Supplementary Table 1: List of ChrI fragment variants identified in various environments at different time points, coordinates and
putative causative genes within the fragment and their functions
Fragment
(Coordinates
in bp)
Conditions (time in
brackets)
F7
(31,798 36,798)
YP Ethanol (48 h),
YPD + 1M NaCl (72
h)
F8
(36,799 41,799)
F12
(56,803 61,803)
YP Galactose
(72 h),
YPD + 1M Sorbitol
(24 h),
YPD + 6 mM H2O2
(72 h)
YPD + 0.05% SDS
(48 h)
Genomic
Coordinate
of gene (in
bp)
31,567 32,940
33,448 34,701
35,155 36,303
36,509 37,147
Genes in
fragment
Functions of the gene
GDH3
NADP(+)-dependent glutamate dehydrogenase
BDH2
Putative medium-chain alcohol dehydrogenase with similarity to BDH1
BDH1
NAD-dependent (R,R)-butanediol dehydrogenase
ECM1
Protein involved in mitochondrial function or organization
37,464 38,972
39,259 41,901
57,385 57,029
57,518 57,850
57,796 57,488
61,052 -
CNE1
Calnexin; integral membrane ER chaperone involved in folding and
quality control of glycoproteins
Multistep regulator of cAMP-PKA signaling; inhibits PKA downstream
of Gpa2p and Cyr1p
Protein involved in mitochondrial function or organization
GPB2
AIM1
YAL044W-A Putative protein of unknown function
YAL045C
Dubious open reading frame
PTA1
Subunit of holo-CPF, a multi protein complex and functional homolog of
58,695
F13
(61,804 66,804)
mammalian CPSF, required for the cleavage and polyadenylation of
mRNA and snoRNA 3' ends
Protein localized to COPII-coated vesicles; involved in the membrane
fusion stage of transport
61,316 62,563
ERV46
62,840 65,404
CDC24
67,520 65,778
87,286 87,752
92,270 87,855
99,697 95,630
99,305 99,868
101,145 00,225
105,872 101,565
CLN3
Guanine nucleotide exchange factor for Cdc42p, required for polarity
establishment and maintenance, and mutants have morphological defects
in bud formation and shmooing
G1 cyclin involved in cell cycle progression
SNC1
Vesicle membrane receptor protein (v-SNARE)
MYO4
Type V myosin motor involved in actin-based transport of cargos
DRS2
Trans-golgi network aminophospholipid translocase (flippase)
HRA1
Non-protein-coding RNA
MAK16
LTE1
Constituent of 66S pre-ribosomal particles; required for maturation of
25S and 5.8S rRNAs
Protein similar to GDP/GTP exchange factors; equired for asymmetric
localization of Bfa1p at daughter-directed spindle pole bodies and for
mitotic exit at low temperatures
108,551 106,272
PMT2
protein O-mannosyltransferase of the ER membrane
YP Galactose (72 h)
F18
(86,809 91,809)
YP Ethanol (24 h, 48
h)
F20
(96,811 10,1811)
YP Galactose (48 h,
72 h),
YP Fructose (48 h,72
h)
F21
(101,812 106,812)
YP Maltose (24 h, 48
h)
F22
(106,813 -
YP Maltose (24 h, 48
h, 72 h)
111,812)
F23
(111,814 116,814)
F24
(116,815 121,815)
F25
(121,816 126,817)
F26
(126,817 131,817)
YP Galactose (24 h,
48 h, 72 h),
YPD + 1M NaCl (72
h)
YP Maltose (24 h, 48
h, 72 h),
YP Galactose (24 h,
48 h, 72 h),
YP Ethanol (24 h,48
h,72 h)
YP Maltose (24 h, 48
h),
YPD + 4NQO (48 h)
YP Maltose (72 h),
YP Galactose (24 h,
48 h)
YP Galactose (72 h)
110,430 108,877
113,359 110,846
114,615 113,614
114,919 118,314
FUN26
Vacuolar membrane transporter with broad nucleoside selectivity
CCR4
Component of the major cytoplasmic deadenylase, CCR4-NOT
transcriptional complex
Protein required for modification of wobble nucleosides in tRNA
ATS1
FUN30
Snf2p family member with ATP-dependent chromatin remodeling
activity; has a role in silencing at the mating type locus, telomeres and
centromeres
119,541 118,564
120,225 124,295
LDS1
Protein involved in spore wall assembly
PSK1
PAS domain-containing serine/threonine protein kinase , co-ordinately
regulates protein synthesis and carbohydrate metabolism and storage in
response to a unknown metabolite that reflects nutritional status
124,492 124,307
125,069 124,755
124,879 126,786
128,102 126,903
129,019 128,252
129,270 -
YAL016C-B
Dubious open reading frame
YAL016C-A
Dubious open reading frame
TPD3
NTG1
Regulatory subunit A of the heterotrimeric PP2A complex; equired for
cell morphogenesis and transcription by RNA polymerase III
DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase
SYN8
Endosomal SNARE related to mammalian syntaxin 8
DEP1
Component of the Rpd3L histone deacetylase complex; required for
F31
(152,257 157,257)
F32
(157,258 162,258)
F34
(167,260 172,260)
YP Ethanol (24 h, 48
h)
130,487
130,799 131,983
152,257 153,876
154,724 154,065
155,005 156,285
CYS3
diauxic shift-induced histone H2B deposition onto rDNA genes
Cystathionine gamma-lyase
NUP60
FG-nucleoporin component of central core of the nuclear pore complex
ERP1
Member of the p24 family involved in ER to Golgi transport
SWD1
Subunit of the COMPASS (Set1C) complex; COMPASS methylates
histone H3 on lysine 4 and is required in transcriptional silencing near
telomeres
Subunit of heterotrimeric Replication Protein A (RPA) which is a highly
conserved single-stranded DNA binding protein involved in DNA
replication, repair, and recombination
158,619 156,754
RFA1
158,966 159,793
164,187 160,597
166,162 160,238
168,871 166,742
169,375 170,295
171,703 170,396
175,135 172,211
SEN34
Subunit of the tRNA splicing endonuclease;
YAR009C
Retrotransposon TYA Gag and TYB Pol genes
YARCTy1-1
Ty1 element
BUD14
Protein involved in bud-site selection
ADE1
Required for de novo purine nucleotide biosynthesis
KIN3
Nonessential serine/threonine protein kinase
CDC12
Protein kinase of the Mitotic Exit Network
YP Galactose (72 h)
YP Dextrose (72 h)