
3.40E-
05
SPCC12
6.06 -0.81
9.48E-
07
SPAC4F
10.06 -0.84
4.16E-
02
SPCC29
0.04 -0.81
3.26E-
02
SPAC19
52.02 -0.84
5.02E-
03
SPBC69
1.04 -0.81
1.39E-
03
SPAC16
E8.04c -0.84
1.94E-
05
SPAC16
A10.04 -0.81
6.17E-
03
SPBC36
B7.08c -0.84
5.79E-
03
SPBC21
1.07c -0.81
1.38E-
03
SPAP8A
3.11c -0.84
1.12E-
03
SPCC24
B10.13 -0.81
7.35E-
04
SPCC75
7.10 -0.84
1.41E-
05
SPBPB1
0D8.07c -0.81
1.48E-
02
SPAC5H
10.10 -0.84
4.97E-
04
SPAC3
G6.10c -0.81
4.32E-
02
SPAC11
D3.05 -0.83
3.88E-
02
SPBC19
G7.04 -0.81
3.74E-
02
SPAP7G
5.04c -0.83
1.17E-
05
SPAC23
C11.08 -0.81
1.21E-
02
SPCC18
27.04 -0.83
1.19E-
02
SPCC96
2.03c -0.81
1.78E-
02
SPAC26
F1.12c -0.83
1.34E-
02
SPAC26
A3.10 -0.80
1.03E-
03
SPBC30
B4.08 -0.83
2.45E-
06
SPAC23
H3.12c -0.80
9.50E-
03
SPAC29
B12.06c -0.82
5.65E-
04
SPBC3B
9.01 -0.80
4.07E-
02
SPAC4G
8.07c -0.82
1.82E-
02

SPCC4G
3.16 -0.82
4.43E-
02

SPBC13
A2.03 -0.82
3.58E-
05

SPAC17
A5.13 -0.82
5.04E-
04

SPAC22
E12.13c -0.81
9.02E-
03

SPCC33
0.07c -0.81
2.68E-
04
Table
A.1:
Continued
161

SPAC2E
1P5.03 -0.81
4.99E-
04

SPAP27
G11.04c -0.81
1.56E-
03

SPBC17
03.05 -0.81
2.06E-
02

SPAC89
0.04c -0.81
4.09E-
03

SPBC83
9.07 -0.80
2.49E-
03

SPAC57
A10.10c -0.80
6.72E-
03

SPAC3G
9.16c -0.80
5.04E-
04

SPBP22
H7.06 -0.80
2.83E-
05

SPBC13
G1.03c -0.80
2.31E-
02

∆gcn5 ∆elp3
∆mst2
Gene
Log2
Chan
ge pvalue Gene
Log2
Chan
ge pvalue Gene
Log2
Change pvalue
SPAC19
52.05 -5.66
4.19E-
03
SPCC28
5.05 -1.25 4.75E-02
SPBP8B
7.31 -0.95 3.75E-02
SPAC29
A4.20 -5.64
3.29E-
13
SPAC3G
6.10c -1.24 1.65E-02
SPBC25
B2.11 -0.95 3.69E-03
SPBPB1
0D8.01 -4.74
5.16E-
06
SPCC96
5.13 -1.24 3.47E-05
SPAC17
G8.05 -0.95 3.74E-03
SPBPB1
0D8.02c -4.74
7.09E-
06
SPAC12
B10.10 -1.23 4.84E-02
SPAC17
A5.09c -0.95 1.02E-03
SPAC17
G8.13c -4.41
1.02E-
02
SPAC15
E1.08 -1.22 1.55E-03
SPAC4H
3.13 -0.95 2.73E-02
SPAC57
A10.06 -3.73
2.28E-
03
SPBC88
7.01 -1.21 1.52E-02
SPAC11
0.01 -0.95 1.64E-04
SPBPB2
-3.65
5.26E-

SPAC22
-1.20 7.38E-04
SPBC17
-0.95 9.76E-03
Table
A.1:
Continued
162

B2.06c 05 7.16c 03.09
SPBC26
H8.11c -3.64
1.20E-
08
SPAC26
H5.02c -1.20 4.71E-06
SPBC23
G7.14 -0.95 1.04E-02
SPAC10
39.02 -3.40
1.56E-
03
SPAC86
9.10c -1.19 3.76E-02
SPAC22
G7.01c -0.95 1.44E-05
SPAC2E
1P3.05c -3.17
1.71E-
10
SPBC16
D10.06 -1.19 1.48E-04
SPBC11
05.12 -0.94 8.94E-03
SPBPB2
B2.01 -2.88
2.83E-
04
SPBC20
F10.06 -1.18 1.68E-02
SPAC32
8.10c -0.94 2.71E-03
SPAC18
6.06 -2.78
1.16E-
03
SPAC5H
10.03 -1.18 1.56E-03
SPAC23
H4.13c -0.93 1.28E-02
SPAC97
7.05c -2.60
5.56E-
03
SPAC11
H11.02c -1.15 4.11E-03
SPAC31
G5.14 -0.92 2.22E-03
SPAC18
6.05c -2.53
1.73E-
03
SPAC5H
10.05c -1.15 6.87E-03
SPAC56
E4.04c -0.92 6.27E-05
SPAC29
B12.10c -2.53
5.33E-
04
SPBC18
61.05 -1.15 1.87E-02
SPAC6C
3.04 -0.92 1.15E-05
SPBC16
A3.16 -2.39
2.04E-
03
SPBPB1
0D8.07c -1.14 7.43E-03
SPAC23
H4.09 -0.92 4.79E-05
SPAC18
6.03 -2.36
3.93E-
05
SPAC29
A4.14c -1.14 9.08E-04
SPBC12
D12.05c -0.91 6.63E-04
SPAC86
9.05c -2.21
1.13E-
02
SPAC2F
3.09 -1.13 8.44E-05
SPAC20
G4.01 -0.91 2.66E-05
SPAC1F
12.03c -2.17
9.71E-
04
SPBC26
H8.09c -1.13 1.50E-03
SPBC33
7.16 -0.91 3.32E-03
SPAC18
G6.12c -2.15
1.37E-
04
SPBC12
71.14 -1.13 8.08E-03
SPAC56
E4.07 -0.90 1.08E-03
SPBC94
7.04 -2.11
1.73E-
03
SPBC3B
8.07c -1.13 1.22E-04
SPCC70.
05c -0.90 5.62E-06
SPCC62
2.01c -2.09
1.73E-
06
SPCC62
2.06c -1.12 3.47E-02
SPAC23
C4.14 -0.89 6.49E-05
SPCC19
02.02 -2.08
2.34E-
04
SPAC2E
12.03c -1.12 2.54E-02
SPAC22
G7.02 -0.89 6.14E-05
SPAC58
9.09 -2.08
6.64E-
05
SPAC17
C9.09c -1.11 9.45E-03
SPBC2G
2.05 -0.89 8.40E-04
SPBC25
B2.08 -2.05
3.28E-
05
SPAC29
B12.14c -1.11 1.26E-04
SPAC56
F8.07 -0.89 2.21E-02
SPCC16
82.09c -2.04
3.76E-
05
SPAC13
G7.09c -1.10 2.72E-02
SPCC24
B10.13 -0.89 2.42E-03
Table
A.1:
Continued
163

SPAC13
99.04c -2.03
5.85E-
03
SPBC28
F2.11 -1.09 7.21E-06
SPAC18
51.02 -0.89 4.49E-05
SPAC13
G7.13c -2.02
3.86E-
05
SPBC17
73.17c -1.09 8.34E-03
SPBC40
9.11 -0.89 7.91E-03
SPBC23
G7.13c -2.01
3.79E-
02
SPBC4B
4.11 -1.09 1.68E-02
SPCC14
94.09c -0.88 4.78E-03
SPCC12
23.13 -1.93
5.77E-
03
SPBC29
A10.13 -1.08 1.96E-04
SPAC23
D3.11 -0.88 3.47E-02
SPBP26
C9.03c -1.89
3.18E-
02
SPBC21
6.04c -1.08 3.21E-02
SPAC24
H6.05 -0.88 2.94E-03
SPBC29
B5.02c -1.83
2.38E-
05
SPAC18
34.07 -1.08 4.95E-04
SPAC3G
6.05 -0.88 1.03E-03
SPBC33
7.09 -1.81
1.10E-
07
SPCC17
95.07 -1.07 8.83E-05
SPAC10
93.01 -0.87 2.68E-03
SPBC21
D10.07 -1.80
3.03E-
07
SPAC13
F5.05 -1.06 6.33E-05
SPAC22
2.10c -0.87 2.52E-04
SPAC18
34.03c -1.76
1.68E-
05
SPBP4H
10.11c -1.06 5.94E-03
SPBC6B
1.02 -0.87 1.34E-03
SPAC17
G6.02c -1.73
3.36E-
06
SPAC23
H3.13c -1.05 2.34E-03
SPBC17
06.01 -0.87 6.33E-05
SPCC66
3.09c -1.68
4.11E-
03
SPAC4G
9.10 -1.04 3.60E-04
SPAC13
G6.15c -0.86 5.17E-03
SPAC8E
11.10 -1.67
4.59E-
04
SPBC71
3.05 -1.04 1.78E-04
SPBC19
G7.07c -0.86 9.20E-04
SPAC23
H3.12c -1.62
2.13E-
04
SPAC82
3.15 -1.04 1.03E-05
SPBC21
1.01 -0.86 3.14E-03
SPCC16
82.08c -1.59
2.61E-
03
SPAC6F
12.05c -1.03 3.67E-05
SPAPB1
E7.07 -0.86 1.11E-03
SPAPY
UG7.04c -1.54
3.02E-
03
SPAC17
82.01 -1.03 1.31E-04
SPCC16
20.01c -0.86 5.31E-03
SPBP4H
10.20 -1.53
1.69E-
07
SPBC16
G5.17 -1.03 1.73E-04
SPBC19
C2.08 -0.86 1.61E-02
SPBC35
9.04c -1.53
7.69E-
04
SPAC17
A2.14 -1.03 5.77E-06
SPAC23
G3.05c -0.86 2.90E-02
SPAC5
H10.06c -1.52
2.42E-
04
SPBC11
05.03c -1.02 5.53E-04
SPBC57
7.08c -0.86 7.90E-04
SPAC12
50.04c -1.50
3.86E-
03
SPBC71
3.12 -1.02 1.10E-02
SPBC2D
10.09 -0.85 5.40E-04
SPCC63
.03 -1.50
1.71E-
02
SPAC5H
10.10 -1.02 1.92E-03
SPAC56
F8.10 -0.85 1.15E-04
Table
A.1:
Continued
164

SPAC58
9.03c -1.47
1.34E-
03
SPBC83
9.07 -1.01 5.77E-03
SPCC16
72.01 -0.85 4.11E-04
SPBC8
D2.09c -1.46
2.16E-
02
SPBC3H
7.12 -1.01 8.09E-03
SPBC11
C11.08 -0.84 1.08E-04
SPBC12
D12.07c -1.45
3.16E-
03
SPCC62
2.12c -1.01 4.65E-06
SPBC3B
9.18c -0.84 7.74E-03
SPAC27
D7.04 -1.44
7.97E-
07
SPCC12
6.10 -1.01 1.11E-04
SPBC31
F10.04c -0.84 1.39E-03
SPBP23
A10.12 -1.44
1.45E-
04
SPBC29
A10.16c -1.00 2.50E-04
SPBC10
6.15 -0.83 1.16E-03
SPAC17
C9.16c -1.44
6.63E-
05
SPAC2E
1P3.04 -1.00 3.43E-03
SPBC65
1.04 -0.83 3.66E-02
SPCC62
2.02 -1.43
4.81E-
05
SPBC83
9.03c -1.00 4.20E-04
SPBC80
0.11 -0.83 9.79E-03
SPCC62
2.07 -1.42
2.44E-
02
SPBC21
C3.04c -1.00 7.78E-03
SPAC7D
4.06c -0.83 2.23E-03
SPBC72
5.16 -1.42
6.90E-
04
SPCC55
3.03 -0.99 9.01E-04
SPAC2F
7.08c -0.83 5.91E-03
SPBC16
83.02 -1.41
8.47E-
03
SPAC22
7.08c -0.99 5.28E-03
SPBC4B
4.10c -0.83 2.42E-04
SPBC2
G2.15c -1.39
1.50E-
06
SPAC92
6.05c -0.99 3.64E-02
SPAC10
39.04 -0.83 2.19E-02
SPBC26
H8.03 -1.38
4.54E-
07
SPAC20
G4.04c -0.99 3.57E-02
SPBC17
D11.03c -0.83 1.48E-03
SPBC11
9.06 -1.37
5.24E-
05
SPAP7G
5.04c -0.98 9.50E-05
SPAC19
B12.12c -0.83 1.07E-02
SPBC19
F8.05 -1.36
8.26E-
04
SPAC32
8.09 -0.98 2.24E-02
SPAC3C
7.10 -0.82 3.96E-03
SPBC16
83.05 -1.36
5.44E-
04
SPAC18
05.16c -0.98 2.53E-04
SPAC66
4.13 -0.82 4.56E-03
SPAC24
H6.11c -1.35
1.60E-
04
SPCC32
0.06 -0.98 5.99E-03
SPBC19
F5.03 -0.82 2.18E-03
SPBP22
H7.06 -1.34
3.46E-
06
SPAC13
G6.06c -0.98 2.45E-02
SPBC36
5.01 -0.82 7.14E-03
SPAC18
34.05 -1.31
8.91E-
07
SPAC10
02.18 -0.98 4.42E-02
SPAC22
F3.07c -0.81 2.59E-03
SPAC8
C9.05 -1.29
2.25E-
03
SPAC22
A12.11 -0.97 2.57E-03
SPAPB1
A10.03 -0.81 1.33E-03
SPBC2
G2.01c -1.28
5.78E-
04
SPBC21
1.06 -0.97 1.09E-03
SPBC1A
4.04 -0.81 3.84E-03
Table
A.1:
Continued
165

SPAC1
B3.10c -1.27
3.22E-
02
SPCC19
19.13c -0.97 1.04E-02
SPBC11
98.06c -0.81 1.14E-03
SPCC12
59.09c -1.27
1.95E-
05
SPBC42
8.04 -0.97 2.99E-03
SPAC3H
1.04c -0.81 1.92E-03
SPCC19
1.03c -1.26
1.69E-
03
SPBC17
34.02c -0.96 1.90E-02
SPAC2H
10.02c -0.81 5.90E-03
SPBC3
H7.07c -1.25
4.55E-
03
SPBC13
E7.11 -0.96 2.45E-04
SPAC10
F6.07c -0.80 1.63E-02
SPBC69
1.04 -1.25
2.31E-
04
SPAC13
99.02 -0.96 7.98E-04
SPAC2E
1P5.03 -0.80 8.31E-03

SPCC70.
03c -0.95 4.19E-02
SPAC19
B12.07c -0.80 1.85E-02

SPBC36.
03c -0.80 1.85E-02

SPBC11
B10.03 -0.80 2.07E-02

mst1
ts

mst1
t
s
mst1
ts

Gene
Log2
Chan
ge pvalue Gene
Log2
Chan
ge pvalue Gene
Log2
Change pvalue
SPAC10
39.02 -2.66
6.36E-
04
SPACU
NK4.14 -1.12 4.95E-05
SPBP35
G2.03c -0.92 6.48E-04
SPBC29
A3.05 -2.18
5.55E-
05
SPCC55
0.02c -1.12 2.19E-06
SPAC17
C9.08 -0.92 7.87E-09
SPCC75
7.06 -2.08
1.87E-
07
SPAC58
9.09 -1.12 9.76E-04
SPACU
NK4.06c -0.91 6.36E-07
SPAC6
B12.09 -1.86
5.44E-
06
SPAC7D
4.05 -1.12 3.57E-04
SPCC57
6.13 -0.91 4.94E-05
SPBC94
7.04 -1.85
2.36E-
04
SPBC31
F10.12 -1.11 1.01E-04
SPAPB2
B4.06 -0.91 7.04E-05
SPAC4
H3.06 -1.78
1.49E-
05
SPBP8B
7.31 -1.11 1.61E-03
SPAC4G
9.13c -0.91 2.44E-03
SPBC14
F5.01 -1.77
4.08E-
05
SPCC66
3.09c -1.11 6.60E-03
SPAC3G
9.02 -0.91 1.56E-04
SPAC14
-1.74
5.14E-

SPBC4B
-1.11 5.68E-03
SPAC22
-0.91 1.21E-02
Table
A.1:
Continued
166

86.08 04 4.05 7.02c
SPCC33
8.04 -1.68
9.00E-
04
SPBC30
B4.02c -1.11 2.43E-04
SPBC57
7.03c -0.91 5.32E-03
SPAC17
G8.09 -1.59
3.35E-
04
SPCC61
3.07 -1.11 2.43E-05
SPAC8C
9.05 -0.91 2.39E-03
SPAC1F
12.08 -1.59
1.53E-
07
SPBC16
83.06c -1.10 3.69E-02
SPBC16
E9.19 -0.91 8.95E-06
SPAC8
C9.07 -1.59
1.14E-
03
SPBC18
61.01c -1.10 2.77E-02
SPBC11
G11.02c -0.91 2.94E-07
SPBC14
6.08c -1.59
2.04E-
04
SPAC1F
12.03c -1.10 1.13E-02
SPCC11
83.03c -0.91 9.54E-04
SPBC36
5.11 -1.58
6.64E-
04
SPBP18
G5.02 -1.10 2.23E-05
SPBC27.
05 -0.91 6.85E-03
SPCC19
19.07 -1.58
3.99E-
05
SPBC16
E9.06c -1.10 1.55E-04
SPBC83
9.03c -0.90 3.04E-05
SPAC12
50.04c -1.57
1.21E-
04
SPBC27
B12.07 -1.09 7.80E-07
SPAC13
G6.14 -0.90 5.25E-04
SPAC2
C4.12c -1.56
2.82E-
06
SPBC36
5.05c -1.09 5.07E-05
SPBC16
A3.06 -0.90 1.34E-04
SPAC2E
1P3.05c -1.56
4.99E-
08
SPBC18
61.07 -1.08 9.22E-05
SPAC17
A5.13 -0.90 1.85E-04
SPBC2
A9.12 -1.53
1.99E-
03
SPAC1F
12.09 -1.08 7.93E-10
SPCC73
6.03c -0.90 1.69E-05
SPBC3
D6.09 -1.53
3.75E-
05
SPBC18
61.04c -1.08 2.46E-05
SPAC17
A2.14 -0.90 3.15E-07
SPAC13
9.06 -1.52
2.60E-
06
SPAC15
E1.08 -1.08 1.94E-04
SPAC19
G12.13c -0.90 7.47E-04
SPBC19
G7.02 -1.52
1.02E-
04
SPAC22
F3.11c -1.08 1.22E-02
SPAC2C
4.14c -0.90 1.09E-04
SPAC3
G6.06c -1.51
5.65E-
06
SPAC92
6.05c -1.08 2.65E-03
SPAC9.1
2c -0.90 5.36E-07
SPBC33
6.08 -1.51
6.85E-
07
SPAC66
4.08c -1.08 2.57E-03
SPBC71
3.09 -0.90 2.54E-03
SPAC12
G12.02 -1.51
3.99E-
05
SPBC36.
12c -1.08 5.12E-05
SPAC13
G7.09c -0.90 1.26E-02
SPBC36
5.04c -1.49
3.84E-
04
SPAC25
B8.15c -1.07 2.24E-05
SPBC72
5.13c -0.90 8.60E-04
SPBC3B
9.21 -1.49
1.89E-
03
SPAC68
8.12c -1.07 6.45E-04
SPCC18
27.01c -0.90 1.10E-02
Table
A.1:
Continued
167

SPBC16
A3.16 -1.47
5.79E-
03
SPCC4G
3.16 -1.07 1.10E-02
SPBC14
F5.08 -0.90 1.92E-06
SPCC16
C4.20c -1.45
5.35E-
04
SPAC2F
7.17 -1.07 5.19E-05
SPBC36.
05c -0.90 8.63E-09
SPAC13
G7.07 -1.45
4.54E-
06
SPBC83.
08 -1.07 2.61E-08
SPCC17
95.01c -0.90 3.27E-05
SPAC17
A5.01 -1.43
5.74E-
08
SPAC16
E8.04c -1.07 9.47E-07
SPBC16
G5.17 -0.90 1.67E-05
SPAC1
B3.10c -1.42
1.83E-
03
SPBC3H
7.07c -1.07 1.03E-03
SPCC12
6.10 -0.89 7.93E-06
SPAC63
0.06c -1.42
1.73E-
04
SPAC22
7.16c -1.07 7.74E-05
SPAC20
G4.04c -0.89 9.54E-03
SPBC56
F2.14 -1.42
4.23E-
03
SPAC56
E4.07 -1.07 3.96E-06
SPAC12
B10.10 -0.89 4.41E-02
SPAC19
52.02 -1.41
4.41E-
05
SPBC30
D10.12c -1.07 5.52E-04
SPCC62
2.06c -0.89 1.93E-02
SPBC4B
4.12c -1.41
5.35E-
07
SPAC3F
10.08c -1.06 2.87E-03
SPAC1A
6.02 -0.89 3.63E-05
SPCC66
3.11 -1.40
7.08E-
06
SPBC20
F10.04c -1.06 6.65E-07
SPBC24
C6.07 -0.89 8.63E-05
SPAC8
C9.10c -1.40
2.19E-
04
SPAC14
C4.02c -1.06 5.40E-05
SPAC82
3.08c -0.89 3.20E-03
SPAC57
A10.03 -1.40
2.96E-
09
SPAC10
02.07c -1.06 1.36E-05
SPAC31
A2.02 -0.89 3.78E-04
SPAC22
7.05 -1.40
3.88E-
03
SPBC19
F8.01c -1.06 1.23E-05
SPAC7D
4.02c -0.89 5.35E-06
SPCC66
3.13c -1.39
1.56E-
03
SPBC17
34.05c -1.06 8.63E-04
SPAC22
7.09 -0.89 9.78E-05
SPCC18
40.10 -1.39
1.92E-
04
SPBC32
F12.15 -1.06 2.09E-02
SPAC23
H4.07c -0.89 4.39E-03
SPACU
NK4.13c -1.38
3.25E-
07
SPBC19
C7.01 -1.06 1.34E-04
SPCC83
0.10 -0.89 1.87E-05
SPCC2
H8.04 -1.38
1.91E-
04
SPCC19
19.14c -1.06 1.87E-04
SPAC11
42.06 -0.88 1.51E-09
SPAC1
D4.01 -1.38
1.49E-
03
SPAC4C
5.04 -1.05 2.90E-07
SPBC31
F10.04c -0.88 2.34E-05
SPAC24
C9.09 -1.37
3.72E-
07
SPAC10
F6.08c -1.05 3.86E-05
SPAC23
C4.09c -0.88 1.13E-02
SPAC31
G5.14 -1.36
7.08E-
07
SPBC11
9.15 -1.05 4.40E-06
SPBC3B
8.01c -0.88 1.26E-05
Table
A.1:
Continued
168

SPCC63
.07 -1.36
3.29E-
04
SPACU
NK4.09 -1.05 2.18E-04
SPBC64
9.03 -0.88 7.34E-03
SPAP8A
3.02c -1.35
1.57E-
03
SPBC21.
03c -1.05 5.86E-04
SPAPB2
4D3.06c -0.88 4.01E-05
SPBC36
B7.08c -1.35
9.15E-
05
SPBC2A
9.09 -1.05 4.13E-05
SPBC19
C2.13c -0.88 1.03E-03
SPAC11
E3.03 -1.35
4.04E-
03
SPBC29
A10.16c -1.05 2.81E-06
SPBC8D
2.13 -0.88 1.16E-05
SPBP8B
7.02 -1.34
3.30E-
04
SPCC16
2.05 -1.04 3.60E-05
SPAC20
H4.05c -0.88 5.09E-05
SPAC22
A12.14c -1.34
2.00E-
04
SPAC17
D4.04 -1.04 7.46E-06
SPAC16
E8.06c -0.88 3.79E-03
SPAC1F
12.06c -1.33
1.35E-
07
SPCC12
23.13 -1.04 2.78E-02
SPAC4F
8.04 -0.88 8.23E-03
SPBC88
7.08 -1.33
2.75E-
02
SPAC29
A4.14c -1.04 7.15E-05
SPBC21
D10.07 -0.88 3.69E-05
SPBC25
H2.10c -1.33
8.84E-
07
SPAC17
82.03 -1.04 3.22E-03
SPBC25
B2.04c -0.88 1.77E-03
SPBC19
F8.02 -1.33
5.75E-
04
SPBC12
71.07c -1.04 2.98E-05
SPAC4G
8.10 -0.88 1.70E-04
SPCP1E
11.07c -1.33
5.31E-
03
SPAC12
B10.04 -1.04 4.00E-04
SPAC34
3.03 -0.87 1.21E-05
SPBC21
B10.13c -1.33
4.92E-
04
SPAC3A
11.13 -1.03 4.06E-03
SPAC27
D7.02c -0.87 7.45E-04
SPAC8
C9.17c -1.32
2.06E-
07
SPBC17
09.07 -1.03 2.93E-05
SPAC25
G10.07c -0.87 2.09E-05
SPCC16
2.01c -1.31
1.43E-
03
SPAC9.0
6c -1.03 1.30E-05
SPBC3B
9.12 -0.87 9.26E-03
SPBC17
03.08c -1.31
1.95E-
03
SPBC17
09.19c -1.03 3.72E-05
SPBC17
03.01c -0.87 3.33E-03
SPAC4
H3.14c -1.31
1.12E-
05
SPCC11
E10.04 -1.03 5.47E-06
SPBC15
C4.01c -0.87 1.15E-06
SPBC17
03.05 -1.31
6.69E-
04
SPAC11
0.02 -1.02 1.66E-05
SPAC10
02.10c -0.87 3.24E-03
SPAC19
52.03 -1.30
4.62E-
04
SPAC13
G6.05c -1.02 2.24E-05
SPAC58
9.02c -0.87 2.05E-03
SPBC35
4.04 -1.30
8.85E-
07
SPBC23
G7.07c -1.02 2.54E-02
SPCC17
39.07 -0.87 1.07E-02
SPAC68
8.06c -1.30
2.58E-
06
SPAC1F
8.06 -1.02 3.79E-03
SPBP23
A10.12 -0.87 6.95E-04
Table
A.1:
Continued
169

SPAC1F
3.01 -1.30
1.88E-
04
SPBC14
C8.15 -1.02 3.69E-07
SPCC24
B10.19c -0.87 3.35E-04
SPAC11
E3.08c -1.30
8.33E-
06
SPBC16
83.02 -1.02 7.47E-03
SPAC31
G5.15 -0.87 1.96E-04
SPCC18
27.04 -1.29
3.90E-
04
SPCC16
A11.12c -1.02 4.75E-04
SPBC6B
1.04 -0.86 6.36E-06
SPCC61
3.11c -1.29
3.23E-
06
SPBC13
G1.03c -1.02 5.29E-03
SPBC2D
10.16 -0.86 2.70E-02
SPAC27
F1.04c -1.29
1.18E-
03
SPCP20
C8.02c -1.01 1.36E-02
SPAC17
C9.05c -0.86 1.44E-06
SPBC29
A3.07c -1.28
2.86E-
03
SPBC19
C7.07c -1.01 5.15E-04
SPCC4B
3.08 -0.86 2.68E-04
SPBC40
5.05 -1.28
1.62E-
03
SPAC22
7.17c -1.01 2.86E-05
SPAC23
G3.10c -0.86 4.18E-05
SPAC14
4.01 -1.27
3.79E-
02
SPAC22
7.12 -1.01 2.21E-05
SPBP8B
7.01c -0.86 5.09E-03
SPBC27
B12.02 -1.27
2.30E-
02
SPBP8B
7.08c -1.01 7.14E-04
SPAC13
A11.03 -0.86 2.45E-02
SPBC32
F12.05c -1.26
2.65E-
05
SPBC27.
04 -1.01 1.46E-02
SPBC36
5.09c -0.86 6.34E-05
SPAC11
D3.02c -1.26
4.53E-
05
SPAC16
7.08 -1.00 1.05E-03
SPCC18
40.11 -0.86 3.25E-04
SPCC16
A11.05c -1.26
3.53E-
04
SPBP16
F5.05c -1.00 4.81E-03
SPBC88
7.18c -0.86 1.98E-04
SPAC15
56.04c -1.25
5.59E-
04
SPCC33
0.03c -1.00 9.84E-04
SPCC18
B5.06 -0.85 5.07E-05
SPBC20
F10.09 -1.25
7.69E-
05
SPCC64
5.10 -1.00 1.67E-07
SPCC77
7.17c -0.85 2.52E-02
SPAC10
39.08 -1.25
6.38E-
04
SPAC3A
12.11c -0.99 1.73E-03
SPBC26
H8.03 -0.85 2.78E-06
SPBC13
E7.06 -1.25
1.27E-
04
SPAC4F
8.01 -0.99 6.42E-05
SPBC12
71.04c -0.85 1.18E-05
SPAC10
F6.10 -1.25
2.27E-
03
SPCC82
5.02 -0.99 1.13E-07
SPBC15
39.10 -0.85 3.03E-02
SPBC21
C3.07c -1.24
8.14E-
09
SPCC12
6.03 -0.99 2.73E-03
SPAC4F
8.05c -0.85 2.56E-02
SPBC14
C8.12 -1.24
5.41E-
05
SPBC16
85.11 -0.99 1.54E-04
SPAC27
E2.02 -0.85 4.32E-05
SPAC15
A10.12c -1.24
1.01E-
03
SPBC30
D10.08 -0.99 2.15E-04
SPAC3H
1.14 -0.85 8.08E-03
Table
A.1:
Continued
170

SPAC68
3.02c -1.24
4.70E-
03
SPBC1D
7.01 -0.99 3.15E-03
SPBC11
05.15c -0.85 1.17E-04
SPAC26
F1.12c -1.23
7.06E-
04
SPCC2H
8.05c -0.98 5.27E-06
SPAC4F
10.19c -0.84 7.74E-04
SPACU
NK4.11c -1.23
5.88E-
03
SPAC31
A2.08 -0.98 3.13E-03
SPBC12
71.13 -0.84 9.26E-05
SPAC23
H4.04 -1.22
6.60E-
04
SPAC6G
9.06c -0.98 1.95E-04
SPCC24
B10.12 -0.84 5.37E-03
SPCC82
5.04c -1.22
1.18E-
06
SPBC2D
10.13 -0.98 5.31E-04
SPAC16
A10.02 -0.84 4.32E-03
SPCC13
93.05 -1.22
3.92E-
06
SPBC3B
9.08c -0.98 3.31E-03
SPAC11
42.04 -0.84 6.78E-03
SPAC64
4.04 -1.22
4.86E-
05
SPBC2D
10.15c -0.98 1.12E-04
SPCC16
A11.16c -0.84 3.93E-05
SPAC5
H10.11 -1.21
1.16E-
06
SPBC36
5.13c -0.98 1.34E-04
SPAC1B
3.02c -0.84 1.36E-03
SPAC68
8.02c -1.21
3.46E-
04
SPBC17
06.03 -0.98 1.66E-05
SPAC6F
12.08c -0.84 9.25E-05
SPBC2
G2.05 -1.20
4.82E-
07
SPAC32
3.01c -0.98 1.34E-05
SPAC82
3.04 -0.84 3.49E-02
SPBC16
H5.15 -1.20
1.27E-
04
SPBC31
F10.04c -0.98 2.62E-06
SPCP31
B10.03c -0.83 1.98E-03
SPAC60
7.02c -1.20
1.02E-
02
SPBC57
7.15c -0.98 3.45E-07
SPBC11
B10.04c -0.83 1.97E-03
SPCC12
6.14 -1.20
1.98E-
07
SPAC22
2.03c -0.98 6.88E-03
SPAC26
H5.06 -0.83 2.68E-05
SPAC3
H1.03 -1.20
1.38E-
02
SPAC1D
4.09c -0.97 2.08E-04
SPBC15
C4.03 -0.83 1.42E-05
SPAC17
A2.08c -1.20
1.00E-
04
SPBP22
H7.05c -0.97 1.50E-04
SPBC3H
7.14 -0.83 4.85E-03
SPBC31
E1.03 -1.20
1.90E-
02
SPBC17
09.04c -0.97 3.65E-05
SPCC4B
3.16 -0.83 1.42E-03
SPBC12
D12.08c -1.19
1.45E-
02
SPAC12
B10.06c -0.97 8.20E-03
SPCC4G
3.02 -0.83 1.47E-05
SPBC12
71.08c -1.19
4.44E-
02
SPCC75
7.05c -0.97 1.50E-08
SPBC4B
4.01c -0.82 8.28E-05
SPBC14
C8.09c -1.19
3.13E-
06
SPCC61.
02 -0.97 1.41E-02
SPAC27
E2.06c -0.82 1.59E-05
SPBC83
.15 -1.19
1.72E-
04
SPAC15
A10.08 -0.96 2.65E-05
SPBC17
18.03 -0.82 1.73E-02
Table
A.1:
Continued
171

SPCC12
23.04c -1.19
2.86E-
06
SPAC20
H4.03c -0.96 8.98E-08
SPAC68
8.09 -0.82 3.42E-05
SPCC13
93.09c -1.19
4.12E-
05
SPAC4F
8.03 -0.96 8.04E-05
SPBC54
3.03c -0.82 2.14E-06
SPAP27
G11.04c -1.18
3.54E-
05
SPAC45
8.07 -0.96 4.48E-05
SPBC16
G5.12c -0.82 3.80E-03
SPCC55
3.07c -1.18
3.02E-
06
SPAC18
34.10c -0.96 7.76E-04
SPBC3B
9.02c -0.82 3.00E-04
SPAC64
4.10 -1.17
1.99E-
04
SPAC3A
12.09c -0.96 5.52E-04
SPBC20
F10.05 -0.82 7.94E-06
SPAC1F
5.07c -1.17
6.26E-
06
SPBC21
5.02 -0.96 7.65E-03
SPBC33
6.13c -0.82 1.02E-04
SPCC16
C4.05 -1.17
2.28E-
04
SPBC20
F10.06 -0.96 7.46E-03
SPBC17
73.17c -0.81 5.91E-03
SPAC68
8.14 -1.16
3.53E-
05
SPBP4H
10.20 -0.95 9.88E-07
SPAC16
7.04 -0.81 1.89E-05
SPAC12
G12.16c -1.16
2.76E-
06
SPAC3H
8.07c -0.95 3.10E-03
SPAC12
G12.13c -0.81 6.70E-04
SPAC32
3.06c -1.16
4.87E-
04
SPAC11
E3.12 -0.95 3.07E-04
SPAC29
E6.03c -0.81 9.24E-03
SPCC56
9.07 -1.16
4.10E-
04
SPBC17
03.14c -0.95 5.27E-04
SPCC29
7.06c -0.81 1.26E-02
SPCC61
3.03 -1.16
6.64E-
06
SPAC82
3.05c -0.95 8.63E-05
SPAC24
H6.08 -0.81 1.15E-04
SPCC83
0.11c -1.16
1.36E-
04
SPBC31
E1.05 -0.95 3.45E-05
SPAC17
H9.06c -0.81 1.72E-03
SPBC11
C11.01 -1.16
5.34E-
05
SPAC4A
8.09c -0.95 2.52E-04
SPBC77
6.14 -0.81 1.83E-04
SPAPB1
E7.10 -1.16
2.88E-
03
SPAC29
A4.06c -0.95 8.85E-04
SPAC92
2.06 -0.81 3.17E-03
SPAC8E
11.07c -1.16
2.14E-
03
SPAC11
H11.03c -0.95 3.32E-04
SPBC2D
10.11c -0.81 2.16E-05
SPBC15
39.02 -1.16
2.14E-
04
SPBC3E
7.11c -0.95 4.13E-06
SPBC30
D10.02 -0.81 4.46E-04
SPCPB1
6A4.04c -1.16
1.97E-
05
SPBC18
H10.15 -0.95 3.22E-06
SPBC94
7.07 -0.81 1.03E-02
SPBC40
9.11 -1.16
3.18E-
05
SPAC2F
7.15 -0.94 1.04E-05
SPBP35
G2.04c -0.81 7.35E-03
SPAC66
4.12c -1.15
2.26E-
04
SPCC64
5.02 -0.94 8.83E-03
SPAC11
H11.05c -0.81 7.11E-04
Table
A.1:
Continued
172

SPAC56
F8.09 -1.15
7.35E-
04
SPAC58
9.08c -0.94 5.32E-03
SPCC62
2.14 -0.81 5.55E-05
SPAC16
87.13c -1.15
7.64E-
07
SPBC12
D12.07c -0.94 6.14E-03
SPAP8A
3.10 -0.81 2.83E-03
SPCC14
42.13c -1.14
1.68E-
04
SPCC17
53.04 -0.93 1.25E-08
SPAC13
G6.04 -0.81 2.58E-02
SPBC13
47.04 -1.14
2.56E-
04
SPAC12
B10.05 -0.93 9.86E-07
SPAC10
71.04c -0.80 2.83E-02
SPBC3
D6.04c -1.14
5.44E-
04
SPBC29
A10.12 -0.93 1.09E-03
SPCC73
7.06c -0.80 2.44E-04
SPBP8B
7.28c -1.14
4.21E-
03
SPCC19
19.13c -0.93 1.10E-03
SPBC40
5.06 -0.80 8.56E-05
SPBC13
47.01c -1.14
1.22E-
03
SPAPB1
E7.11c -0.93 1.76E-04
SPAC20
H4.08 -0.80 3.23E-02
SPBC3B
9.10 -1.13
1.19E-
05
SPAC63
0.10 -0.93 1.72E-05
SPBC9B
6.05c -0.80 1.66E-04
SPBC35
4.03 -1.13
7.44E-
05
SPBC17
A3.08 -0.93 3.80E-09
SPAC57
A10.11c -0.80 1.89E-04
SPAC27
D7.07c -1.13
1.41E-
04
SPAC10
F6.07c -0.93 4.19E-04
SPCC19
19.02 -0.80 5.13E-04
SPBC17
34.02c -1.13
4.70E-
04
SPCC96
2.05 -0.92 1.14E-06
SPCC64
5.12c -0.80 1.45E-04
SPBC6B
1.12c -1.12
1.87E-
03
SPBC77
6.12c -0.92 2.75E-04
SPCC61
3.12c -1.12
9.16E-
06
SPBC72
5.17c -0.92 1.47E-05
SPBC19
G7.04 -1.12
2.57E-
03
SPBC11
05.18c -0.92 2.61E-02
SPBC16
C6.05 -1.12
6.84E-
04
SPAC23
C4.02 -0.92 2.06E-02

SPBC16
A3.12c -0.92 6.95E-09

SPAC17
H9.13c -0.92 6.40E-06

SPAC4A
8.05c -0.92 2.14E-03

Table
A.1:
Continued
173

Up-
regula
ted

∆elp
3
Gene
Log2
Chan
ge pvalue Gene
Log2
Chan
ge pvalue Gene
Log2
Change pvalue
SPBCPT
2R1.08c 4.50
1.90E-
04
SPCC58
4.02 1.18 2.64E-05
SPBC19
G7.13 0.93 2.54E-05
SPAC97
7.16c 3.86
3.35E-
10
SPAC34
3.07 1.18 4.11E-05
SPAC11
D3.09 0.93 3.75E-04
SPAC75
0.07c 3.83
1.50E-
08
SPCC70.
08c 1.17 5.62E-04
SPAPB1
5E9.02c 0.92 9.68E-04
SPAC18
6.01 3.35
3.47E-
10
SPAC57
A7.05 1.17 1.78E-02
SPBC3B
8.09 0.92 3.31E-03
SPAC21
2.08c 2.97
1.73E-
14
SPBC27.
03 1.16 3.44E-06
SPCC13
B11.04c 0.92 6.37E-04
SPAC2E
1P3.02c 2.62
2.24E-
09
SPCC16
2.02c 1.15 3.38E-07
SPCC16
2.03 0.92 6.07E-05
SPAC18
6.02c 2.30
3.71E-
09
SPBC6B
1.03c 1.15 1.56E-05
SPAC3F
10.10c 0.92 3.13E-05
SPAC86
9.01 2.29
2.04E-
12
SPCC56
9.07 1.15 4.69E-04
SPAC10
39.04 0.92 9.91E-04
SPAC6
C3.03c 2.25
1.97E-
07
SPAP7G
5.03 1.15 9.86E-07
SPAC15
E1.02c 0.92 6.58E-03
SPCC13
93.10 2.22
1.28E-
07
SPCC16
72.03c 1.14 9.29E-05
SPAC10
39.01 0.91 2.98E-02
SPBPB2
B2.01 2.20
1.27E-
04
SPBC16
E9.10c 1.14 8.08E-05
SPAC10
06.03c 0.91 1.72E-05
SPBC23
G7.10c 2.17
1.62E-
02
SPAC1F
8.05 1.14 5.70E-03
SPAC21
E11.04 0.91 4.13E-04
SPAC24
C9.15c 2.17
8.66E-
05
SPBC8E
4.03 1.12 1.48E-04
SPAC56
E4.06c 0.91 4.17E-06
SPAC75
0.04c 2.08
4.04E-
07
SPBC16
83.01 1.12 5.83E-05
SPAC6F
6.04c 0.91 1.04E-06
SPBC35
9.02 2.08
3.34E-
09
SPBC3D
6.11c 1.11 4.91E-06
SPAC7D
4.08 0.90 5.57E-03
SPBC17
78.04 2.05
1.97E-
08
SPAC8C
9.10c 1.11 1.83E-03
SPAC29
A4.19c 0.90 1.19E-07
Table
A.1:
Continued
174

SPBPB8
B6.03 2.05
2.21E-
08
SPBC29
A10.02 1.11 1.05E-04
SPAC27
D7.13c 0.90 1.69E-05
SPBC2
G2.17c 2.02
8.36E-
06
SPAPB2
4D3.02c 1.11 9.64E-08
SPBC11
G11.05 0.90 1.36E-02
SPCC13
2.04c 2.01
3.61E-
06
SPBC29
A10.14 1.11 1.96E-05
SPAC32
3.04 0.89 3.46E-04
SPBC32
H8.11 1.93
3.06E-
06
SPBC13
E7.02 1.10 5.34E-06
SPCC89
5.06 0.89 1.85E-04
SPAPB1
A11.01 1.88
4.70E-
07
SPBC94
7.13 1.10 3.93E-05
SPCC55
0.10 0.89 2.11E-05
SPBC18
61.06c 1.87
1.43E-
06
SPAC6G
9.01c 1.10 1.00E-03
SPBC23
G7.11 0.88 1.16E-02
SPAC11
H11.04 1.86
1.93E-
02
SPBC13
47.03 1.09 1.06E-04
SPAC16.
04 0.88 3.77E-04
SPAC10
F6.15 1.85
3.86E-
08
SPAC11
D3.05 1.08 9.83E-03
SPAC5H
10.04 0.88 8.05E-03
SPAC56
F8.12 1.83
1.07E-
07
SPCC79
0.02 1.08 6.01E-08
SPAC3C
7.13c 0.88 2.24E-05
SPCC83
0.04c 1.77
3.11E-
06
SPBC35
9.04c 1.08 7.84E-04
SPBC65
1.01c 0.88 1.02E-03
SPBC31
F10.08 1.76
3.63E-
05
SPAC29
B12.12 1.08 4.98E-04
SPBC28
E12.02 0.88 4.93E-04
SPBC35
4.08c 1.75
5.80E-
06
SPCC28
5.09c 1.08 2.49E-04
SPAC11
E3.09 0.88 2.33E-04
SPBC21
C3.02c 1.73
3.75E-
08
SPAC92
2.07c 1.07 5.34E-04
SPAC4F
10.15c 0.87 6.93E-04
SPBC8E
4.02c 1.73
3.53E-
08
SPAC25
H1.09 1.07 9.45E-05
SPAC3C
7.04 0.87 3.33E-06
SPBC14
6.11c 1.70
3.31E-
08
SPBC35
9.01 1.07 2.11E-05
SPAC15
A10.10 0.87 2.20E-04
SPAC2
H10.01 1.68
3.07E-
02
SPCC18.
10 1.06 2.66E-07
SPAC17
A5.04c 0.87 6.79E-07
SPAC32
A11.01 1.65
6.28E-
04
SPCC2H
8.02 1.06 3.34E-06
SPBC16
52.01 0.87 5.24E-03
SPCC33
0.07c 1.62
4.64E-
08
SPBC16
85.12c 1.06 9.17E-03
SPBC26
H8.08c 0.87 5.46E-03
SPBC36
.01c 1.57
1.78E-
05
SPAC31
A2.12 1.06 4.71E-06
SPAC32
8.08c 0.87 3.86E-03
SPCC74
.02c 1.57
1.52E-
07
SPCC11
E10.01 1.06 8.56E-06
SPCC61
3.12c 0.87 1.77E-04
Table
A.1:
Continued
175

SPBC16
85.13 1.56
1.51E-
02
SPBC19
F5.02c 1.05 1.22E-04
SPBC17
11.07 0.86 6.60E-03
SPCC41
7.04 1.55
5.01E-
09
SPAC9E
9.12c 1.05 1.39E-06
SPBC55
7.02c 0.86 9.61E-06
SPBC18
61.01c 1.55
3.44E-
03
SPCC18
27.01c 1.05 3.92E-03
SPBC13
47.12 0.86 3.15E-05
SPAC97
7.17 1.54
8.49E-
06
SPCC29
0.02 1.04 2.94E-04
SPAC63
7.11 0.86 1.19E-04
SPBPB8
B6.04c 1.52
3.79E-
04
SPAC2E
1P3.04 1.04 1.08E-04
SPCC14
94.06c 0.86 2.63E-03
SPBC31
7.01 1.52
2.25E-
05
SPCC55
3.01c 1.03 5.72E-09
SPBC16
04.01 0.86 1.93E-05
SPAC11
42.05 1.51
8.79E-
07
SPCC14
50.07c 1.03 1.79E-04
SPAC14
C4.02c 0.85 5.06E-04
SPAPB1
A10.08 1.48
1.68E-
07
SPBC3D
6.03c 1.03 5.04E-04
SPAC3C
7.02c 0.85 1.09E-03
SPAPB1
8E9.03c 1.47
2.97E-
04
SPBPB2
1E7.10 1.03 4.48E-02
SPAC4G
9.10 0.85 7.81E-05
SPBC8
D2.19 1.44
9.74E-
07
SPAC4H
3.11c 1.03 9.08E-05
SPBC1D
7.05 0.85 4.24E-03
SPBCPT
2R1.02 1.42
3.18E-
05
SPBC30
B4.01c 1.03 1.35E-02
SPAC56
F8.14c 0.85 1.14E-02
SPBC94
7.04 1.41
2.62E-
03
SPAC11
D3.06 1.02 2.26E-07
SPBC17
D1.07c 0.85 6.63E-03
SPBC16
85.06 1.41
5.92E-
05
SPAC6C
3.02c 1.01 2.40E-03
SPBP35
G2.03c 0.85 1.32E-03
SPAC10
06.04c 1.38
1.28E-
05
SPCC16
2.04c 1.00 2.14E-04
SPBC10
6.08c 0.84 5.05E-04
SPAC4
G9.05 1.38
5.05E-
05
SPBC71
3.06 1.00 2.60E-04
SPAC14
0.02 0.84 1.05E-02
SPAC4F
10.09c 1.38
4.66E-
06
SPAC8E
11.03c 1.00 4.80E-03
SPBC30
B4.02c 0.84 2.75E-03
SPBC9B
6.03 1.37
4.59E-
04
SPBC2G
2.15c 1.00 1.26E-06
SPAC5H
10.07 0.84 1.37E-03
SPBC18
E5.10 1.37
1.93E-
06
SPBP8B
7.18c 1.00 5.53E-06
SPAC11
D3.03c 0.84 1.28E-02
SPAC14
4.09c 1.37
2.09E-
06
SPAC19
G12.01c 0.99 4.59E-08
SPAC3A
11.09 0.84 4.19E-05
SPBC21
5.13 1.36
3.67E-
08
SPAC22
F8.11 0.99 4.49E-07
SPCC41
7.03 0.84 2.59E-05
Table
A.1:
Continued
176

SPCC96
5.12 1.36
3.34E-
05
SPAC32
8.09 0.99 2.22E-03
SPBC11
98.12 0.84 6.15E-04
SPBPB2
B2.18 1.35
1.78E-
02
SPBC58
2.06c 0.99 2.09E-06
SPAC89
0.05 0.84 5.02E-03
SPCC57
6.17c 1.34
2.81E-
06
SPAC2E
1P5.05 0.99 7.15E-04
SPAC29
A4.10 0.83 2.39E-03
SPAC1F
8.04c 1.34
1.11E-
02
SPAC57
A7.06 0.99 1.28E-03
SPCC33
0.09 0.83 1.70E-04
SPACU
NK4.09 1.34
1.48E-
05
SPBC11
9.17 0.99 1.91E-04
SPBC21
H7.04 0.83 1.21E-03
SPCC96
5.11c 1.34
2.06E-
04
SPBC16
A3.17c 0.98 1.89E-03
SPAC18
B11.03c 0.83 1.41E-02
SPAPB2
4D3.07c 1.33
5.52E-
02
SPAC18
05.03c 0.98 7.31E-06
SPBC4F
6.07c 0.83 2.98E-04
SPCC96
5.14c 1.33
6.05E-
03
SPBP8B
7.04 0.98 8.34E-05
SPAC6G
10.06 0.83 3.45E-05
SPBC56
F2.03 1.32
6.49E-
07
SPAC15
27.03 0.97 1.48E-04
SPBC2G
2.01c 0.83 1.31E-03
SPBC13
48.01 1.32
3.43E-
02
SPAC10
02.16c 0.97 6.08E-04
SPBC53
0.07c 0.83 3.35E-05
SPCC19
19.14c 1.30
1.83E-
05
SPAC57
A10.04 0.97 1.50E-05
SPCC18.
05c 0.83 1.11E-04
SPAC4F
10.08 1.29
9.03E-
07
SPAC6G
9.12 0.96 2.57E-05
SPBP23
A10.11c 0.82 3.27E-05
SPCC75
7.11c 1.29
3.59E-
05
SPAC3G
6.04 0.96 1.22E-03
SPAC23
D3.01 0.82 2.51E-05
SPAC12
50.01 1.29
1.17E-
06
SPBC13
A2.04c 0.96 5.43E-02
SPCC10
20.05 0.82 3.69E-03
SPBC24
C6.02 1.28
7.38E-
05
SPAC3A
11.07 0.96 1.08E-02
SPBC3D
6.12 0.82 2.00E-04
SPCC10
20.09 1.28
4.64E-
03
SPBC2G
5.03 0.96 7.12E-03
SPBC6B
1.05c 0.82 5.12E-05
SPAC11
D3.01c 1.25
1.07E-
02
SPAC22
F8.09 0.96 2.89E-02
SPAC17
A2.12 0.82 2.45E-03
SPBC14
C8.01c 1.24
3.74E-
04
SPAC19
A8.07c 0.96 2.80E-03
SPCC32
0.08 0.81 1.71E-03
SPAPB1
8E9.04c 1.23
1.20E-
04
SPCC12
23.02 0.96 3.43E-04
SPAC26
A3.12c 0.81 1.09E-04
SPBC66
0.15 1.23
5.51E-
05
SPBC19
C7.03 0.95 7.54E-04
SPAC1B
3.15c 0.81 1.47E-03
Table
A.1:
Continued
177

SPCC66
3.14c 1.22
2.00E-
06
SPAC11
H11.03c 0.95 3.05E-04
SPBC11
9.14 0.81 1.08E-04
SPAC97
7.07c 1.21
4.27E-
05
SPBC21
D10.08c 0.95 2.84E-02
SPAC97
7.03 0.81 1.13E-03
SPAC9.
10 1.21
8.22E-
06
SPBC18
H10.09 0.95 5.73E-06
SPAC24
H6.13 0.81 5.39E-03
SPAC92
6.08c 1.21
2.07E-
03
SPCC18.
13 0.95 1.30E-03
SPCC16
C4.14c 0.81 6.87E-04
SPAC2
C4.06c 1.21
1.38E-
05
SPAC16
7.08 0.95 1.66E-03
SPBC19
C2.11c 0.81 1.36E-03
SPAC26
H5.06 1.21
2.04E-
07
SPBC12
C2.03c 0.94 1.30E-04
SPCP20
C8.02c 0.81 4.25E-02
SPCC33
0.03c 1.20
1.63E-
04
SPBC21
C3.10c 0.94 2.46E-02
SPBC17
D1.01 0.81 4.49E-04
SPAC1F
12.10c 1.20
5.05E-
02
SPBC28
F2.12 0.94 3.76E-04
SPAC3F
10.16c 0.80 4.48E-04
SPAC8
C9.11 1.20
1.49E-
04
SPCC96
2.02c 0.94 1.79E-04
SPBC21
B10.12 0.80 1.04E-05
SPAC19
52.15c 1.19
1.25E-
05
SPAC86
9.11 0.94 2.42E-04
SPCC62
2.19 0.80 4.22E-04
SPAC86
9.02c 1.19
3.86E-
03
SPAC15
27.01 0.93 3.77E-05
SPCC63.
06 0.80 5.30E-05
SPAC6
C3.05 1.19
3.90E-
05
SPBC29
A3.11c 0.93 7.67E-04
SPBC3F
6.04c 0.80 5.89E-03
SPBC83
.12 1.19
1.95E-
04
SPAC10
93.05 0.93 6.90E-04
SPAC13
99.02 0.80 1.70E-04

SPBC18
H10.07 0.93 6.75E-06
SPAPB2
4D3.03 0.80 1.18E-06

SPAC23
H3.11c 0.93 2.82E-04
SPBC17
73.08c 0.80 1.27E-05

∆gcn
5
∆mst
2
Gene
Log2
Chan
ge pvalue Gene
Log2
Chan
ge pvalue
SPAC51
3.03 4.73
8.99E-
03
SPBCPT
2R1.08c 2.69 1.20E-02
Table
A.1:
Continued
178

SPBC17
11.02 4.18
8.90E-
03
SPBC35
9.06 2.29 2.33E-02
SPBCPT
2R1.08c 3.89
7.73E-
04
SPAC3G
6.07 1.37 2.68E-02
SPAC1F
8.01 3.87
8.30E-
03
SPAC6B
12.03c 1.36 1.52E-02
SPBPJ4
664.03 3.40
3.66E-
03
SPBC32
F12.15 1.22 9.22E-03
SPBC35
9.06 3.20
2.79E-
03
SPAC15
65.04c 1.21 1.46E-03
SPAPB8
E5.05 3.04
2.62E-
03
SPBC27
B12.02 1.21 2.89E-02
SPCC17
39.08c 2.94
2.22E-
02
SPAC14
C4.08 1.19 6.86E-03
SPAC27
D7.03c 2.57
5.66E-
03
SPAC11
E3.06 1.16 2.62E-02
SPAC11
H11.04 2.45
3.38E-
03
SPCC16
2.10 1.14 2.51E-02
SPCC79
4.01c 2.34
3.09E-
02
SPCC19
06.04 1.13 8.22E-03
SPAC31
G5.09c 2.26
4.08E-
03
SPAC4H
3.03c 1.13 3.71E-02
SPCC18
8.12 2.05
4.71E-
03
SPAC16
7.06c 1.09 9.36E-03
SPBC23
G7.10c 1.80
4.08E-
02
SPBC40
9.03 1.06 1.26E-02
SPCC14
42.01 1.76
3.57E-
03
SPBC3E
7.02c 1.05 4.17E-02
SPAC11
E3.06 1.72
2.01E-
03
SPAC18
G6.13 1.03 9.99E-03
SPAC56
F8.15 1.71
2.55E-
02
SPBC31
F10.08 1.03 5.15E-03
SPCC16
2.10 1.65
2.36E-
03
SPBC17
73.12 1.03 2.04E-02
SPBC32
C12.02 1.63
5.27E-
03
SPBC40
5.05 1.01 8.87E-03
SPAC22
F3.12c 1.58
8.83E-
03
SPBC40
9.14c 0.96 5.74E-03
SPCC77
7.04 1.42
8.73E-
03
SPAC3H
1.03 0.96 4.27E-02
Table
A.1:
Continued
179

SPAC97
7.16c 1.36
3.70E-
04
SPAC3H
1.08c 0.95 1.02E-02
SPCC70
.04c 1.31
2.14E-
04
SPCP1E
11.07c 0.94 3.68E-02
SPCC19
06.04 1.29
3.25E-
03
SPCC62
2.06c 0.92 1.64E-02
SPAP11
E10.02c 1.26
3.91E-
03
SPBC11
05.16c 0.92 1.87E-02
SPAC23
E2.03c 1.25
3.36E-
02
SPCC14
42.11c 0.91 7.26E-03
SPAC20
H4.11c 1.19
3.84E-
03
SPAC22
F3.11c 0.90 3.14E-02
SPAPB1
A10.14 1.16
1.25E-
03
SPBC36
B7.06c 0.90 6.07E-03
SPCC10
20.01c 1.15
4.37E-
03
SPBC2A
9.12 0.89 4.95E-02
SPAC3
G9.11c 1.07
9.81E-
03
SPCC33
8.18 0.89 4.28E-02
SPCC33
8.18 1.02
2.22E-
02
SPCC62
2.03c 0.89 1.44E-02
SPBC25
B2.02c 1.02
1.38E-
02
SPAC4G
9.13c 0.87 3.34E-03
SPAC14
C4.01c 0.98
2.93E-
03
SPBC30
D10.04 0.87 8.41E-03
SPACU
NK4.10 0.95
1.37E-
02
SPAC13
C5.03 0.87 4.43E-04
SPAC15
65.04c 0.92
1.07E-
02
SPAC15
F9.01c 0.86 2.80E-03
SPBC21
C3.10c 0.92
2.80E-
02
SPCC77
7.11 0.86 2.38E-02
SPAC1F
8.05 0.88
2.57E-
02
SPAC12
B10.06c 0.85 1.76E-02
SPBC19
C2.05 0.87
4.88E-
02
SPAPB1
A10.14 0.85 1.20E-02
SPAC26
H5.09c 0.86
3.31E-
02
SPBC88
7.16 0.84 2.97E-02
SPCC15
29.01 0.84
3.97E-
02
SPBC21
B10.13c 0.84 1.55E-02
SPAC19
52.04c 0.81
4.07E-
02
SPCC83
0.04c 0.82 6.52E-03
Table
A.1:
Continued
180

SPAC13
C5.03 0.81
9.05E-
04
SPAC15
A10.12c 0.81 1.99E-02

SPAPB2
4D3.04c 0.80 1.38E-03

∆gcn5 ∆elp3 ∆gcn5 ∆mst2 ∆mst2 ∆elp3
Gene
Log2
Chang
e
pvalu
e Gene
Log2
Change pvalue Gene
Log2
Change pvalue
SPBCPT
2R1.08c 4.68
3.86
E-04
SPBCPT
2R1.08c 6.70
1.71E-
06
SPAC97
7.16c 4.40 3.91E-11
SPAC97
7.05c 4.56
1.72
E-06
SPCC17
95.06 6.36
9.50E-
17
SPCC33
0.05c 4.25 1.65E-02
SPAC97
7.16c 3.64
4.94
E-09
SPAC1F
8.01 6.19
1.63E-
04
SPBCPT
2R1.08c 2.92 7.13E-03
SPBC35
9.02 3.05
4.16
E-11
SPAC31
G5.09c 4.76
1.85E-
06
SPCC13
93.10 2.88 2.52E-09
SPBPB8
B6.04c 2.81
1.09
E-06
SPBC35
9.06 4.72
7.39E-
05
SPAC97
7.15 2.79 9.58E-03
SPBPB8
B6.02c 2.78
2.18
E-13
SPCC17
39.08c 4.27
1.92E-
03
SPBC35
4.08c 2.71 1.31E-08
SPAC2E
1P3.02c 2.76
5.64
E-09
SPBC4.0
1 4.20
1.88E-
08
SPAC2E
1P3.02c 2.32 1.45E-08
SPCC18
8.12 2.74
1.17
E-03
SPAC22
F3.12c 4.08
5.34E-
07
SPBC18
61.06c 2.19 1.62E-07
SPAC19
52.04c 2.66
4.36
E-06
SPCC79
4.01c 4.08
6.89E-
04
SPBC35
9.02 2.16 1.83E-09
SPAC10
06.04c 2.62
8.20
E-09
SPAC27
D7.03c 4.01
1.14E-
04
SPCC73
7.04 2.15 3.53E-04
SPAC24
C9.15c 2.58
4.26
E-05
SPCC16
2.10 3.93
1.21E-
07
SPAPB2
4D3.07c 2.07 4.94E-03
SPCC77
7.04 2.48
2.27
E-04
SPCC18
8.12 3.84
1.08E-
05
SPBC17
78.04 2.03 2.28E-08
SPBC17
78.04 2.46
6.92
E-09
SPAC1F
5.09c 3.80
2.81E-
11
SPBC2G
2.17c 2.02 8.49E-06
SPBPB8
B6.03 2.35
1.43
E-08
SPAC3G
9.11c 3.74
8.98E-
09
SPBC31
F10.08 2.00 7.89E-06
SPAC75
2.35
3.46

SPBC56
3.68
2.97E-

SPAC56
1.98 3.35E-08
Table
A.1:
Continued
181

0.04c E-07 F2.06 06 F8.12
SPBC31
F10.08 2.27
6.61
E-06
SPBC11
98.14c 3.67
5.79E-
13
SPAPB1
A11.01 1.97 2.41E-07
SPAC75
0.07c 2.27
6.97
E-05
SPAPB2
4D3.10c 3.59
1.78E-
03
SPAC6C
3.03c 1.92 1.73E-06
SPCC13
93.10 2.20
6.91
E-07
SPCC14
42.01 3.56
2.49E-
06
SPAC11
42.05 1.87 4.14E-08
SPBC14
6.11c 2.20
3.50
E-09
SPCC33
0.05c 3.53
4.12E-
02
SPCC13
2.04c 1.86 9.18E-06
SPAC18
6.01 2.18
1.12
E-06
SPCC54
8.07c 3.38
1.44E-
02
SPCC83
0.04c 1.85 1.78E-06
SPAC97
7.07c 2.16
1.03
E-07
SPBC32
C12.02 3.19
7.81E-
06
SPBC14
6.11c 1.84 9.60E-09
SPAC11
H11.04 2.15
1.63
E-02
SPAC11
E3.06 3.11
4.16E-
06
SPAC11
H11.04 1.83 2.09E-02
SPBC35
4.08c 2.03
3.56
E-06
SPCC73
7.04 2.99
8.94E-
06
SPCC33
0.03c 1.81 1.20E-06
SPBC13
48.01 2.02
5.55
E-03
SPAC23
E2.03c 2.99
3.26E-
05
SPAC32
A11.01 1.81 2.58E-04
SPBC32
H8.11 2.00
7.97
E-06
SPCC19
06.04 2.90
5.26E-
07
SPAC18
B11.03c 1.79 1.44E-05
SPCC83
0.04c 1.91
4.97
E-06
SPAC6B
12.03c 2.86
2.44E-
05
SPAC4G
9.05 1.78 2.15E-06
SPAC4
G9.05 1.89
4.35
E-06
SPBC19
C2.05 2.79
2.48E-
06
SPAC10
F6.15 1.78 6.86E-08
SPCC10
20.01c 1.86
1.69
E-04
SPAC20
H4.11c 2.70
5.84E-
07
SPAC97
7.17 1.76 1.58E-06
SPCC74
.02c 1.86
6.50
E-08
SPAC3F
10.10c 2.65
5.28E-
12
SPCPB1
C11.02 1.71 2.25E-05
SPBC18
61.06c 1.85
6.74
E-06
SPAC1F
8.08 2.65
6.91E-
08
SPBC18
61.01c 1.71 1.59E-03
SPCC10
20.09 1.85
5.86
E-04
SPBC21
D10.06c 2.64
1.15E-
12
SPAPB1
A10.08 1.70 2.16E-08
SPAC57
A7.05 1.79
2.17
E-03
SPCC33
8.18 2.63
4.83E-
06
SPBC21
C3.02c 1.69 5.34E-08
SPAC4F
10.08 1.76
5.76
E-08
SPBC16
83.08 2.63
6.85E-
04
SPCC66
3.06c 1.67 2.19E-02
SPCC12
23.02 1.74
1.11
E-06
SPBPB2
B2.12c 2.63
2.11E-
02
SPCC41
7.04 1.66 1.68E-09
Table
A.1:
Continued
182

SPBC13
47.03 1.70
1.87
E-06
SPAC4H
3.03c 2.57
7.41E-
05
SPBC8E
4.02c 1.66 6.10E-08
SPAC8E
11.03c 1.70
1.17
E-04
SPAC97
7.16c 2.56
1.74E-
07
SPAC86
9.02c 1.66 2.21E-04
SPBC21
C3.02c 1.65
3.77
E-07
SPCC79
4.04c 2.42
8.62E-
04
SPAC11
D3.05 1.64 3.58E-04
SPBC18
E5.10 1.64
7.52
E-07
SPBC14
6.02 2.33
5.56E-
08
SPBC8D
2.19 1.64 1.62E-07
SPCC16
2.04c 1.64
2.53
E-06
SPACU
NK4.17 2.32
3.65E-
05
SPAC18
6.06 1.62 5.18E-03
SPBC2
G2.17c 1.62
3.31
E-04
SPCC70.
04c 2.32
1.90E-
07
SPAC24
C9.15c 1.62 1.40E-03
SPCC77
7.03c 1.61
1.49
E-04
SPAC13
F5.03c 2.24
2.84E-
05
SPBC19
C7.04c 1.60 9.14E-03
SPCC19
19.14c 1.61
5.39
E-06
SPAC13
C5.03 2.23
2.19E-
09
SPCC74.
02c 1.57 1.47E-07
SPBC36
.01c 1.60
5.09
E-05
SPAC14
C4.01c 2.19
4.47E-
07
SPAC34
3.07 1.56 1.31E-06
SPBC8E
4.02c 1.60
5.36
E-07
SPCC77
7.04 2.19
2.67E-
04
SPBC36.
01c 1.53 2.38E-05
SPAC97
7.06 1.58
1.23
E-08
SPBC12
89.16c 2.18
1.83E-
04
SPAC25
H1.09 1.52 1.38E-06
SPAC5
H10.04 1.58
1.55
E-04
SPAC1F
8.05 2.18
1.15E-
05
SPAC6C
3.05 1.49 2.55E-06
SPAC5
H10.07 1.56
6.58
E-06
SPBC72
5.10 2.12
6.57E-
04
SPAC15
A10.10 1.48 3.51E-07
SPBC23
G7.11 1.54
3.44
E-04
SPCC13
93.12 2.09
1.29E-
09
SPBC32
H8.11 1.47 8.25E-05
SPCC41
7.04 1.54
3.12
E-08
SPCC12
23.12c 2.09
3.59E-
07
SPBC9B
6.03 1.46 2.51E-04
SPAC34
3.07 1.54
6.73
E-06
SPAC31
G5.07 2.07
6.02E-
09
SPAC5H
10.04 1.46 1.08E-04
SPAC56
F8.14c 1.53
2.57
E-04
SPCP31
B10.06 2.06
1.01E-
06
SPCC33
0.07c 1.44 2.45E-07
SPCC13
2.04c 1.52
2.99
E-04
SPAC5H
10.01 2.06
2.73E-
02
SPCC58
4.02 1.44 2.33E-06
SPBC31
7.01 1.52
7.96
E-05
SPBC16
E9.16c 2.04
3.18E-
08
SPAC4F
10.08 1.44 2.05E-07
SPAC1F
12.10c 1.52
2.89
E-02
SPAC15
65.04c 1.97
9.48E-
06
SPACU
NK4.09 1.43 6.27E-06
Table
A.1:
Continued
183

SPBC58
2.06c 1.52
2.40
E-08
SPAC22
F8.05 1.82
2.21E-
03
SPAC57
A7.05 1.43 5.01E-03
SPAC27
D7.13c 1.50
7.42
E-08
SPAC16
7.06c 1.80
1.42E-
04
SPBC8E
4.03 1.41 1.07E-05
SPBC27
.03 1.50
5.24
E-07
SPAC56
F8.15 1.78
2.08E-
02
SPAC4F
10.09c 1.39 4.10E-06
SPAPB1
A11.03 1.49
8.74
E-07
SPAC29
A4.12c 1.77
1.12E-
04
SPAPB1
8E9.03c 1.39 5.16E-04
SPBC21
5.13 1.49
5.37
E-08
SPCC56
9.03 1.74
1.64E-
05
SPBC66
0.15 1.38 1.40E-05
SPCC14
50.08c 1.48
1.35
E-04
SPBC19
C7.04c 1.69
6.22E-
03
SPAC11
D3.01c 1.37 5.96E-03
SPAC4F
10.09c 1.47
8.06
E-06
SPAC4H
3.04c 1.66
4.45E-
05
SPAC14
4.09c 1.37 2.09E-06
SPAC1
A6.11 1.47
7.89
E-07
SPAC16
10.03c 1.66
1.23E-
07
SPBC18
E5.10 1.36 2.03E-06
SPBC3
D6.11c 1.46
5.95
E-07
SPBC24
C6.06 1.65
2.64E-
06
SPAC19
52.15c 1.32 3.49E-06
SPAC31
G5.10 1.46
4.44
E-05
SPAC19
52.04c 1.65
2.86E-
04
SPAC10
06.04c 1.32 2.26E-05
SPBPB2
B2.18 1.44
2.34
E-02
SPCC14
50.08c 1.61
1.48E-
05
SPBC6B
1.03c 1.31 3.08E-06
SPBPB2
B2.07c 1.43
4.35
E-07
SPCC75
7.03c 1.60
2.25E-
05
SPAC3H
1.06c 1.30 2.41E-02
SPAC3
H1.06c 1.42
2.71
E-02
SPBC19
C2.04c 1.60
2.07E-
05
SPAC14
C4.01c 1.30 2.38E-04
SPBC72
5.10 1.42
2.39
E-02
SPBPB2
B2.13 1.58
4.84E-
02
SPCC19
19.14c 1.29 2.07E-05
SPBC53
0.11c 1.41
1.76
E-04
SPBC17
11.11 1.56
4.60E-
07
SPBC16
85.13 1.29 4.03E-02
SPBC56
F2.03 1.40
1.29
E-06
SPBC13
A2.04c 1.54
3.92E-
03
SPCC75
7.11c 1.28 3.98E-05
SPAC25
H1.09 1.40
1.70
E-05
SPBC11
C11.06c 1.54
7.57E-
03
SPAC6G
9.12 1.27 7.86E-07
SPBC16
85.13 1.39
4.63
E-02
SPAC30
D11.02c 1.52
5.32E-
04
SPBC13
47.03 1.25 2.23E-05
SPBC66
0.15 1.39
4.73
E-05
SPBC72
5.03 1.52
1.37E-
03
SPBC21
D10.08c 1.24 6.16E-03
SPAC18
05.03c 1.37
3.64
E-07
SPAC13
G7.02c 1.51
1.89E-
02
SPBC60
9.04 1.23 1.35E-02
Table
A.1:
Continued
184

SPBC14
C8.05c 1.37
4.13
E-07
SPCC28
5.07c 1.50
2.25E-
05
SPCC10
20.09 1.23 6.34E-03
SPBC29
A10.02 1.36
3.82
E-05
SPBC13
47.03 1.49
2.50E-
06
SPBC14
C8.01c 1.22 4.12E-04
SPAC2
C4.06c 1.36
1.29
E-05
SPBC16
85.06 1.48
3.30E-
05
SPBP8B
7.18c 1.22 3.70E-07
SPCC16
2.02c 1.35
1.72
E-07
SPCC77
7.03c 1.47
1.17E-
04
SPAPB1
8E9.04c 1.21 1.46E-04
SPBC1
D7.05 1.34
2.29
E-04
SPAC2F
7.06c 1.47
1.41E-
03
SPCC56
9.07 1.20 2.90E-04
SPBC6B
1.03c 1.33
1.00
E-05
SPBC16
85.05 1.45
5.80E-
07
SPAC22
F8.11 1.20 2.99E-08
SPBC13
48.09 1.33
5.45
E-08
SPCC12
23.02 1.45
2.97E-
06
SPCC41
7.06c 1.20 4.80E-05
SPAC16
E8.05c 1.33
1.32
E-05
SPAC17
51.01c 1.45
4.96E-
03
SPBC16
85.06 1.19 3.25E-04
SPBC21
B10.12 1.32
5.47
E-08
SPAC63
7.03 1.44
2.98E-
03
SPBC3D
6.11c 1.19 2.01E-06
SPCC12
59.14c 1.32
2.23
E-06
SPCC57
6.01c 1.42
1.24E-
04
SPAC2E
1P3.04 1.16 2.98E-05
SPBC16
85.06 1.32
3.69
E-04
SPCC79
4.02 1.42
3.45E-
05
SPAC8C
9.11 1.16 1.99E-04
SPBC18
H10.09 1.32
3.29
E-07
SPCC4G
3.03 1.42
8.82E-
06
SPCC18.
10 1.16 7.43E-08
SPCC13
B11.03c 1.32
7.25
E-08
SPCC97
0.11c 1.41
7.07E-
05
SPAC2C
4.06c 1.16 2.31E-05
SPAC22
F3.03c 1.31
4.83
E-03
SPAC1A
6.06c 1.41
1.42E-
05
SPAC15
F9.01c 1.16 1.96E-04
SPBC8
D2.19 1.29
1.71
E-05
SPAC32
A11.01 1.40
2.47E-
03
SPAC92
6.08c 1.15 3.02E-03
SPCC56
9.04 1.28
9.07
E-08
SPCC17
39.15 1.40
1.46E-
06
SPAC4H
3.11c 1.15 2.56E-05
SPAC26
A3.03c 1.28
3.43
E-08
SPAC4G
9.07 1.40
3.48E-
05
SPBC13
E7.02 1.15 3.21E-06
SPAC9.
10 1.28
1.64
E-05
SPCC11
83.10 1.39
1.37E-
08
SPCC16
2.02c 1.13 4.56E-07
SPAC22
F3.02 1.28
1.00
E-06
SPAC29
A4.17c 1.39
4.24E-
04
SPAPB2
4D3.02c 1.11 9.51E-08
SPBC12
89.16c 1.27
2.50
E-02
SPAP11
E10.02c 1.38
1.95E-
03
SPCC55
3.01c 1.09 2.44E-09
Table
A.1:
Continued
185

SPAC97
7.17 1.26
2.89
E-04
SPCP20
C8.02c 1.38
1.34E-
05
SPBC3D
6.03c 1.09 2.95E-04
SPBC36
.02c 1.26
2.55
E-02
SPAC4D
7.02c 1.38
9.19E-
05
SPCC96
2.02c 1.06 4.54E-05
SPBC16
85.14c 1.25
5.32
E-04
SPBC18
H10.05 1.37
7.18E-
06
SPBC56
F2.03 1.06 1.05E-05
SPAC19
52.15c 1.25
2.78
E-05
SPCC10
20.01c 1.37
1.08E-
03
SPCC16
72.03c 1.06 2.11E-04
SPBC13
A2.04c 1.25
2.77
E-02
SPBP19
A11.07c 1.37
5.09E-
08
SPCC28
5.09c 1.05 3.17E-04
SPCC58
4.16c 1.25
1.62
E-02
SPACU
NK4.10 1.35
1.16E-
03
SPBC21
5.13 1.05 1.47E-06
SPBC18
H10.07 1.24
6.45
E-07
SPAPB1
5E9.02c 1.34
2.13E-
05
SPAC12
50.01 1.05 1.73E-05
SPCC4B
3.10c 1.23
1.41
E-03
SPBC13
47.01c 1.33
2.83E-
04
SPAC18
G6.09c 1.04 1.62E-02
SPAC10
06.03c 1.23
1.70
E-06
SPAP7G
5.03 1.33
1.25E-
07
SPCC2H
8.02 1.04 4.18E-06
SPBC19
G7.13 1.22
3.39
E-06
SPCC10
20.05 1.33
4.17E-
05
SPCC75
7.02c 1.04 1.52E-04
SPAC11
H11.03c 1.22
7.70
E-05
SPBC8E
4.05c 1.32
4.73E-
06
SPAC3C
7.04 1.03 3.40E-07
SPAC19
G12.01c 1.21
1.23
E-08
SPCC29
0.04 1.32
5.40E-
04
SPAC63
7.11 1.03 1.51E-05
SPAC26
H5.06 1.21
9.36
E-07
SPAPB1
8E9.04c 1.32
5.58E-
05
SPBC94
7.13 1.02 8.86E-05
SPCC28
5.09c 1.21
2.43
E-04
SPCPB1
C11.02 1.31
4.02E-
04
SPAC6C
3.02c 1.02 2.14E-03
SPAC29
B12.12 1.20
5.02
E-04
SPCC74.
09 1.31
1.88E-
02
SPCC70.
08c 1.02 1.98E-03
SPAC10
F6.15 1.20
5.11
E-05
SPMIT.0
6 1.31
1.09E-
02
SPAC17
A5.13 1.01 5.36E-05
SPAC1F
8.04c 1.20
3.59
E-02
SPBC21
D10.08c 1.31
4.37E-
03
SPBC3H
7.06c 1.00 4.55E-03
SPAC6
C3.07 1.20
1.91
E-05
SPAC10
06.04c 1.30
2.55E-
05
SPAC9.1
0 1.00 7.44E-05
SPAC6
G9.01c 1.19
1.32
E-03
SPAC27
D7.11c 1.29
3.52E-
03
SPBC19
C2.11c 1.00 1.86E-04
SPCC96
2.02c 1.18
4.84
E-05
SPAC16
E8.03 1.29
5.33E-
05
SPCC12
23.02 1.00 2.21E-04
Table
A.1:
Continued
186

SPCC57
6.17c 1.18
5.14
E-05
SPAPB1
A10.14 1.28
5.07E-
04
SPBC24
C6.02 1.00 8.98E-04
SPACU
NK4.09 1.17
2.26
E-04
SPAC68
8.03c 1.28
1.65E-
05
SPCC10
20.05 1.00 7.73E-04
SPAPB8
E5.10 1.17
2.57
E-04
SPAC8E
11.03c 1.28
6.46E-
04
SPAP7G
5.03 0.99 6.36E-06
SPBC9B
6.03 1.16
4.65
E-03
SPAC19
B12.08 1.27
1.47E-
03
SPBC17
D1.01 0.99 5.20E-05
SPAC56
F8.13 1.16
1.37
E-06
SPBC36
5.12c 1.25
2.02E-
03
SPBPB8
B6.03 0.99 2.31E-04
SPAC32
A11.01 1.16
1.83
E-02
SPCC70.
02c 1.25
2.42E-
05
SPBC16
83.01 0.99 2.14E-04
SPAC92
6.08c 1.15
6.76
E-03
SPBC14
C8.05c 1.25
3.12E-
07
SPAC22
F3.02 0.99 6.54E-06
SPCC33
0.07c 1.15
2.16
E-05
SPAC1F
7.05 1.25
1.60E-
03
SPAC18
05.03c 0.99 6.68E-06
SPBC21
D10.08c 1.14
2.01
E-02
SPBC36.
02c 1.25
1.46E-
02
SPBP8B
7.04 0.99 7.41E-05
SPAC11
D3.06 1.14
2.30
E-07
SPCC12
6.07c 1.24
2.16E-
08
SPAC26
H5.06 0.98 3.34E-06
SPBC18
H10.21c 1.13
2.83
E-05
SPAC15
65.03 1.24
4.38E-
04
SPCC14
50.07c 0.98 2.82E-04
SPAC1
A6.08c 1.13
1.51
E-02
SPCPB1
6A4.06c 1.23
6.25E-
04
SPBC28
E12.02 0.98 1.64E-04
SPACU
NK4.10 1.13
9.83
E-03
SPMIT.0
2 1.23
6.56E-
03
SPCC18
27.01c 0.98 6.16E-03
SPCC18
8.09c 1.12
4.54
E-07
SPBC66
0.07 1.23
5.63E-
04
SPAC92
2.07c 0.98 1.24E-03
SPBC14
C8.01c 1.11
2.58
E-03
SPAC15
F9.01c 1.22
1.13E-
04
SPBP35
G2.13c 0.97 1.89E-03
SPBC16
52.01 1.11
2.03
E-03
SPCC13
93.07c 1.21
3.70E-
06
SPAC19
G12.01c 0.97 7.03E-08
SPAC57
A7.06 1.10
1.28
E-03
SPAC15
A10.03c 1.21
3.37E-
05
SPCC66
3.14c 0.96 3.78E-05
SPBC3
D6.03c 1.10
7.60
E-04
SPAC26
H5.09c 1.21
4.35E-
03
SPBC16
85.14c 0.96 1.95E-03
SPBC17
D1.07c 1.10
2.25
E-03
SPAC2C
4.17c 1.21
1.81E-
05
SPCC11
E10.01 0.96 2.68E-05
SPAC23
D3.01 1.10
2.79
E-06
SPBC12
71.01c 1.21
1.05E-
07
SPAC26
H5.08c 0.96 8.91E-04
Table
A.1:
Continued
187

SPBC68
5.03 1.10
9.65
E-07
SPBC2G
2.17c 1.21
1.71E-
03
SPCC79
0.02 0.96 3.31E-07
SPBCPT
2R1.02 1.10
1.32
E-03
SPAC17
H9.19c 1.21
4.66E-
03
SPBC3B
8.09 0.96 2.52E-03
SPAC22
F8.09 1.10
2.55
E-02
SPBC16
85.14c 1.20
2.63E-
04
SPBC58
2.06c 0.96 3.28E-06
SPCC19
06.04 1.09
1.98
E-02
SPBC13
47.11 1.20
4.08E-
03
SPBC16
A3.17c 0.96 2.32E-03
SPAC21
2.08c 1.09
9.05
E-07
SPAC11
D3.14c 1.20
2.97E-
02
SPBC31
7.01 0.96 2.23E-03
SPBC23
E6.09 1.09
7.17
E-03
SPAC32
A11.02c 1.19
1.75E-
04
SPAC9E
9.12c 0.95 4.72E-06
SPAC63
7.11 1.08
3.21
E-05
SPBC11
9.07 1.19
1.53E-
04
SPAC29
A4.19c 0.95 5.06E-08
SPAC31
A2.12 1.08
1.40
E-05
SPBC15
D4.02 1.19
1.21E-
03
SPAC57
A10.04 0.95 1.93E-05
SPCC18
.10 1.08
1.03
E-06
SPBC35
4.12 1.18
7.69E-
05
SPBC16
E9.10c 0.95 5.32E-04
SPBC21
6.02 1.07
1.43
E-04
SPAC4A
8.04 1.18
1.01E-
03
SPBC35
9.01 0.95 8.06E-05
SPAPB1
E7.01c 1.07
5.66
E-04
SPAC10
02.12c 1.18
5.46E-
05
SPBC11
9.17 0.94 2.96E-04
SPBC16
E9.10c 1.07
4.80
E-04
SPAC4F
10.16c 1.18
2.55E-
05
SPBC18
H10.09 0.94 6.33E-06
SPAC6
C3.05 1.07
3.87
E-04
SPAC25
G10.04c 1.18
1.96E-
04
SPAC32
8.09 0.94 3.27E-03
SPAC4
H3.11c 1.07
1.91
E-04
SPBC14
C8.11c 1.15
3.09E-
04
SPAC12
50.02 0.94 4.92E-04
SPCC31
H12.02c 1.07
2.16
E-05
SPAC29
B12.12 1.15
2.67E-
04
SPCC18.
13 0.93 1.50E-03
SPCC11
E10.09c 1.06
6.81
E-06
SPAC9.1
0 1.14
1.67E-
05
SPAC4G
9.10 0.93 2.85E-05
SPCC29
0.02 1.06
6.79
E-04
SPAC5H
10.07 1.13
7.77E-
05
SPCC96
5.11c 0.93 4.57E-03
SPBC17
D1.01 1.06
8.69
E-05
SPAC2E
1P3.02c 1.13
1.67E-
04
SPAC21
E11.04 0.93 3.43E-04
SPBC28
E12.02 1.06
2.41
E-04
SPAC17
A5.04c 1.13
1.67E-
08
SPAC15
27.03 0.93 2.37E-04
SPAC57
A10.04 1.05
2.14
E-05
SPAC18
05.15c 1.12
4.53E-
05
SPAC56
E4.06c 0.92 3.24E-06
Table
A.1:
Continued
188

SPAC12
50.01 1.05
5.80
E-05
SPAP8A
3.04c 1.12
3.58E-
02
SPAC14
C4.02c 0.92 2.57E-04
SPAC15
27.03 1.05
2.09
E-04
SPMIT.0
5 1.11
4.20E-
02
SPAC57
A7.06 0.91 2.39E-03
SPAC1F
8.06 1.05
6.62
E-03
SPAC1F
7.06 1.11
5.51E-
07
SPAC29
A4.10 0.91 1.13E-03
SPCC33
0.09 1.05
4.29
E-05
SPBC32
F12.09 1.09
3.21E-
05
SPBC27.
03 0.91 6.32E-05
SPBC29
A3.14c 1.05
3.35
E-07
SPAC16
E8.02 1.09
2.42E-
04
SPAC32
3.04 0.91 2.86E-04
SPAC1
B3.15c 1.05
4.06
E-04
SPCC56
9.02c 1.09
2.26E-
05
SPAC27
D7.13c 0.91 1.39E-05
SPCC18
27.01c 1.05
8.20
E-03
SPBC14
C8.07c 1.08
1.46E-
03
SPAC8C
9.10c 0.91 7.80E-03
SPCC18
.05c 1.05
2.63
E-05
SPCC30
6.08c 1.08
9.75E-
04
SPBC19
G7.06 0.91 5.88E-06
SPAC27
D7.05c 1.05
2.84
E-03
SPBC36
B7.06c 1.08
1.61E-
03
SPAC31
A2.12 0.91 3.11E-05
SPBC24
C6.02 1.05
1.52
E-03
SPBC21
C3.10c 1.07
1.17E-
02
SPBC19
C7.03 0.91 1.21E-03
SPAC22
H10.10 1.05
1.91
E-05
SPBC94
7.15c 1.07
1.15E-
03
SPCC13
B11.04c 0.90 7.51E-04
SPBC94
7.13 1.05
2.26
E-04
SPBC14
C8.01c 1.07
1.43E-
03
SPAC23
D3.01 0.90 8.16E-06
SPBC6B
1.05c 1.04
1.08
E-05
SPAC22
F3.03c 1.06
9.08E-
03
SPBC16
04.01 0.90 1.04E-05
SPBC11
9.14 1.04
2.29
E-05
SPBC1D
7.05 1.06
7.39E-
04
SPBC26
H8.08c 0.90 4.23E-03
SPBC21
C3.10c 1.04
2.55
E-02
SPAC10
06.01 1.05
1.71E-
05
SPAC92
2.03 0.90 4.12E-06
SPAC12
D12.09 1.04
1.44
E-05
SPBC24
C6.09c 1.05
5.72E-
04
SPAC6G
9.01c 0.90 5.00E-03
SPCC24
B10.14c 1.04
7.59
E-05
SPBC1A
4.01 1.05
4.79E-
04
SPCC57
6.17c 0.89 3.00E-04
SPCC12
6.02c 1.04
4.35
E-05
SPAC26
F1.04c 1.05
1.33E-
04
SPCC13
22.03 0.89 4.63E-03
SPAC8F
11.05c 1.03
7.83
E-04
SPAC17
A2.07c 1.05
2.17E-
05
SPCC12
81.07c 0.89 1.32E-02
SPAC25
B8.06c 1.03
9.70
E-05
SPAC26
H5.04 1.04
3.82E-
06
SPCC61
3.12c 0.89 1.30E-04
Table
A.1:
Continued
189

SPCC10
20.05 1.03
1.54
E-03
SPCC19
1.01 1.04
3.16E-
03
SPAC6B
12.08 0.89 2.84E-04
SPBC17
03.04 1.03
3.15
E-08
SPBP23
A10.04 1.04
7.76E-
07
SPBC65
1.01c 0.89 9.17E-04
SPAC3
A11.07 1.02
1.42
E-02
SPAC51
3.02 1.03
3.47E-
03
SPAC4A
8.07c 0.89 2.87E-04
SPAC1F
8.02c 1.02
4.31
E-03
SPCPJ73
2.02c 1.03
2.86E-
05
SPAC7D
4.08 0.89 6.16E-03
SPCC58
4.02 1.02
4.23
E-04
SPAC3A
11.07 1.03
6.82E-
03
SPBC19
F5.02c 0.89 6.72E-04
SPBC65
1.01c 1.02
7.35
E-04
SPAC23
C11.06c 1.03
9.35E-
03
SPBC35
4.09c 0.88 9.76E-07
SPBC3F
6.04c 1.02
2.21
E-03
SPBC27
B12.01c 1.02
1.84E-
03
SPBC16
85.12c 0.88 2.53E-02
SPBC29
A10.14 1.02
1.71
E-04
SPBC3D
6.03c 1.01
5.93E-
04
SPCC29
0.02 0.88 1.31E-03
SPBC16
D10.07c 1.01
7.85
E-08
SPCC33
0.04c 1.01
1.22E-
05
SPAC10
93.05 0.88 1.13E-03
SPBC3
D6.10 1.01
9.35
E-04
SPAC26
F1.14c 1.01
9.34E-
03
SPAC10
06.03c 0.88 2.78E-05
SPAC22
G7.11c 1.01
1.86
E-03
SPBC33
6.12c 1.01
8.55E-
07
SPAC2E
1P5.05 0.87 2.06E-03
SPCC29
7.06c 1.01
6.67
E-03
SPAC18
05.09c 1.01
5.47E-
04
SPBC53
0.07c 0.87 1.81E-05
SPAC30
D11.07 1.00
7.39
E-05
SPAC4G
8.04 1.00
1.11E-
06
SPBC17
11.07 0.87 6.41E-03
SPAC27
D7.11c 1.00
3.16
E-02
SPCC33
8.08 1.00
1.28E-
04
SPCC73
7.03c 0.87 1.40E-04
SPAC89
0.05 1.00
3.10
E-03
SPCC28
5.16c 1.00
5.57E-
07
SPBC17
03.08c 0.87 2.74E-02
SPBC33
6.05c 1.00
2.80
E-02
SPBC19
C2.09 1.00
2.43E-
02
SPAPJ76
0.03c 0.86 6.24E-03
SPBC3
H7.06c 0.99
1.00
E-02
SPBC80
0.14c 0.99
8.10E-
04
SPCC41
7.03 0.86 1.81E-05
SPAC26
A3.12c 0.99
4.17
E-05
SPCC16
2.04c 0.99
2.34E-
04
SPBP8B
7.30c 0.86 1.80E-05
SPBC25
H2.08c 0.99
8.82
E-04
SPAC3A
11.06 0.99
8.27E-
04
SPAC24
H6.13 0.85 3.80E-03
SPCC23
B6.03c 0.99
1.85
E-04
SPAC22
G7.11c 0.99
8.41E-
04
SPBC94
7.04 0.85 4.95E-02
Table
A.1:
Continued
190

SPBC13
E7.02 0.98
7.76
E-05
SPBC25
H2.08c 0.99
3.31E-
04
SPAC3G
6.04 0.85 3.25E-03
SPAC17
A5.04c 0.98
6.53
E-07
SPAC3A
11.10c 0.99
2.36E-
03
SPCC10
20.13c 0.85 3.53E-04
SPCC14
50.09c 0.98
6.63
E-05
SPBC19
C7.03 0.98
5.76E-
04
SPBC12
71.07c 0.85 2.62E-04
SPBC17
18.02 0.97
1.14
E-03
SPAC31
G5.19 0.98
2.16E-
04
SPCC12
59.14c 0.85 1.16E-04
SPAC17
A5.11 0.96
9.07
E-04
SPAC13
F5.07c 0.98
1.21E-
02
SPBC90
2.06 0.85 3.79E-04
SPCC16
C4.05 0.96
3.24
E-03
SPAC13
99.01c 0.98
1.43E-
04
SPBC6B
1.05c 0.85 3.50E-05
SPAC4
H3.05 0.95
4.22
E-06
SPBC65
1.05c 0.98
1.87E-
04
SPAC22
F8.09 0.85 5.01E-02
SPCC61
3.12c 0.95
2.03
E-04
SPBC18
A7.01 0.97
5.17E-
04
SPBC11
98.12 0.84 5.63E-04
SPAC16
.04 0.95
5.06
E-04
SPAC24
C9.07c 0.97
2.49E-
04
SPCC14
94.06c 0.84 2.97E-03
SPBC11
9.17 0.95
7.86
E-04
SPBC16
83.01 0.97
2.71E-
04
SPAC29
B12.12 0.84 3.97E-03
SPCC14
94.06c 0.95
2.86
E-03
SPBC25
H2.09 0.97
2.22E-
04
SPAC17
A2.12 0.84 2.00E-03
SPBC33
7.11 0.95
2.04
E-06
SPCPJ73
2.03 0.97
6.75E-
04
SPAC14
0.02 0.84 1.10E-02
SPAC9E
9.12c 0.95
1.98
E-05
SPAC19
52.15c 0.96
1.46E-
04
SPCC75
7.09c 0.83 1.22E-03
SPBC11
C11.04c 0.95
1.99
E-05
SPAC3C
7.05c 0.96
1.99E-
04
SPAC19
B12.01 0.83 5.83E-03
SPCC13
93.05 0.95
2.55
E-04
SPBC17
73.08c 0.96
1.16E-
06
SPBC19
C2.01 0.83 5.22E-04
SPBC19
C7.03 0.95
2.12
E-03
SPBC23
G7.06c 0.95
1.53E-
04
SPAC26
A3.03c 0.83 3.14E-06
SPBC26
H8.08c 0.94
6.64
E-03
SPBC16
04.18c 0.94
4.20E-
04
SPAC1D
4.11c 0.83 1.19E-04
SPBP19
A11.07c 0.94
3.19
E-05
SPBC2F
12.05c 0.94
5.74E-
05
SPCC55
0.10 0.83 4.58E-05
SPAC24
H6.06 0.94
5.61
E-05
SPAC51
3.05 0.94
1.15E-
03
SPBC18
H10.07 0.83 2.78E-05
SPBC17
73.08c 0.94
6.57
E-06
SPCC58
4.15c 0.94
2.45E-
04
SPAC16.
04 0.83 6.80E-04
Table
A.1:
Continued
191

SPCC62
2.19 0.94
2.77
E-04
SPCC13
22.08 0.94
1.06E-
02
SPAC11
E3.09 0.83 4.23E-04
SPAC4
D7.10c 0.94
6.09
E-04
SPAC6G
9.16c 0.94
2.13E-
04
SPAC30
D11.03 0.82 2.24E-03
SPAP8A
3.11c 0.94
1.17
E-03
SPAC16
A10.01 0.94
4.99E-
04
SPBC30
B4.01c 0.82 4.11E-02
SPCC89
5.06 0.93
3.39
E-04
SPCC14
42.05c 0.93
8.43E-
04
SPBC1D
7.05 0.82 5.43E-03
SPBC10
6.08c 0.93
5.68
E-04
SPAC19
A8.05c 0.93
1.83E-
04
SPAPB1
E7.01c 0.82 2.10E-03
SPAP7G
5.03 0.93
5.23
E-05
SPCC11
83.11 0.93
1.45E-
03
SPAC16
7.08 0.82 4.99E-03
SPCC57
6.19c 0.93
1.54
E-03
SPAC22
7.15 0.93
4.12E-
05
SPAC22
E12.09c 0.82 1.57E-03
SPCP20
C8.02c 0.93
3.76
E-02
SPBC11
05.10 0.93
1.11E-
05
SPAC17
A5.04c 0.82 1.52E-06
SPBP8B
7.27 0.93
1.77
E-05
SPAC10
93.06c 0.93
1.90E-
04
SPBPB8
B6.05c 0.82 1.20E-02
SPBC35
9.04c 0.92
6.29
E-03
SPBC66
0.06 0.92
2.82E-
03
SPBC18
H10.21c 0.81 2.95E-04
SPCC55
0.12 0.92
4.92
E-03
SPAPB2
B4.06 0.92
6.13E-
05
SPBC16
G5.16 0.81 3.19E-05
SPAC32
8.08c 0.92
5.57
E-03
SPCC73
7.09c 0.92
6.96E-
05
SPAC26
F1.12c 0.81 1.48E-02
SPAC24
H6.13 0.92
5.05
E-03
SPBP8B
7.24c 0.92
1.65E-
03
SPBP23
A10.12 0.81 1.24E-03
SPBC19
G7.06 0.92
2.13
E-05
SPAC16
C9.01c 0.92
4.20E-
03
SPAC86
9.11 0.81 9.45E-04
SPBC36
.07 0.92
1.15
E-04
SPCC24
B10.14c 0.92
8.40E-
05
SPAPB1
A10.06c 0.81 1.39E-04
SPAC29
A4.13 0.92
2.51
E-04
SPAC22
E12.03c 0.92
6.85E-
04
SPAC32
8.08c 0.81 6.19E-03
SPAC18
B11.09c 0.91
9.67
E-04
SPBC90
2.05c 0.92
3.85E-
04
SPBC14
C8.08c 0.81 3.66E-04
SPAC15
27.01 0.91
1.68
E-04
SPAC15
A10.05c 0.91
1.25E-
02
SPAC8E
11.03c 0.81 1.80E-02
SPCC19
19.07 0.91
1.22
E-02
SPAC82
4.07 0.91
1.48E-
05
SPAC82
1.04c 0.81 2.29E-02
SPBC11
98.12 0.90
8.31
E-04
SPCC4B
3.01 0.90
6.97E-
04
SPBC2G
2.01c 0.80 1.63E-03
Table
A.1:
Continued
192

SPAC82
3.04 0.90
4.09
E-02
SPBC3H
7.08c 0.90
3.06E-
04
SPCC89
5.06 0.80 4.86E-04
SPCC97
0.01 0.90
2.98
E-05
SPBC23
E6.09 0.90
1.15E-
02
SPAC11
D3.06 0.80 5.61E-06
SPCC70
.09c 0.90
8.42
E-04
SPAC11
H11.01 0.90
1.54E-
03
SPAC20
H4.04 0.80 1.11E-07
SPAC16
7.08 0.90
5.84
E-03
SPAC17
G6.12 0.90
2.27E-
04
SPCC64
5.06c 0.80 3.91E-04
SPBC31
F10.11c 0.90
5.38
E-05
SPAPB2
B4.03 0.90
6.99E-
03
SPBC17
73.13 0.80 6.50E-05
SPBC29
A10.09c 0.89
5.25
E-04
SPBC83
9.06 0.89
6.58E-
05
SPCC63.
06 0.80 5.51E-05
SPCC12
23.11 0.89
9.64
E-03
SPBC32
F12.03c 0.89
9.60E-
04
SPCC17
39.03 0.80 4.76E-06
SPAC11
E3.09 0.89
5.72
E-04
SPAC95
9.05c 0.89
2.20E-
05
SPAC12
50.02 0.89
1.99
E-03
SPAC23
C4.13 0.89
1.19E-
02
SPCC16
2.03 0.89
2.71
E-04
SPBC19
F5.01c 0.88
1.39E-
03
SPAC29
A4.19c 0.89
6.59
E-07
SPAC31
G5.10 0.88
1.91E-
03
SPAPB1
A10.06c 0.89
1.72
E-04
SPAC22
A12.02c 0.88
1.08E-
04
SPAC92
2.07c 0.89
6.15
E-03
SPCC12
81.04 0.88
1.23E-
03
SPAC23
H3.11c 0.88
1.23
E-03
SPCC73
6.15 0.88
1.19E-
02
SPAC2E
1P5.05 0.88
4.49
E-03
SPAC20
G4.02c 0.87
9.70E-
03
SPCC4B
3.08 0.88
6.47
E-04
SPCC16
A11.15c 0.87
6.26E-
04
SPCC24
B10.22 0.88
7.65
E-04
SPCP1E
11.03 0.87
7.00E-
07
SPCC12
6.07c 0.88
1.18
E-05
SPCC23
B6.03c 0.87
2.24E-
04
SPCC33
0.03c 0.88
6.23
E-03
SPBC10
6.08c 0.87
3.82E-
04
SPAC16
E8.06c 0.88
8.30
E-03
SPBC27
B12.04c 0.86
2.96E-
06
Table
A.1:
Continued
193

SPBP8B
7.04 0.88
7.41
E-04
SPAC17
G6.04c 0.86
6.89E-
04
SPBC29
A10.10c 0.87
2.59
E-03
SPBC12
71.05c 0.86
5.59E-
03
SPBC71
3.06 0.87
2.32
E-03
SPAC19
B12.10 0.86
3.43E-
04
SPCC64
5.13 0.87
8.86
E-05
SPBC16
G5.07c 0.86
8.04E-
06
SPCC11
E10.01 0.87
2.67
E-04
SPBC16
A3.02c 0.85
6.22E-
04
SPBP35
G2.03c 0.87
2.63
E-03
SPCC33
8.12 0.85
8.62E-
03
SPAC3F
10.10c 0.87
1.95
E-04
SPBC17
18.01 0.85
1.88E-
06
SPAC6F
6.04c 0.87
7.95
E-06
SPAC63
0.05 0.85
1.75E-
03
SPAC19
A8.07c 0.86
1.19
E-02
SPAP14
E8.02 0.84
1.91E-
02
SPAC3
G6.04 0.86
6.58
E-03
SPCC73
7.03c 0.84
1.86E-
04
SPCC59
4.04c 0.86
5.09
E-04
SPBC42
8.07 0.84
1.37E-
04
SPBC57
7.09 0.86
3.21
E-05
SPAC19
52.16 0.84
1.14E-
04
SPBC21
H7.04 0.86
2.32
E-03
SPBC77
6.15c 0.84
6.71E-
03
SPAPB2
4D3.02c 0.85
1.39
E-05
SPAC45
8.04c 0.84
8.96E-
03
SPBC11
98.04c 0.85
7.63
E-06
SPAC12
96.01c 0.84
3.61E-
06
SPAC18
05.15c 0.85
1.95
E-03
SPCC16
82.11c 0.84
4.61E-
04
SPCC70
.08c 0.85
1.41
E-02
SPCC16
2.02c 0.84
2.12E-
05
SPAC16
C9.01c 0.85
1.43
E-02
SPAC4F
10.02 0.84
2.72E-
05
SPBC28
F2.12 0.85
2.46
E-03
SPAC4F
10.07c 0.84
3.46E-
06
SPCC19
19.11 0.84
7.62
E-06
SPBC15
D4.01c 0.83
7.54E-
03
Table
A.1:
Continued
194

SPCC11
E10.03 0.84
2.53
E-04
SPBC21
6.03 0.83
5.43E-
04
SPAC22
2.05c 0.84
4.44
E-06
SPBC6B
1.05c 0.83
4.28E-
05
SPAC14
C4.01c 0.84
1.70
E-02
SPBC83.
05 0.83
6.11E-
04
SPCC55
3.01c 0.84
6.21
E-07
SPBC16
C6.02c 0.83
2.60E-
05
SPBC58
2.10c 0.84
3.30
E-03
SPBC21
C3.11 0.83
1.69E-
03
SPCC41
7.11c 0.83
8.90
E-03
SPBC17
18.07c 0.83
1.26E-
07
SPAC19
52.07 0.83
8.84
E-07
SPAC20
G4.05c 0.82
1.01E-
04
SPBC17
D1.02 0.83
2.69
E-03
SPAC22
F8.04 0.81
1.50E-
03
SPCC66
3.14c 0.83
5.39
E-04
SPBC17
18.06 0.81
2.95E-
06
SPAC19
G12.07c 0.83
6.46
E-05
SPAC60
7.08c 0.81
2.43E-
03
SPCC18
.13 0.83
8.00
E-03
SPBC1E
8.05 0.80
8.54E-
03
SPAC97
7.03 0.83
2.37
E-03
SPAC82
3.16c 0.80
1.05E-
04
SPAC2F
7.17 0.83
1.82
E-03
SPAC56
E4.06c 0.83
4.76
E-05
SPBC23
G7.06c 0.83
1.55
E-03
SPCC4E
9.01c 0.83
2.64
E-04
SPBC12
71.07c 0.82
1.01
E-03
SPBC8
D2.05c 0.82
9.74
E-05
SPAC22
F8.11 0.82
2.36
E-05
SPCC36
4.04c 0.81
5.08
E-05
Table
A.1:
Continued
195

SPCC13
22.03 0.81
1.67
E-02
SPBC65
1.05c 0.81
2.59
E-03
SPBC30
B4.02c 0.81
7.95
E-03
SPCC14
42.04c 0.81
3.50
E-04
SPCC63
.06 0.81
1.57
E-04
SPAC6
G9.12 0.81
5.39
E-04
SPAC1
D4.11c 0.81
4.84
E-04
SPBC21
.03c 0.80
1.04
E-02
SPAC20
H4.04 0.80
5.11
E-07
SPAC25
B8.05 0.80
3.42
E-04
SPCP31
B10.05 0.80
4.38
E-05
SPAC16
E8.14c 0.80
3.88
E-04
SPAC23
C11.03 0.80
7.87
E-03
SPAC17
G6.12 0.80
1.89
E-03
SPBC16
85.04 0.80
1.10
E-03
SPCC55
3.08c 0.80
1.08
E-03
SPAC3
A11.05c 0.80
1.50
E-03

∆gcn5 ∆elp3
∆mst2
Gene Log2
Chang pvalu
Gene
Log2
pvalue Gene
Log2
pvalue
Table
A.1:
Continued
196

e e Change Change
SPAC1F
8.03c 7.18
1.76
E-07
SPCC41
7.04 1.47
1.65E-
06
SPAC29A4
.19c 1.03 2.24E-06
SPBCPT
2R1.08c 6.37
1.88
E-04
SPBC3H
7.06c 1.47
3.50E-
03
SPBC146.0
5c 1.02 4.38E-03
SPAC1F
8.02c 6.36
4.47
E-12
SPAC22
F3.02 1.46
3.66E-
06
SPAC1805.
15c 1.02 2.97E-03
SPAC51
3.03 6.13
1.53
E-02
SPBC66
0.07 1.46
2.43E-
03
SPCC962.0
2c 1.02 1.94E-03
SPBC17
11.02 5.33
1.64
E-02
SPAC2F
7.06c 1.45
1.73E-
02
SPAC637.1
1 1.02 6.69E-04
SPAC3
G9.11c 4.62
6.82
E-08
SPBPB2
B2.02 1.44
4.01E-
02
SPBC23G7
.06c 1.02 1.91E-03
SPCC17
95.06 4.47
1.54
E-11
SPAC1F
7.06 1.44
1.71E-
06
SPCC576.0
4 1.02 3.56E-03
SPBC16
83.09c 4.31
2.61
E-04
SPBC16
85.06 1.44
1.42E-
03
SPCC1739.
03 1.02 1.70E-05
SPAC1F
8.01 4.18
3.58
E-02
SPCC10
20.01c 1.43
1.01E-
02
SPCC1442.
04c 1.01 3.83E-04
SPBC23
G7.10c 4.12
2.21
E-03
SPAC8C
9.03 1.43
3.28E-
03
SPBC609.0
1 1.01 4.17E-06
SPBC83
9.06 3.64
1.71
E-11
SPBC21
B10.12 1.43
5.28E-
07
SPBC660.1
5 1.01 6.78E-03
SPCC17
39.08c 3.56
4.61
E-02
SPAC5H
10.04 1.43
3.12E-
03
SPAC16C9
.01c 1.00 2.11E-02
SPCC18
8.12 3.56
9.35
E-04
SPAC4G
9.05 1.42
1.17E-
03
SPBC1271.
01c 1.00 9.67E-05
SPCC73
7.04 3.55
7.02
E-05
SPBC24
C6.09c 1.42
8.69E-
04
SPAC57A7
.08 1.00 3.98E-03
SPBC56
F2.06 3.51
2.76
E-04
SPCC56
9.04 1.42
6.19E-
07
SPAC977.0
6 1.00 1.19E-04
SPAC97
7.16c 3.41
4.14
E-07
SPBC13
A2.04c 1.41
4.62E-
02
SPAC1006.
01 0.99 1.13E-03
SPBC94
7.05c 3.29
1.29
E-08
SPCC83
0.07c 1.40
6.04E-
03
SPCC1393.
07c 0.99 1.37E-03
SPAC1F
7.08 3.06
1.45
E-03
SPAC23
G3.03 1.39
1.54E-
03
SPAC6C3.
02c 0.98 2.53E-02
SPBC35
9.06 2.98
3.49
E-02
SPBC94
7.13 1.39
1.38E-
04
SPAC6G10
.03c 0.98 7.71E-03
Table
A.1:
Continued
197

SPAPB8
E5.05 2.89
3.07
E-02
SPCC57
6.17c 1.39
1.15E-
04
SPCC1235.
01 0.98 6.12E-03
SPAC27
D7.03c 2.82
2.54
E-02
SPAC25
H1.03 1.38
9.10E-
05
SPBC13E7.
02 0.98 8.26E-04
SPAC31
G5.09c 2.76
1.09
E-02
SPBC13
47.11 1.38
1.54E-
02
SPBC25H2
.08c 0.98 6.14E-03
SPBC19
C7.04c 2.68
2.75
E-03
SPCC24
B10.14c 1.38
4.26E-
05
SPAC222.1
5 0.98 8.65E-04
SPAC1F
8.08 2.67
6.91
E-06
SPBC72
5.03 1.38
2.54E-
02
SPCC11E1
0.09c 0.98 2.57E-04
SPCC14
42.01 2.67
2.09
E-03
SPCC12
6.07c 1.38
7.12E-
07
SPBC119.1
4 0.97 5.68E-04
SPBC13
47.03 2.67
9.57
E-08
SPAC13
D6.01 1.38
2.81E-
04
SPCC548.0
5c 0.97 4.97E-04
SPCC19
06.04 2.58
1.04
E-05
SPBC10
6.02c 1.37
3.46E-
02
SPAPB8E5
.10 0.97 7.90E-03
SPAC22
H10.13 2.53
2.35
E-03
SPBC4F
6.17c 1.36
1.43E-
02
SPAC24H6
.13 0.97 1.57E-02
SPAC19
52.04c 2.53
1.24
E-04
SPBC21
5.13 1.36
4.54E-
06
SPCC553.0
7c 0.97 1.15E-03
SPAC92
2.03 2.52
1.72
E-10
SPAC15
A10.10 1.36
7.97E-
05
SPAC3A11
.05c 0.97 2.10E-03
SPBC2
G2.17c 2.42
5.92
E-05
SPCC28
5.07c 1.36
1.95E-
03
SPAC24H6
.06 0.97 4.79E-04
SPAC13
G7.02c 2.41
9.23
E-03
SPAC4D
7.02c 1.36
2.65E-
03
SPAC328.0
2 0.96 2.66E-05
SPBC16
85.13 2.39
9.44
E-03
SPCC33
0.03c 1.35
1.43E-
03
SPAC2C4.
06c 0.96 3.74E-03
SPAC11
H11.04 2.39
3.15
E-02
SPBC11
98.14c 1.34
1.86E-
04
SPBC1861.
06c 0.96 1.98E-02
SPAC6
B12.03c 2.37
4.00
E-03
SPAC29
B12.12 1.33
1.61E-
03
SPBC1D7.
05 0.95 1.85E-02
SPAC11
E3.06 2.34
2.81
E-03
SPCC12
59.14c 1.32
4.21E-
05
SPBC354.1
2 0.95 9.50E-03
SPAC8E
11.03c 2.33
4.79
E-05
SPBC36
B7.06c 1.31
4.97E-
03
SPAC18B1
1.09c 0.95 4.68E-03
SPAC27
D7.09c 2.32
6.89
E-03
SPBC32
H8.06 1.30
4.54E-
04
SPAPB1E7
.01c 0.94 9.35E-03
SPAC4
H3.03c 2.32
4.33
E-03
SPCC77
7.03c 1.29
7.02E-
03
SPAC17A2
.07c 0.94 1.94E-03
Table
A.1:
Continued
198

SPCC77
7.04 2.26
3.99
E-03
SPCC73
6.05 1.29
2.29E-
04
SPCP1E11.
03 0.94 2.20E-05
SPCC33
0.04c 2.25
2.32
E-08
SPAC1F
8.05 1.29
2.13E-
02
SPBC19C2
.11c 0.94 5.95E-03
SPCC18
40.12 2.25
8.28
E-05
SPACU
NK4.10 1.29
1.79E-
02
SPBC36.01
c 0.94 2.45E-02
SPCC16
2.10 2.22
3.47
E-03
SPAC30
D11.02c 1.29
2.17E-
02
SPAC1565.
03 0.94 3.36E-02
SPBC31
F10.08 2.20
1.44
E-04
SPAC31
G5.10 1.27
1.66E-
03
SPAC56F8.
14c 0.93 4.31E-02
SPCC33
8.18 2.19
1.39
E-03
SPCC10
20.05 1.27
1.86E-
03
SPAC3F10.
17 0.93 1.31E-03
SPAC10
06.04c 2.18
3.18
E-06
SPBC21
D10.08c 1.27
3.81E-
02
SPCC11E1
0.03 0.92 9.64E-04
SPAC1F
7.07c 2.17
7.51
E-03
SPAC23
G3.02c 1.26
7.51E-
05
SPBC83.09
c 0.92 1.70E-02
SPAC14
C4.01c 2.07
6.99
E-05
SPCC33
8.08 1.26
4.14E-
04
SPAC328.0
8c 0.92 2.26E-02
SPBC16
85.05 2.07
5.19
E-07
SPBC6B
1.05c 1.25
2.02E-
05
SPBC12C2
.03c 0.92 3.51E-03
SPCC70
.04c 2.06
7.02
E-05
SPAC22
H12.01c 1.25
4.08E-
03
SPBC685.0
3 0.92 1.42E-04
SPBC17
78.04 2.04
2.92
E-06
SPAC4H
3.08 1.25
3.05E-
04
SPBC17D1
.01 0.92 2.88E-03
SPBC14
C8.01c 2.04
7.84
E-05
SPBC32
H8.11 1.24
7.27E-
03
SPCP31B1
0.06 0.91 3.64E-02
SPAC20
H4.11c 2.03
8.15
E-04
SPAC27
D7.11c 1.23
3.55E-
02
SPBC6B1.
06c 0.90 1.16E-03
SPBC32
C12.02 2.03
1.20
E-02
SPBC15
D4.01c 1.23
5.60E-
03
SPCC737.0
3c 0.90 2.31E-03
SPCC74
.02c 2.02
5.55
E-07
SPBC9B
6.03 1.23
1.44E-
02
SPBC1604.
18c 0.90 9.35E-03
SPCPB1
6A4.06c 2.02
1.50
E-04
SPBC1A
4.01 1.22
2.57E-
03
SPAC17C9
.02c 0.90 1.13E-03
SPAC29
A4.12c 2.02
9.22
E-04
SPAPB1
A10.08 1.22
1.47E-
04
SPAC56E4
.06c 0.90 2.53E-04
SPCC10
20.09 1.99
2.30
E-03
SPBC19
C2.06c 1.22
3.32E-
02
SPAC6G9.
12 0.89 1.77E-03
SPBC35
4.08c 1.97
8.65
E-05
SPAC4H
3.11c 1.21
5.74E-
04
SPCC16A1
1.08 0.89 3.06E-03
Table
A.1:
Continued
199

SPBC16
85.14c 1.96
6.09
E-05
SPCC28
5.09c 1.21
2.04E-
03
SPCC162.0
5 0.89 4.18E-03
SPBC72
5.10 1.95
1.55
E-02
SPAC82
1.04c 1.20
1.73E-
02
SPBP8B7.0
4 0.89 4.46E-03
SPBC12
89.16c 1.92
9.16
E-03
SPAC11
D3.09 1.20
8.54E-
04
SPAC4H3.
02c 0.89 3.06E-03
SPAC1F
12.10c 1.92
2.92
E-02
SPCC13
93.13 1.20
1.34E-
03
SPCPJ732.
02c 0.89 3.35E-03
SPAC4F
10.08 1.91
4.96
E-07
SPBC65
1.05c 1.20
7.43E-
04
SPAPB24D
3.04c 0.89 8.76E-03
SPBC60
9.04 1.89
8.18
E-03
SPBC40
9.03 1.18
4.28E-
02
SPBC8E4.0
2c 0.88 3.79E-03
SPAC23
H3.15c 1.86
3.19
E-02
SPAC19
G12.01c 1.18
5.96E-
07
SPBC660.0
6 0.88 3.09E-02
SPAC24
C9.15c 1.84
7.31
E-03
SPBC21
C3.11 1.16
1.77E-
03
SPCC1442.
07c 0.88 4.26E-02
SPAC16
10.03c 1.83
3.64
E-06
SPBP19
A11.07c 1.15
4.44E-
05
SPCC338.1
2 0.88 4.48E-02
SPAC19
52.15c 1.83
4.67
E-06
SPBC11
05.14 1.15
3.40E-
02
SPCC1281.
04 0.88 1.46E-02
SPBC23
G7.11 1.81
6.89
E-04
SPAC17
A5.04c 1.15
1.74E-
06
SPBC3D6.
10 0.87 1.49E-02
SPBC16
D10.08c 1.80
2.21
E-02
SPAC4A
8.04 1.15
1.48E-
02
SPAC23H4
.11c 0.87 3.97E-02
SPMIT.
10 1.79
3.82
E-05
SPBC14
C8.11c 1.15
5.68E-
03
SPBP22H7.
04 0.87 1.55E-03
SPAC6
C3.07 1.79
2.44
E-06
SPAC31
A2.12 1.15
1.04E-
04
SPACUNK
4.16c 0.87 3.94E-02
SPBC14
C8.05c 1.78
2.72
E-07
SPAC17
H9.19c 1.14
4.48E-
02
SPAC6G9.
08 0.87 1.94E-03
SPAC1F
8.04c 1.78
1.61
E-02
SPBC1E
8.05 1.14
8.60E-
03
SPCC550.1
2 0.87 2.86E-02
SPAC22
F3.12c 1.77
3.16
E-02
SPBC6B
1.03c 1.13
7.01E-
04
SPAC1805.
09c 0.87 1.98E-02
SPAC13
C5.03 1.76
9.05
E-06
SPCC79
4.02 1.13
6.53E-
03
SPAC10F6.
15 0.87 7.47E-03
SPBC16
85.12c 1.76
3.02
E-03
SPAC22
7.13c 1.13
9.05E-
04
SPAC631.0
2 0.86 2.33E-02
SPCC4
G3.03 1.75
4.36
E-05
SPBC16
83.12 1.13
4.88E-
02
SPCC417.1
1c 0.86 2.76E-02
Table
A.1:
Continued
200

SPAC3F
10.10c 1.74
7.67
E-07
SPCC54
8.04 1.12
2.73E-
03
SPAC4F10.
09c 0.86 1.08E-02
SPCC58
4.02 1.73
1.85
E-05
SPCC17
39.15 1.12
8.50E-
04
SPBC16E9.
08 0.86 2.15E-03
SPAC25
H1.09 1.72
2.27
E-05
SPBC18
H10.09 1.12
5.21E-
05
SPBC26H8
.08c 0.86 4.12E-02
SPCC19
19.14c 1.72
4.18
E-05
SPAC6C
3.05 1.12
2.08E-
03
SPBC16D1
0.07c 0.85 1.81E-05
SPBC14
6.11c 1.71
3.61
E-06
SPBC11
05.17 1.12
1.71E-
03
SPBC16A3
.17c 0.85 3.80E-02
SPCC83
0.04c 1.71
2.58
E-04
SPAC64
4.14c 1.12
1.04E-
04 SPCC63.06 0.85 8.88E-04
SPBC27
.03 1.71
2.12
E-06
SPBC19
G7.13 1.11
1.60E-
04
SPAC328.0
3 0.85 3.05E-02
SPBC3
H7.08c 1.69
1.40
E-05
SPAC22
E12.03c 1.11
2.59E-
03
SPAC56F8.
13 0.85 6.71E-04
SPAC86
9.02c 1.69
3.83
E-03
SPAC17
G6.13 1.10
2.19E-
02
SPCC830.0
3 0.85 2.44E-03
SPBC21
C3.02c 1.68
6.85
E-06
SPCC18.
10 1.10
1.63E-
05
SPAC23D3
.01 0.84 7.34E-04
SPBC3
D6.11c 1.66
2.48
E-06
SPCC96
5.05c 1.09
5.91E-
05
SPAC15A1
0.04c 0.84 3.61E-02
SPAC18
G6.09c 1.66
8.05
E-03
SPAC8C
9.12c 1.09
6.22E-
04
SPAC8C9.
11 0.84 2.94E-02
SPAC2E
1P3.02c 1.64
1.28
E-04
SPAC92
6.08c 1.08
3.51E-
02
SPAC328.0
4 0.83 4.68E-04
SPCPB1
C11.02 1.62
1.31
E-03
SPAC25
G10.04c 1.08
7.18E-
03
SPAC1250.
02 0.83 1.62E-02
SPBC53
0.11c 1.61
4.67
E-04
SPCC12
23.12c 1.08
1.04E-
02
SPAC24B1
1.06c 0.83 7.40E-04
SPBC4F
6.09 1.61
2.36
E-02
SPAC20
G4.03c 1.08
3.75E-
02
SPAC13D6
.02c 0.83 3.94E-03
SPAC1
A6.11 1.60
5.63
E-06
SPBC17
11.11 1.08
1.41E-
03
SPBC3F6.0
4c 0.82 3.46E-02
SPAC4
H3.04c 1.60
1.88
E-03
SPAC12
50.01 1.08
5.08E-
04
SPCC61.01
c 0.82 8.37E-03
SPAC5
H10.07 1.58
8.84
E-05
SPCC4F
11.02 1.08
7.99E-
03
SPAC56F8.
16 0.82 1.56E-02
SPAC22
A12.02c 1.56
7.62
E-06
SPBC33
7.11 1.08
8.06E-
06
SPBC18H1
0.21c 0.82 5.14E-03
Table
A.1:
Continued
201

SPAC6
G9.01c 1.54
1.12
E-03
SPAC15
65.04c 1.07
3.04E-
02
SPAC1002.
12c 0.82 1.95E-02
SPAPB1
A11.03 1.52
1.40
E-05
SPCC13
22.03 1.06
1.38E-
02
SPAPB2B4
.06 0.81 4.54E-03
SPCC12
23.02 1.52
1.04
E-04
SPAC19
B12.08 1.06
3.93E-
02
SPCC132.0
3 0.81 1.40E-02
SPBC18
E5.10 1.52
3.93
E-05
SPAC15
F9.01c 1.06
7.42E-
03
SPCC70.09
c 0.81 1.06E-02
SPCC97
0.11c 1.51
1.10
E-03
SPAC18
6.01 1.05
1.34E-
02
SPAC6B12
.08 0.81 9.73E-03
SPCC96
5.08c 1.51
5.89
E-08
SPBC8D
2.19 1.04
1.55E-
03
SPAC13G7
.07 0.81 2.00E-02
SPBC17
18.02 1.51
1.62
E-04
SPCC12
6.02c 1.04
4.81E-
04
SPCC584.1
5c 0.81 1.29E-02
SPAC22
G7.11c 1.50
4.45
E-04
SPAC58
9.08c 1.04
2.30E-
02
SPAC1B3.
15c 0.81 1.70E-02
SPAC16
E8.05c 1.49
5.39
E-05
SPAC1F
7.05 1.04
4.25E-
02
SPAC688.0
3c 0.80 1.92E-02
SPAC15
56.06b 1.49
3.37
E-03
SPCC10
20.13c 1.04
1.35E-
03
SPAC1527.
03 0.80 1.23E-02
SPAC27
D7.05c 1.49
1.14
E-03
SPBC35
4.06 1.04
3.10E-
03
SPBC800.1
4c 0.80 3.46E-02
SPBC32
H8.07 1.48
7.42
E-05
SPAC4D
7.10c 1.04
1.91E-
03
SPCC16A1
1.15c 0.80 1.54E-02
SPAC34
3.07 1.48
1.58
E-04
SPCC73
6.15 1.04
3.12E-
02
SPAC13G6
.05c 0.80 5.77E-03

SPBC16
A3.02c 1.03
2.41E-
03
SPBC27B1
2.03c 0.80 1.05E-03

mst1
ts

Gene
Log2
Chang
e
pvalu
e Gene
Log2
Change pvalue Gene
Log2
Change pvalue
SPAC86
9.09 6.68
2.91
E-12
SPAC22
F8.05 1.90
1.56E-
03
SPBC56F2.
05c 1.13 2.88E-07
SPAC86
9.06c 6.61
2.79
E-13
SPBC13
48.09 1.89
3.69E-
11
SPCC830.0
4c 1.13 4.93E-04
SPAC1F
8.05 5.36
1.87
E-11
SPAC14
C4.01c 1.87
3.69E-
06
SPAC458.0
4c 1.13 9.70E-04
Table
A.1:
Continued
202

SPBC23
G7.10c 5.25
4.94
E-06
SPAC27
E2.04c 1.87
1.98E-
08
SPCC417.0
4 1.13 5.53E-07
SPAC22
G7.11c 5.22
4.34
E-14
SPCC57
6.17c 1.87
2.59E-
08
SPAC1565.
04c 1.12 2.73E-03
SPAC3
G9.11c 5.13
5.88
E-11
SPAC11
D3.13 1.86
2.69E-
03
SPBC1271.
05c 1.12 6.81E-04
SPBPB2
1E7.01c 5.11
3.01
E-13
SPAC18
6.08c 1.85
7.53E-
13
SPBC14C8
.01c 1.11 1.01E-03
SPAC18
6.02c 5.11
6.43
E-15
SPAC13
F5.03c 1.85
2.29E-
04
SPCC338.0
8 1.08 5.52E-05
SPAC97
7.16c 5.02
4.45
E-12
SPAC97
7.03 1.84
7.01E-
08
SPAC4D7.
02c 1.08 1.01E-03
SPBC24
C6.09c 4.94
1.55
E-13
SPAC75
0.04c 1.84
2.17E-
06
SPBC19G7
.06 1.07 6.95E-07
SPAC22
H10.13 4.85
1.83
E-08
SPAC6B
12.03c 1.84
1.97E-
03
SPAC15A1
0.05c 1.07 4.43E-03
SPBCPT
2R1.08c 4.76
1.05
E-04
SPBC16
04.01 1.81
4.55E-
10
SPAC10F6.
15 1.07 5.54E-05
SPAC1F
8.01 4.72
1.97
E-03
SPAC26
F1.04c 1.81
1.42E-
07
SPAC57A1
0.05c 1.07 9.94E-05
SPBC12
89.14 4.61
8.12
E-16
SPBC72
5.03 1.80
2.78E-
04
SPBC359.0
2 1.06 3.40E-05
SPCPB1
6A4.06c 4.53
1.21
E-11
SPAC10
02.20 1.78
1.18E-
07
SPCC1682.
11c 1.06 4.16E-05
SPAC13
9.05 4.49
1.53
E-09
SPBC16
85.12c 1.78
1.13E-
04
SPAC57A7
.05 1.06 2.98E-02
SPAC86
9.07c 4.43
2.62
E-15
SPBC88
7.16 1.78
9.01E-
05
SPAC25H1
.09 1.05 1.16E-04
SPBC56
F2.06 4.36
2.99
E-07
SPAC8E
11.03c 1.76
2.30E-
05
SPAC3A11
.10c 1.05 1.37E-03
SPBC11
98.14c 4.32
3.57
E-14
SPBCPT
2R1.02 1.75
2.46E-
06
SPAP7G5.
03 1.05 3.04E-06
SPBC3
H7.08c 4.09
9.33
E-14
SPBC19
C2.06c 1.74
1.97E-
04
SPAC16E8
.03 1.05 4.37E-04
SPAC86
9.08 4.08
1.01
E-15
SPAC3C
7.05c 1.73
1.30E-
07
SPBC32F1
2.09 1.05 5.21E-05
SPAC29
A4.12c 4.06
1.45
E-09
SPCC12
35.13 1.72
9.81E-
09
SPAC19D5
.06c 1.05 1.26E-08
SPBC16
E9.16c 4.00
6.07
E-13
SPBC12
89.16c 1.69
1.86E-
03
SPAPB1E7
.08c 1.04 2.41E-03
Table
A.1:
Continued
203

SPAPB8
E5.10 3.98
1.31
E-12
SPAC1F
7.08 1.68
9.05E-
03
SPCC584.1
2 1.04 1.37E-03
SPBC1
A4.01 3.96
4.49
E-12
SPAC1F
7.07c 1.67
4.16E-
03
SPAC26F1.
10c 1.03 2.03E-03
SPBC35
9.06 3.91
5.00
E-04
SPAC16
A10.01 1.67
5.76E-
07
SPCC4G3.
12c 1.03 4.78E-06
SPCC73
7.04 3.85
3.10
E-07
SPAC75
0.07c 1.67
5.11E-
04
SPAC1751.
01c 1.03 3.57E-02
SPBC16
83.09c 3.69
3.37
E-05
SPAC97
7.07c 1.65
9.39E-
07
SPCC550.1
0 1.02 3.46E-06
SPBPB2
1E7.04c 3.67
3.08
E-06
SPAC26
F1.14c 1.63
1.76E-
04
SPAC5D6.
10c 1.02 4.49E-06
SPCC66
3.06c 3.66
3.28
E-05
SPBC12
89.15 1.62
2.28E-
04
SPAC56F8.
13 1.02 1.65E-06
SPBP4G
3.03 3.65
2.74
E-13
SPAPB1
A10.14 1.61
5.00E-
05 SPAC9.08c 1.02 2.89E-02
SPBPB8
B6.03 3.64
2.07
E-12
SPBPB2
B2.11 1.60
3.89E-
06
SPBC9B6.
03 1.02 5.43E-03
SPAC11
D3.01c 3.61
1.72
E-07
SPBPB2
B2.01 1.59
2.51E-
03
SPBC2F12.
15c 1.01 1.47E-04
SPAC1F
8.04c 3.59
5.41
E-07
SPBC3E
7.02c 1.59
3.78E-
03
SPCC417.0
2 1.01 2.72E-04
SPAPB1
A11.03 3.59
1.50
E-13
SPAC22
G7.08 1.59
1.64E-
08
SPBC115.0
3 1.01 1.55E-02
SPAC22
A12.17c 3.57
1.96
E-11
SPAC13
F5.07c 1.57
2.96E-
04
SPAC1006.
01 1.01 2.69E-05
SPBC11
98.01 3.55
7.19
E-16
SPBC35
4.11c 1.57
6.76E-
06
SPAC11G7
.05c 1.01 1.66E-07
SPAPJ6
95.01c 3.52
2.00
E-09
SPAC3C
7.02c 1.56
1.32E-
06
SPAC29B1
2.12 1.01 8.96E-04
SPCC17
95.06 3.52
2.50
E-12
SPBC19
C2.05 1.55
1.41E-
03
SPAC27D7
.11c 1.00 1.78E-02
SPAC1F
8.03c 3.48
2.47
E-05
SPCC41
7.10 1.55
1.01E-
05
SPAC6C3.
05 1.00 2.58E-04
SPBC60
9.04 3.44
4.99
E-07
SPAC6G
10.03c 1.53
3.38E-
06
SPBC1198.
07c 1.00 2.47E-04
SPAC23
H3.15c 3.42
1.03
E-05
SPAC97
7.06 1.52
4.06E-
09
SPCC1739.
10 1.00 1.24E-03
SPACU
NK4.17 3.33
3.64
E-07
SPBC4F
6.09 1.52
4.04E-
03
SPAC4F10.
07c 1.00 3.28E-07
Table
A.1:
Continued
204

SPAC3
G6.07 3.33
1.53
E-05
SPAP11
E10.02c 1.51
9.62E-
04
SPAC1F7.1
0 0.98 6.97E-04
SPAC1F
8.08 3.32
2.20
E-09
SPCC32
0.07c 1.50
3.94E-
08
SPBC1778.
04 0.98 2.40E-04
SPAC97
7.05c 3.29
2.46
E-05
SPAC13
A11.06 1.50
2.85E-
05
SPAC22E1
2.03c 0.98 3.60E-04
SPAC27
D7.03c 3.25
8.89
E-04
SPAC27
D7.09c 1.49
1.26E-
02
SPAPB24D
3.02c 0.98 5.43E-07
SPAC31
G5.09c 3.17
2.17
E-04
SPAC27
F1.05c 1.49
6.79E-
06
SPBC23G7
.08c 0.98 4.93E-06
SPBPB2
B2.12c 3.16
7.06
E-03
SPCC96
5.06 1.48
8.33E-
05
SPAC5D6.
04 0.98 1.70E-05
SPAC4
H3.08 3.16
4.98
E-12
SPAC31
G5.10 1.48
9.73E-
06
SPAC2F7.0
6c 0.97 2.29E-02
SPCC75
7.03c 3.11
2.10
E-09
SPCC18
8.09c 1.48
1.31E-
09
SPBC800.1
4c 0.97 1.02E-03
SPCC13
22.07c 3.10
9.51
E-09
SPBC31
F10.08 1.47
2.58E-
04
SPCC1281.
07c 0.97 7.95E-03
SPBPB2
B2.18 3.05
1.46
E-05
SPBC21
5.11c 1.47
4.82E-
03
SPCC338.1
2 0.96 3.69E-03
SPCC33
8.18 3.04
7.26
E-07
SPBC16
83.01 1.47
2.17E-
06
SPAC26H5
.09c 0.96 1.85E-02
SPBPB8
B6.04c 3.04
7.61
E-08
SPAC23
E2.03c 1.47
1.47E-
02
SPAC22F8.
02c 0.96 3.73E-05
SPBC11
05.13c 3.02
1.10
E-07
SPBC19
F8.06c 1.45
1.04E-
06
SPAPB1A1
0.13 0.96 2.42E-03
SPAC15
E1.02c 3.00
8.68
E-09
SPCP31
B10.06 1.45
7.41E-
05
SPBC3H7.
06c 0.95 6.77E-03
SPAC23
C11.06c 2.99
1.15
E-07
SPAC22
G7.07c 1.44
2.63E-
07
SPCC31H1
2.06 0.95 4.50E-05
SPCC17
39.08c 2.96
2.15
E-02
SPBC16
52.01 1.43
5.97E-
05
SPBC1E8.0
5 0.94 2.77E-03
SPCC16
A11.15c 2.94
5.09
E-11
SPBC11
05.14 1.43
8.01E-
04
SPCC736.1
3 0.94 9.33E-05
SPAC4F
10.17 2.88
6.57
E-09
SPAC29
A4.17c 1.42
3.30E-
04
SPBC21C3
.10c 0.94 2.41E-02
SPBC16
85.05 2.86
1.62
E-11
SPCC77
7.03c 1.42
1.75E-
04
SPCC1183.
09c 0.94 1.08E-03
SPBC17
73.06c 2.76
4.69
E-04
SPBC2F
12.09c 1.42
1.58E-
10
SPAC29E6
.01 0.94 8.52E-06
Table
A.1:
Continued
205

SPAPJ6
91.02 2.72
1.52
E-05
SPCC4G
3.03 1.42
8.84E-
06
SPAC3G9.
08 0.94 2.44E-04
SPAC56
F8.15 2.68
1.28
E-03
SPAC56
F8.14c 1.41
1.86E-
04
SPCC417.1
1c 0.94 1.74E-03
SPBC2
G2.17c 2.66
2.11
E-07
SPBC36
B7.06c 1.41
1.26E-
04
SPAC1556.
06b 0.93 7.79E-03
SPAC32
A11.02c 2.65
4.69
E-09
SPAC19
G12.09 1.40
2.69E-
05
SPBC146.1
1c 0.93 8.17E-05
SPCC10
20.01c 2.64
6.19
E-07
SPAC1A
6.06c 1.39
1.65E-
05
SPCC757.1
3 0.92 1.20E-05
SPAC26
F1.05 2.64
1.00
E-07
SPAC2E
1P3.01 1.39
8.75E-
05
SPAC4G8.
04 0.92 3.46E-06
SPCC77
7.04 2.63
3.77
E-05
SPBC21.
07c 1.38
5.91E-
08
SPAP27G1
1.12 0.92 3.35E-06
SPBPB2
B2.08 2.60
7.87
E-03
SPAC3F
10.10c 1.37
1.64E-
07
SPCC663.0
3 0.92 1.04E-03
SPCC13
93.12 2.58
4.35
E-11
SPAPB1
8E9.04c 1.37
3.66E-
05
SPBC12C2
.14c 0.92 3.64E-07
SPBC83
.19c 2.58
3.49
E-12
SPAC20
H4.11c 1.37
1.26E-
03
SPBC16E9.
13 0.92 1.89E-07
SPBC72
5.10 2.57
9.52
E-05
SPCPJ73
2.03 1.36
1.74E-
05
SPCC1223.
02 0.91 5.23E-04
SPCC66
3.08c 2.54
9.81
E-03
SPAC34
3.12 1.32
8.35E-
03
SPBC2D10
.04 0.91 8.49E-06
SPAC5
H10.02c 2.46
3.89
E-11
SPCC79
4.03 1.32
2.22E-
04
SPCC757.0
2c 0.91 5.53E-04
SPCC19
06.04 2.44
5.08
E-06
SPBC1D
7.02c 1.32
1.30E-
03
SPAC57A7
.09 0.91 3.86E-03
SPBC13
48.14c 2.41
2.14
E-15
SPBC66
0.09 1.31
4.89E-
08
SPAC25B8
.19c 0.90 5.75E-06
SPAC97
7.17 2.40
1.80
E-08
SPBC11
C11.06c 1.30
2.04E-
02
SPCC1529.
01 0.90 2.94E-02
SPAPB2
4D3.10c 2.37
2.63
E-02
SPBC66
0.06 1.30
1.25E-
04
SPAC23C1
1.07 0.90 2.19E-04
SPBC83
9.06 2.36
6.88
E-11
SPBC94
7.09 1.29
3.43E-
07
SPAC14C4
.08 0.89 3.44E-02
SPAC13
G7.02c 2.34
8.34
E-04
SPBC17
73.05c 1.29
1.35E-
05
SPBC19C7
.03 0.88 1.47E-03
SPAC1F
7.06 2.33
5.44
E-12
SPCC11
83.11 1.29
6.12E-
05
SPCC550.0
7 0.88 7.70E-03
Table
A.1:
Continued
206

SPCC16
2.10 2.28
1.19
E-04
SPAC30
D11.02c 1.28
2.33E-
03
SPBC2G2.
10c 0.88 2.21E-06
SPBC32
C12.02 2.27
3.35
E-04
SPBC16
A3.02c 1.28
7.49E-
06
SPAC4G9.
07 0.87 3.14E-03
SPCPB1
C11.02 2.25
7.04
E-07
SPCC14
42.07c 1.28
2.97E-
04
SPBC409.0
7c 0.87 1.11E-06
SPAC51
3.06c 2.24
1.52
E-09
SPCC83
0.05c 1.27
3.16E-
09
SPCC330.0
4c 0.87 7.08E-05
SPCC13
93.07c 2.23
4.88
E-10
SPAPB2
B4.04c 1.27
5.22E-
05
SPAC11E3
.13c 0.87 4.61E-06
SPBC36
.02c 2.23
1.36
E-04
SPAC4A
8.04 1.26
5.82E-
04
SPAC29A4
.13 0.87 1.42E-04
SPBPB8
B6.02c 2.23
1.43
E-12
SPBP4H
10.10 1.25
3.33E-
02
SPBC19C7
.05 0.86 1.49E-02
SPBC4.
01 2.20
9.35
E-05
SPBC21
B10.12 1.25
2.42E-
08
SPAPB1A1
1.01 0.86 2.50E-03
SPAC1F
8.02c 2.18
3.57
E-07
SPCC12
81.08 1.25
1.62E-
07
SPBC354.0
8c 0.86 6.08E-03
SPCC79
4.01c 2.18
4.23
E-02
SPBC10
6.02c 1.25
8.64E-
03
SPBC8D2.
20c 0.86 1.96E-03
SPAPB1
5E9.02c 2.17
3.00
E-08
SPBC66
0.07 1.24
4.93E-
04
SPCC794.0
2 0.85 4.13E-03
SPAC4
H3.03c 2.14
4.86
E-04
SPAC63
7.12c 1.23
1.21E-
06
SPAC18G6
.09c 0.85 4.39E-02
SPAC51
3.02 2.12
1.94
E-06
SPAC11
E3.14 1.22
1.11E-
06
SPAC23A1
.06c 0.85 2.28E-04
SPBC36
5.12c 2.11
9.95
E-06
SPBC14
6.02 1.21
2.11E-
04
SPBC8D2.
19 0.85 4.47E-04
SPAC3
H8.09c 2.11
1.77
E-10
SPBC60
9.01 1.21
2.27E-
09
SPBP19A1
1.07c 0.85 2.98E-05
SPBC94
7.05c 2.11
5.62
E-08
SPAC1F
7.12 1.21
6.28E-
07
SPAC20G4
.05c 0.84 7.65E-05
SPAC5
H10.04 2.10
1.33
E-06
SPCC12
6.07c 1.20
3.53E-
08
SPBC1A4.
02c 0.84 5.93E-06
SPBC19
C7.04c 2.09
1.28
E-03
SPACU
NK4.19 1.20
1.53E-
05
SPBC29A3
.08 0.84 4.84E-03
SPBPB2
B2.02 2.06
3.06
E-04
SPAC19
B12.08 1.19
2.44E-
03
SPAC20G4
.03c 0.83 2.51E-02
SPCC18
40.12 2.05
4.17
E-06
SPAC17
A2.01 1.19
2.40E-
07
SPBC16E9.
11c 0.83 6.41E-06
Table
A.1:
Continued
207

SPCC12
23.12c 2.05
4.69
E-07
SPBC40
5.02c 1.18
7.98E-
05
SPAC328.0
3 0.83 4.68E-03
SPBC4C
3.08 2.04
6.23
E-08
SPBC35
4.12 1.18
7.96E-
05
SPCC736.1
1 0.83 6.80E-06
SPAC63
7.03 2.03
1.33
E-04
SPAC16
7.06c 1.18
5.55E-
03
SPCC285.1
6c 0.83 6.73E-06
SPBC8E
4.05c 1.99
1.54
E-08
SPBC68
5.03 1.16
8.69E-
08
SPBC146.0
6c 0.82 5.62E-04
SPAC11
E3.06 1.98
6.19
E-04
SPAC17
86.04 1.16
3.48E-
05
SPAC688.0
4c 0.82 5.52E-04
SPAC9.
10 1.98
8.57
E-09
SPAC26
H5.08c 1.16
1.50E-
04
SPAC2C4.
17c 0.82 1.01E-03
SPBC16
A3.13 1.96
2.81
E-05
SPCC13
22.08 1.15
2.57E-
03
SPAC186.0
9 0.82 5.01E-08
SPCC70
.04c 1.95
2.09
E-06
SPAP8A
3.04c 1.15
3.11E-
02
SPCC417.0
5c 0.81 3.23E-03
SPCC19
1.01 1.94
5.61
E-06
SPCC57
6.01c 1.15
1.01E-
03
SPCC364.0
2c 0.81 3.45E-04
SPBC23
E6.03c 1.94
3.20
E-06
SPBC15
D4.02 1.14
1.67E-
03
SPAC1610.
03c 0.81 6.80E-04
SPBPB2
B2.07c 1.93
9.41
E-10
SPBC12
C2.03c 1.14
1.51E-
05
SPAC343.0
7 0.80 1.77E-03
SPBPB2
B2.06c 1.93
9.87
E-04
SPAC3A
12.06c 1.14
2.93E-
07
SPBP8B7.3
0c 0.80 3.90E-05
SPAC3
C7.13c 1.92
3.23
E-10
SPBC32
H8.13c 1.14
6.14E-
06
SPCC737.0
3c 0.80 3.26E-04

SPBC24
C6.06 1.13
2.19E-
04
SPBC21H7
.06c 0.80 2.18E-02

208

Appendix B: Creation of Histone H4 K5R K8R K12R mutant plasmid

B.1 Purpose: To study the affect of Histone H4 acetylation at lysine 5, 8 and 12 I created
a plasmid with residues mutated to arginine.
B.2 Histone H4 KR mutant construction: Genomic DNA was isolated from WT (261)
cells and had hhf2 cloned out using primers 1335 and 1336. The PCR product was
purified using Qiagen PCR purification kit and then transformed into vector using topo
cloning kit (Invitrogen). Using Phusion site-directed- mutagenesis kit (Finnzymes)
mutations at lysines 5, 8 and 12 were introduced using PCR with primers 1406 and 1407,
and transformed into e. coli. Isolates were sequenced using standard M13 primers.
Plasmsid is pRLN101 #1588 in plasmid collection.

209

Figure B.1 H4K5R K8R K12R plasmid (pRLN101). A. Topo cloning vector
(Invitrogen). B. PCR product inserted.

h4.2
*
R R R
5' 3'
-300bp +250
A.
B

210

Figure B.2 Sequence alignment of wild-type histone H4 and h4kr mutant

Table B.1 Primers used in Appendix B:
Oligo number Sequence
1406 /5’phos/ gcg ctt acg acc acc cct tcc caa tcc tgt acc acc tct tcc acg acc aga cat
1407 /5’phos/ cat cgt aag atc ctt cgt gat aac att caa ggt att act aag cct gcc att cgt cg
1335 ctt tcc acg tcg ggt gtg ga
1336 cag agc tta ctc cca gag taa gtc aga cac

CLUSTAL 2.0.12 multiple sequence alignment
H4KR AGCTCGGATCCNCTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTCTTTCCACGTCG 60
hhf2 ------------------------------------------------------------

H4KR GGTGTGGACACTTCCTGCTATATATACCTCAGTCAATCACAACCCTAACCCTGATTTAAG 120
hhf2 ------------------------------------------------------------

H4KR ATTGCGATTTCGGCTTCCCCGCTACCTGAAAAAATGTATATATATATGGAGATGGACGCC 180
hhf2 ------------------------------------------------------------

H4KR TAACTACAGCACTTACACAGTAACTACTACGACTAGTACGAGAAGCCATTGAAATTCAAA 240
hhf2 ------------------------------------------------------------

H4KR TCATAGGAATTTCAGTGTTTGCGCTTGAAAATTAGTTTTTGATATTGTAAATTGATCAAT 300
hhf2 ------------------------------------------------------------

H4KR TGGTAGTCAGTTTGTTTGAACTTACAGGAATCCCATTACTCATATAAGATGTCTGGTCGT 360
hhf2 ------------------------------------------------ATGTCTGGTCGT 12
************
H4KR GGAAGAGGTGGTAGAGGATTGGGAAGGGGTGGTGCTAAGCGCCATCGTAAGATCCTTCGT 420
hhf2 GGAAAAGGTGGTAAAGGATTGGGAAAGGGTGGTGCTAAGCGCCATCGTAAGATCCTTCGT 72
**** ******** *********** **********************************
H4KR GATAACATTCAAGGTATTACTAAGCCTGCCATTCGTCGTCTTGCTCGTCGTGGCGGTGTT 480
hhf2 GATAACATTCAAGGTATTACTAAGCCTGCCATTCGTCGTCTTGCTCGTCGTGGCGGTGTT 132
************************************************************
H4KR AAGCGTATTTCTGCTTTGGTTTACGAAGAGACTCGTGCCGTTCTCAAGCTTTTCTTGGAA 540
hhf2 AAGCGTATTTCTGCTTTGGTTTACGAAGAGACTCGTGCCGTTCTCAAGCTTTTCTTGGAA 192
************************************************************
H4KR AACGTTATCCGTGATGCAGTTACCTACACTGAACACGCCAAGCGTAAGACTGTCACTTCC 600
hhf2 AACGTTATCCGTGATGCAGTTACCTACACTGAACACGCCAAGCGTAAGACTGTCACTTCC 252
************************************************************
H4KR TTGGACGTTGTCTACTCTTTGAAGCGTCAAGGCCGTACCATTTATGGTTTCGGTGGTTAA 660
hhf2 TTGGACGTTGTCTACTCTTTGAAGCGTCAAGGCCGTACCATTTATGGTTTCGGTGGTTAA 312
************************************************************
H4KR ACTGGTTGCACACTTTTCGATATTGAAGTGAATTGTATTTTCTTTTTCTTTTTTTCCTAC 720
hhf2 ------------------------------------------------------------

H4KR TTTGCATATTAATAGTTGTTTCTCTTTTTATCTTTACTCATTTCTCTTTTANTATCCATT 780
hhf2 ------------------------------------------------------------

H4KR CAATGANTATTTATTTGCACGAAATGGNTGGTTTTCCTTGAANAAATGCNATTTTATTGA 840
hhf2 ------------------------------------------------------------

Abstract (if available)

Abstract Within the cell DNA exists as chromatin, a complex mass of nucleic acids and proteins. Chromatin is highly structured and is compacted through the interaction of double stranded DNA with histone proteins, to form a nucleosome. Histones are post- translationally modified on the amino acids of their N-terminal tails to create a heritable epigenetic code. Histone acetylation regulates the interaction between DNA and histones in nucleosomes. Histone acetyltransferases are the enzymes that transfer acetyl groups on to histones.

Linked assets

University of Southern California Dissertations and Theses

Conceptually similar

PDF

KAT5 acetyltransferase in DNA damage repair in Schizosaccharomyces pombe

PDF

Investigating the role of ploidy on genome stability in fission yeast

PDF

Identification and characterization of PR-Set7 and histone H4 lysine 20 methylation-associated proteins

PDF

The intra-S phase checkpoint and its effect on replication fork dynamics in saccharomyces cerevisiae

PDF

Essential and non-essential helicases maintain genome stability in Schizosaccharomyces pombe

PDF

New tools for whole-genome analysis of DNA replication timing and fork elongation in saccharomyces cerevisiae

PDF

The role of histone H4 lysine 20 monomethylation in gene expression and differentiation

PDF

The function of Rpd3 in balancing the replicaton initiation of different genomic regions

PDF

C. elegans topoisomerase II regulates chromatin architecture and DNA damage for germline genome activation

PDF

Biochemical mechanism of TopBP1 recruitment to sites of DNA damage

Asset Metadata

Creator Nugent, Rebecca Lynn (author)

Core Title The S. pombe Mst1 histone acetyltransferase is required for genome stability

School College of Letters, Arts and Sciences

Degree Doctor of Philosophy

Degree Program Molecular Biology

Publication Date 08/09/2010

Defense Date 06/16/2010

Publisher University of Southern California (original), University of Southern California. Libraries (digital)

Tag centromere,chromatin,DNA damage repair,fission yeast,genome stability,histone acetyltransferase,Mst1,MYST,OAI-PMH Harvest,Transcription

Language English

Contributor Electronically uploaded by the author (provenance)

Advisor Forsburg, Susan L. (committee chair), Aparicio, Oscar Martin (committee member), Rice, Judd C. (committee member)

Creator Email rebanug@gmail.com,rnugent@usc.edu

Permanent Link (DOI) https://doi.org/10.25549/usctheses-m3355

Unique identifier UC1481629

Identifier etd-Nugent-3942 (filename),usctheses-m40 (legacy collection record id),usctheses-c127-380147 (legacy record id),usctheses-m3355 (legacy record id)

Legacy Identifier etd-Nugent-3942.pdf

Dmrecord 380147

Document Type Dissertation

Rights Nugent, Rebecca Lynn

Type texts

Source University of Southern California (contributing entity), University of Southern California Dissertations and Theses (collection)

Repository Name Libraries, University of Southern California

Repository Location Los Angeles, California

Repository Email cisadmin@lib.usc.edu