Supporting Information

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1 Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mm HU and incubated at 30 C or 37 C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5 end of genes. Vertical bars represent the binding ratio of proteins in each locus. The binding of Arp6-Flag (Top), Swr1-Flag (middle), and Arp6-Flag in swr1 cells (bottom) in the region 228K-244K of Chr 6R were compared. The orientation of transcription of the genes of Watson strand and Crick strand in the region was shown by arrows in the map over the panels. Regions of divergent promoters are indicated with gray shadow. Figure S7. Correlation of the localizations of Arp6 and Swr1. The Arp6-binding log2 ratios of Arp6-binding loci (change p- value <0.025) in wild-type (A) and in swr1 cells (B) are represented as scatterplots versus the Swr1 binding log2 ratio in each Arp6 binding locus of wild-type cells. The yellow lines represent the hypothetical pattern of the data if Arp6 and Swr1 bind equally on the chromosomes. Figure S8. ChIP analysis for Htz1 in cells lacking Arp6 or Swr1. Htz1 association to the promoter of GAL1, SWR1, and ribosomal protein (RPL13A and RPS16B) genes was analyzed using ChIP with an anti-htz1 antibody (abcam, ab4626) and quantified using real-time quantitative PCR in wild-type (WT), arp6, and swr1 cells. The values are indicated as percentage of input DNA obtained by ChIP with anti-htz1 antibody. The data points represent the mean ± SD for at least three independent experiments. Figure S9. Quantitative analysis of RDS1 (YCR106W) and UBX3 (YDL091C) in arp6- and htz1-deletion mutants. The same amount of total RNA from wild-type, arp6, and htz1 cells was analyzed using real-time quantitative RT PCR. The ACT1 gene was analyzed as a control. The relative amount of the transcript of the genes to ACT1 is shown. The data points represent the mean ± SD for at least three independent experiments. Figure S10. ChIP analysis for nuclear pore complex with GAL1 gene in arp6 cells. The association of GAL1 gene with NPC was analyzed using ChIP with an antibody against nuclear pore complex proteins (Mab414, abcam, ab24609) in wild-type (WT) and arp6 cells grown on the glucose- or galactose containing media. Immunoprecipitated DNA was quantified using real-time PCR probed for GAL1 gene. The percentage of recovered DNA over input is plotted relative to wild-type cells on glucose as 1. The data points represent the mean ± SD for at least three independent experiments.

2 Table S1. Presence of Arp6 in nonrepetitive 10 kb subtelomere zones. (0.05 MB DOC) Table S2. Microarray analysis in arp6δ and swr1δ cells. (1.10 MB XLS) Table S3. Binding of Arp6 and Swr1 on ribosomal protein genes. (0.04 MB DOC) Table S4. Expression of RP genes in arp6δ and swr1δ cells. (0.04 MB XLS) Table S5. Genes markedly down-regulated in arp6 cells. (0.09 MB DOC) Table S6. Strains used in this study. (0.06 MB DOC) Text S1. Primer sequences. (0.04 MB DOC)

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6 SWR1 Arp6 Swr1 Arp6 in swr1 Yoshida et al., Supplementary Fig. S3B

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8 Arp6 Swr1 Arp6 in swr1 Yoshida et al., Supplementary Fig. S5

9 A 4 Arp6 (log2) r =0.278, n= Swr1 (log2) B 4 Arp6 in swr1 (log2) r =0.138, n= Swr1 (log2) Yoshida et al., Supplementary Fig. S6

10 ChIP analysis for Htz1 in arp6 and swr1 mutants % precipitated by anti-htz1 / input WT arp6 swr1 0 GAL1 SWR1 RPL13A RPS16B Yoshida et al. Supplementary Fig. S7

11 Quantitative rtpcr for Arp6/Swr1-bound genes (x10-3 ) Relative expression to ACT WT arp6 htz1 0 RDS1 UBX3 Yoshida et al., Supplementary Fig. S8

12 ChIP for GAL1-nuclear pore association 2.0 WT arp6 p<0.05 % (IP/ input) / WT gluc glucose galactose Yoshida et al., Supplementary Fig. S9

13 Supplementary Table S1. Presence of Arp6 in nonrepetitive 10 kb subtelomere zones Chr3L (32) 1) Chr3R (34) Chr4L (4) Chr4R (13) Chr5L (15) Chr5R (13) Chr6R (34) Total (145) SWR1 Arp6 binding loci coincidence with Swr1 binding 1 2) (3%) 3) 3 (9%) 0 (0%) 3 (9%) 1 (25%) 1 (8%) 0 (0%) 0 (0%) 3 (20%) 0 (0%) 2 (13%) 0 (0%) 7 (21%) 16 (11%) 2 (6%) 7 (5%) swr1 Arp6 binding loci 3 (9%) 4 (12%) 0 (0%) 5 (38%) 0 (0%) 1 (8%) 9 (26%) 22 (15%) 1) number of subtelomeric probes in the array, 2) number of probes on which the ChIP-chip signal is significantly positive, 3) percentage of binding-positive probes

14 SupplemantaTable S2 arp6 log2 ratio arp6 t-test p-value swr1 log2 ratio swr1 t-test p-value YAL001C TFC3 transcription factor tau (TFIIIC) subunit 138 YAL002W VPS8 Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif. YAL003W EFB1 Translation elongation factor EF-1beta, GDP/GTP exchange factor for Tef1p/Tef2p YAL004W strong similarity to A.klebsiana glutamate dehydrogenase YAL007C ERP2 p24 protein involved in membrane trafficking YAL008W FUN14 hypothetical protein YAL009W SPO7 sporulation protein YAL010C MDM10 Mitochondrial outer membrane protein involved in mitochondrial morphology and inheritance YAL011W possible mitochondrial transit peptide/weak similarity to Mus musculus p53-associated cellular protein YAL012W CYS3 cystathionine gamma-lyase YAL013W DEP1 regulation of phospholipid metabolism YAL014C hypothetical protein YAL015C NTG1 DNA glycosylase YAL016W TPD3 protein phosphatase 2A regulatory subunit A YAL017W FUN31 Serine/threonine kinase YAL018C transmembrane domains/weak similarity to hypothetical proteins YOL047c and YOL048c YAL019W FUN30 SNF2 protein family YAL021C CCR4 95 kda containng leucine rich tandem repeats YAL022C FUN26 predicted membrane protein YAL023C PMT2 dolichyl phosphate-d-mannose:protein O-D-mannosyltransferase YAL024C LTE1 putative GTP-exchange protein YAL025C MAK16 putative nuclear protein YAL026C DRS2 Membrane-spanning Ca-ATPase (P-type),member of the cation transport (E1-E2) ATPases YAL027W hypothetical protein YAL028W similarity to hypothetical protein YOR324c YAL029C MYO4 myosin YAL030W SNC1 homolog of Snc2p, vesicle-associated membrane protein (synaptobrevin) homolog, forms a complex with Snc2p and Sec9p YAL031C FUN21 FUN21 YAL032C PRP45 pre-mrna splicing factor YAL033W POP5 An integral subunit of RNase P and apparent subunit of RNase MRP YAL034C FUN19 Function unknown now YAL034W-A MTW1 determining metaphase spindle length YAL035C-A YAL035W FUN12 97 kda protein YAL036C FUN11 similar to Xenopus GTP-binding protein DRG YAL037W strong similarity to GTP-binding proteins YAL038W CDC19 Pyruvate kinase YAL039C CYC3 cytochrome c heme lyase (CCHL) YAL040C CLN3 G(sub)1 cyclin YAL041W CDC24 Guanine nucleotide exchange factor (a.k.a. GDP-release factor) for cdc42 YAL042W ERV46 ER-Golgi transport vesicle protein YAL043C PTA1 pre-trna processing YAL043C-A YAL044C GCV3 H-protein subunit of the glycine cleavage system YAL045C hypothetical protein YAL047C SPC72 component of spindle pole bodies YAL048C PEP4 vacuolar aspartic proteasse YAL049C weak similarity to Legionella small basic protein sbpa YAL053W strong similarity to hypothetical proteins YOR365c,YGL139w,YPL221w YAL054C ACS1 inducible acetyl-coenzyme A synthetase YAL055W PEX22 peroxisomal matrix protein import YAL058C-A YAL058W CNE1 Calnexin and calreticulin homolog YAL059W ECM1 putative transmembrane domain protein involved in cell wall biogenesis YAL060W FUN49 stereospecific (2R, 3R)-2,3-butanediol dehydrogenase YAL061W FUN50 similarity to alcohol/sorbitol dehydrogenase YAL062W GDH3 NADP-linked glutamate dehydrogenase YAL064C-A strong similarity to Flo1p, Flo5p - putative pseudogene YAL064W hypothetical protein YAL065C strong similarity to Flo1p and Flo9p - putative pseudogene YAL066W weak similarity to membrane protein yybf - Bacillus subtilis YAL067C SEO1 putative permease/suppressor of Sulfoxyde Ethionine resistance YAL069W YAR002C-A ERP1 p24 protein involved in membrane trafficking YAR002W NUP60 nuclear pore protein YAR003W FUN16 beta transducin domain/similarity to human RB protein binding protein YAR007C RFA1 69 kda subunit of the heterotrimeric RPA (RF-A) single-stranded DNA binding protein, binds URS1 and CAR1 YAR008W SEN34 34kDa subunit of the tetrameric trna splicing endonuclease YAR009C TY1B Ty1B protein YAR010C TY1A TY1A protein YAR014C BUD14 maximal growth/similarity to hypothetical protein S.pombe YAR015W ADE1 phosphoribosyl amino imidazolesuccinocarbozamide synthetase YAR018C KIN3 protein kinase YAR019C CDC15 protein kinase domain YAR020C PAU7 similar to Pau3, member of Pau1 family YAR023C membrane protein YAR027W FUN55 membrane protein/strong similarity to YAR028w, YCR007c, YGL053w, YAR031w, FUN59p and YGL051w YAR028W membrane protein/strong similarity to Fun55p, YGL053w, YCR007c, YAR031w, Fun59p and YGL051w YAR030C hypothetical protein YAR031W PRM9 membrane protein/strong similarity to YGL053w, Fun59p, YGL051w, Fun55p, YAR028w and YCR007c YAR033W FUN59 membrane protein/strong similarity to YGL051w, YGL053w, YAR031w, Fun55p, YAR028w and YCR007c YAR035W YAT1 Outer carnitine acetyltransferase, mitochondrial YAR042W SWH1 ankyrin repeat YAR044W OSH1 Shows homology to the human oxysterol binding protein (OSBP) YAR047C predicted nuclear targeting signal YAR053W predicted membrane protein YAR060C strong similarity to hypothetical protein YHR212c YAR061W E strong similarity to N-terminus of Flo1p - putative pseudogene

15 YAR062W strong similarity to Flo1p - putative pseudogene YAR064W Potential membrane protein YAR066W identical to YHR214w hypothetical protein, similarity to Sta1p YAR068W Potential membrane protein YAR069C Potential membrane protein YAR070C potential mitochondrial transit peptide YAR071W PHO11 Acid phosphatase, secreted YAR073W IMD1 IMP dehydrogenase homolog YAR075W strong similarity to IMP dehydrogenases YBL001C ECM15 involved in cell wall biogenesis YBL002W HTB2 Histone H2B (HTB1 and HTB2 code for nearly identical proteins) YBL005W-A TyA gag protein. Gag processing produces capsid proteins. YBL005W-B The TyB Gag-Pol protein. Gag processing produces capsid proteins. Pol is cleaved to produce protease, reverse transcriptase, and integrase activities. YBL007C SLA1 contains 3 SH3 domains, interacts with Bee1p YBL008W HIR1 putative repressor protein homologous to yeast Tup1p and mammalian retinal transducin ; contains nuclear targeting signal YBL009W strong similarity to DNA damage responsive Alk1p YBL011W SCT1 suppressor of choline-transport mutants YBL012C questionable ORF YBL013W FMT1 Methionyl-tRNA Transformylase YBL014C RRN6 member of yeast Pol I core factor (CF) also composed of Rrn11p, Rrn7p and TATA-binding protein YBL015W ACH1 acetyl CoA hydrolase YBL016W FUS3 cdc2+ /CDC28 related kinase with positive role in conjugation YBL017C PEP1 carboxypeptidase Y sorting receptor in late Golgi ; Type I integral membrane protein 166aa cytoplasmic tail, 1300 aa lumenal domain YBL018C POP8 integral subunit of RNase P and apparent subunit of RNase MRP YBL019W APN2 AP endonuclease YBL020W RFT1 67 kda integral membrane protein YBL021C HAP3 transcriptional activator protein of CYC1 YBL022C PIM1 mitochondrial ATP-dependent protease YBL023C MCM2 Minichromosome maintenance protein, transcription factor YBL024W NCL1 Probable proliferating-cell nucleolar antigen (human p120) YBL025W RRN10 Upstream activation factor subunit YBL026W LSM2 snrna-associated protein of the Sm class YBL027W RPL19B Ribosomal protein L19B (YL14) (L23B) (rpl5l) YBL028C hypothetical protein - involved in mating-type regulation YBL029W hypothetical protein YBL030C PET9 mitochondrial ADP /ATP translocator YBL031W SHE1 hypothetical protein YBL032W weak similarity to hnrnp complex protein homolog YBR233w YBL033C RIB1 GTP cyclohydrolase II YBL034C STU1 component of the mitotic spindle YBL035C POL12 B subunit of DNA polymerase alpha-primase complex YBL036C Homolog to twitching motility protein (P. aeroginosa) YBL037W APL3 Large subunit of clathrin associated protein complex YBL038W MRPL16 Mitochondrial ribosomal protein MRPL16 YBL039C URA7 CTP synthase, highly homologus to URA8 CTP synthase YBL040C ERD2 encodes the HDEL receptor required for retention of ER proteins YBL041W PRE7 proteasome subunit YBL042C FUI1 uridine permease YBL043W ECM13 (putative) involved in cell wall biogenesis YBL044W hypothetical protein YBL045C COR1 44 kda core protein of yeast coenzyme QH2 cytochrome c reductase YBL046W weak similarity to hypothetical protein YOR054c YBL048W hypothetical protein YBL049W strong similarity to hypothetical protein - human YBL050W SEC17 peripheral membrane protein required for vesicular transport between ER and Golgi YBL051C E-05 hypothetical protein YBL052C SAS3 involved in silencing at HMR YBL053W questionable ORF YBL054W Homolog to myb transforming proteins YBL055C similarity to hypothetical S.pombe protein YBL056W PTC3 protein phosphatase type 2C YBL057C strong similarity to hypothetical S.pombe protein YBL058W SHP1 putative regulatory subunit for Glc7p, a phosphatase required for glucose repression YBL059W weak similarity to hypothetical protein YER093c-a YBL060W has homology to the sec7 domain of gtp exchange factors YBL061C SKT5 Probable Ca++ binding membrane protein (prenylated) YBL062W questionable ORF YBL063W KIP1 kinesin related protein YBL064C similar to thiol-specific antioxidant enzymes such as rehydrin /peroxiredoxin YBL065W questionable ORF YBL066C SEF1 putative transcription factor YBL067C UBP13 ubiquitin carboxyl-terminal hydrolase YBL068W PRS4 ribose-phosphate pyrophosphokinase 4 YBL069W AST1 involved in targeting of plasma membrane [H+]ATPase YBL070C questionable ORF YBL071C hypothetical protein YBL072C RPS8A Ribosomal protein S8A (S14A) (rp19) (YS9) YBL073W questionable ORF YBL074C AAR2 MATa1-mRNA splicing factor YBL075C SSA3 heat-inducible cytosolic member of the 70 kda heat shock protein family YBL076C ILS1 cytoplasmic isoleucyl-trna synthetase YBL077W questionable ORF YBL078C AUT7 Aut7p has homology to LC3, a microtubule-associated protein from rat. YBL079W NUP170 Nucleoporin highly similar to Nup157p and to mammalian Nup155p (nup170 mutant can be complemented with NUP155) YBL080C PET kDa protein YBL081W hypothetical protein YBL082C RHK1 putative Dol-P-Man dependent alpha(1-3) mannosyltransferase involved in the biosynthesis of the lipid-linked oligosaccharide YBL083C questionable ORF YBL085W BOI1 BEM1-binding protein YBL086C involved in sugar metabolism YBL087C RPL23A Ribosomal protein L23A (L17aA) (YL32) YBL089W similar to amino acid transport proteins

16 YBL090W MRP21 Component of the small subunit of mitochondrial ribosomes YBL091C MAP2 methionine aminopeptidase 2 YBL092W RPL32 Ribosomal protein L32 YBL093C ROX3 RNA polymerase II holoenzyme /mediator subunit YBL094C questionable ORF YBL095W similarity to C.albicans hypothetical protein YBL096C questionable ORF YBL097W BRN1 involved in chromosome maintenance ; similar to Drosophila barren, Xenopus XCAP-H, and human BRRN1 YBL098W similar to kynurenine 3-monoxygenase YBL099W ATP1 mitochondrial F1F0-ATPase alpha subunit YBL100C YBL101C ECM21 involved in cell wall biogenesis YBL101W-A TyA gag protein. Gag processing produces capsid proteins. YBL102W SFT2 similar to mammalian syntaxin 5 YBL103C RTG3 Probable cytochrome c subunit, copper binding YBL104C weak similarity to S.pombe hypothetical protein SPAC12G12.01c YBL105C PKC1 Protein Kinase C YBL106C SRO77 yeast homolog of the Drosphila tumor suppressor, lethal giant larvae YBL107C hypothetical protein YBL111C strong similarity to subtelomeric encoded proteins YBL112C strong similarity to subtelomeric encoded proteins YBR001C NTH2 Neutral trehalase, highly homologous to Nth1p YBR002C RER2 cis-prenyltransferase YBR003W COQ1 hexaprenyl pyrophosphate synthetase YBR004C similarity to S.pombe hypothetical protein SPAC18B11.05 YBR005W strong similarity to hypothetical protein YDR003w YBR006W UGA2 succinate semialdehyde dehydrogenase YBR007C hypothetical protein YBR008C FLR1 Major Facilitator Transporter YBR009C HHF1 Histone H4 (HHF1 and HHF2 code for identical proteins) YBR010W HHT1 Histone H3 (HHT1 and HHT2 code for identical proteins) YBR011C IPP1 Inorganic pyrophosphatase YBR012C hypothetical protein YBR012W-A TyA gag protein. Gag processing produces capsid proteins. YBR012W-B The TyB Gag-Pol protein. Gag processing produces capsid proteins. Pol is cleaved to produce protease, reverse transcriptase, and integrase activities. YBR013C hypothetical protein YBR014C Glutaredoxin homolog YBR015C MNN2 putative Golgi alpha-1,2-mannosyltransferase YBR016W strong similarity to hypothetical proteins YDL012c and YDR210w YBR017C KAP104 karyopherin beta 2, yeast transportin YBR018C GAL7 galactose-1-phosphate uridyl transferase YBR019C GAL10 UDP-glucose 4-epimerase YBR020W GAL1 galactokinase YBR021W FUR4 uracil permease YBR022W hypothetical protein YBR023C CHS3 chitin synthase 3 YBR024W SCO2 SCO1 protein homolog (S. cerevisiae) YBR025C probable purine nucleotide-binding protein YBR026C MRF1' Nuclear protein that binds to T-rich strand of core consensus sequence of autonomously replicating sequence YBR027C hypothetical protein YBR028C Probable ser /thr-specific protein kinase, homolog to YKR2 and YPK1 (S. cerevisiae) YBR029C CDS1 CDP-diacylglycerol synthase, CTP-phosphatidic acid cytidylyltransferase, CDP-diglyceride synthetase YBR030W involved in inositol biosynthesis YBR031W RPL4A Ribosomal protein L4A (L2A) (rp2) (YL2) YBR032W hypothetical protein YBR033W Probable regulatory Zn-finger protein, / homolog to YKL251 / YBR034C HMT1 nuclear protein arginine methyltransferase (mono- and asymmetrically dimethylating enzyme) YBR035C PDX3 pyridoxine (pyridoxiamine) phosphate oxidase YBR036C CSG2 contains 9 or 10 putative membrane spanning regions ; putative Ca2+ binding protein (homology to EF-hand Ca2+ binding site) YBR037C SCO1 inner mitochondrial membrane protein YBR038W CHS2 chitin synthase 2 YBR039W ATP3 gamma subunit of mitochondrial ATP synthase YBR040W FIG1 integral membrane protein YBR041W FAT1 Fatty acid transporter YBR042C Probable membrane-bound small GTPase YBR043C similarity to benomyl/methotrexate resistance protein YBR044C TCM62 mitochondrial protein ; (putative) chaperone YBR045C GIP1 putative Glc7 regulatory subunit YBR046C ZTA1 Homolog to quinone oxidoreductase (E. coli) YBR047W hypothetical protein YBR048W RPS11B Ribosomal protein S11B (S18B) (rp41b) (YS12) YBR050C REG2 putative Glc7 regulatory subunit YBR051W questionable ORF YBR052C Homolog to YCR004, obr1 (S. pombe), trp repressor binding protein (E. coli) YBR053C YBR054W YRO2 Homolog to HSP30 heat shock protein YRO1 (S. cerevisiae) 7 YBR055C PRP6 RNA splicing factor YBR056W Homolog to glucan-1,3--glucosidase (EC ; S. cerevisiae) 2 YBR057C MUM2 similar to ubiquitin C-terminal hydrolase, involved in meiosis YBR058C UBP14 Ubiquitin-specific protease YBR058C-A TSC3 involved in sphingolipid biosynthesis YBR059C AKL1 Serine-threonine protein kinase YBR060C ORC2 origin recognition complex subunit 2 YBR061C Homolog to ftsj protein (E. coli), / YCR054 / YBR062C similarity to rat neurodegeneration associated protein 1 YBR063C Probable phosphopanthethein-binding protein YBR064W questionable ORF YBR065C ECM2 (putative) involved in cell wall biogenesis and mrna splicing YBR066C NRG2 homologue of NRG1 YBR067C TIP1 cell wall mannoprotein YBR068C BAP2 probable amino acid permease for leucine, valine, and isoleucine YBR069C TAT1 Amino acid transport protein for valine, leucine, isoleucine, and tyrosine

17 YBR070C involved in osmotolerance YBR071W hypothetical protein YBR072W E HSP26 heat shock protein 26 YBR073W RDH54 Putative helicase similar to RAD54 YBR074W Homolog to aminopeptidase Y (S. cerevisiae) YBR075W hypothetical protein YBR076W ECM8 involved in cell wall biogenesis YBR077C hypothetical protein YBR078W ECM33 Homolog to sporulation specific protein SPS2 (S. cerevisiae) YBR079C RPG1 translation initiation factor eif3 YBR080C SEC18 cytoplasmic protein involved in protein transport between ER and Golgi ; ATPase YBR081C SPT7 transcription factor, member of the histone acetyltransferase SAGA complex YBR082C UBC4 ubiquitin-conjugating enzyme YBR083W TEC1 transcription factor of the TEA /ATTS DNA-binding domain family, regulator of Ty1 expression YBR084C-A RPL19A Ribosomal protein L19A (L23A) (rpl5l) (YL14) YBR084W MIS1 mitochondrial C1-tetrahydroflate synthase YBR085C-A YBR085W AAC3 mitochondrial ADP /ATP translocator YBR086C IST2 Probable transmembrane protein YBR087W RFC5 Subunit 5 of Replication Factor C ; homologous to human RFC 38 kda subunit YBR088C POL30 Proliferating cell nuclear antigen YBR089C-A NHP6B 11-kDa nonhistone chromosomal protein YBR089W questionable ORF YBR090C-A NHP6B 11-kDa nonhistone chromosomal protein YBR091C MRS5 Nuclear protein involved in mitochondrial intron splicing YBR092C PHO3 Acid phosphatase, constitutive YBR093C PHO5 Acid phosphatase, repressible YBR094W weak similarity to pig tubulin-tyrosine ligase YBR095C hypothetical protein YBR096W hypothetical protein YBR097W VPS15 Myristoylated Serine /threonine protein kinase involved in vacuolar protein sorting YBR098W MMS4 putative transcriptional (co)activator for DNA damage YBR099C weak similarity to T.brucei mitochondrion hypothetical protein 6 YBR100W questionable ORF YBR101C weak similarity to S.pombe hypothetical protein SPBC3B9.01 YBR102C EXO84 Component of the exocyst complex ; homolog in rat brain called rexo84. YBR103W SIF2 535 amino acid protein containing 4 WD-40 repeats and a nuclear localization signal YBR104W YMC2 mitochondrial carrier protein YBR105C VID24 peripheral vesicle membrane protein YBR106W PHO88 regulator of Pho81, involved in regulating phosphate transport YBR107C IML3 weakly similar to chitin synthases, involved in chromosomal segregation and mitosis YBR108W Probable transcription factor YBR109C CMD1 Calmodulin YBR110W ALG1 beta-1,4-mannosyltransferase YBR111C YSA1 Homolog to serendipity protein (D. melanogaster) YBR112C CYC8 Transcription regulatory protein YBR113W questionable ORF YBR114W RAD16 Radiation repair protein, putative DNA helicase YBR115C LYS2 alpha aminoadipate reductase YBR116C questionable ORF YBR117C TKL2 transketolase, homologous to tkl1 YBR118W TEF2 translational elongation factor EF-1 alpha YBR119W MUD1 U1 snrnp A protein YBR120C CBP6 Translational activator of COB mrna YBR121C GRS1 Glycyl-tRNA synthase YBR122C MRPL36 Mitochondrial ribosomal protein MRPL36 (YmL36) YBR123C TFC1 transcription factor tau (TFIIIC) subunit 95 YBR124W questionable ORF YBR125C PTC4 Type 2C protein phosphatase YBR126C TPS1 56 kd synthase subunit of trehalose-6-phosphate synthase /phosphatase complex YBR127C VMA2 vacuolar ATPase V1 domain subunit B (60 kda) YBR128C APG14 involved in autophagy YBR129C OPY1 involved in mating pathway YBR130C SHE3 involved in cell polarity YBR131W CCZ1 involved in sporulation, caffeine, calcium, and zinc sensitivity YBR132C AGP2 Amino acid permease YBR133C HSL7 regulator of Swe1p kinase YBR134W questionable ORF YBR135W CKS1 subunit of the Cdc28 protein kinase YBR137W hypothetical protein YBR138C HDR1 High-Dosage Reductional segregation defective YBR139W Probable serine-type carboxypeptidase (EC ) YBR141C hypothetical protein YBR142W MAK5 Probable pre-mrna splicing RNA-helicase YBR143C SUP45 Homolog of erf1 (eukaryotic Release Factor 1) in other metazoans. YBR144C hypothetical protein YBR145W ADH5 alcohol dehydrogenase isoenzyme V YBR146W MRPS9 Probable mitochondrial ribosomal protein S9 YBR147W strong similarity to hypothetical protein YOL092w YBR148W YSW1 Spore-specific protein YBR149W ARA1 D-arabinose dehydrogenase YBR150C TBS1 Probable Zn-finger protein YBR151W APD1 Actin Patches Distal YBR152W SPP381 U4 /U6.U5-associated snrnp protein ; contains a PEST proteolysis motif YBR153W RIB7 Riboflavin biosynthesis protein YBR154C RPB5 25-kDa RNA polymerase subunit (common to polymerases I, II and III) YBR155W CNS1 component of Hsp90p chaperone machinery YBR156C SLI15 Mitotic spindle protein involved in chromosome segregation. YBR157C ICS2 Increased Copper Sensitivity YBR158W CST13 Chromosome STability protein YBR159W similarity to human 17-beta-hydroxysteroid dehydrogenase YBR160W CDC28 protein kinase catalytic subunit YBR161W Homolog to suppressor of reduced viability of starvation (SUR1, S. cerevisiae)

18 YBR162C TOS1 similarity to hypothetical protein YJL171c YBR162W-A YSY6 involved in the secretory pathway YBR163W DEM1 Weak similarity to Pta1p (pre-trna processing protein) YBR164C ARL1 ADP-ribosylation factor-like protein 1 YBR165W UBS1 positive regulator of CDC34, involved in ubiquitin-mediated degradation YBR166C TYR1 Prephenate dehydrogenase (NADP+) YBR167C POP7 Pop7 protein, an integral subunit of RNase P and apparent subunit of RNase MRP YBR168W weak similarity to hypothetical protein YLR324w YBR169C SSE2 HSP70 family member, highly homologous to Sse1p YBR170C NPL4 Suppressor of SEC63 (S.cerevisiae), novel ER translocation component YBR171W SEC66 glycoprotein complexed with Sec62p and Sec63p in the Sec63 complex, an integral endoplasmic reticulum membrane protein complex required for translocation of presecretory proteins YBR172C SMY2 Kinesin-related protein suppressing myosin defects (MYO2) YBR173C UMP1 20S proteasome maturation factor YBR174C weak similarity to hypothetical protein YLR324w YBR175W Probable GTP-binding protein YBR176W ECM31 Alpha-Ketoisovalerate Hydroxymethyltransferase YBR177C EHT1 alcohol acyl transferase YBR178W questionable ORF YBR179C FZO1 homolog of Drosophila melanogaster fuzzy onions gene ; integral protein of the mitochondrial outer membrane which can be isolated as part of a high molecular weight complex YBR180W DTR1 dityrosine transporter MFS-MDR YBR181C RPS6B 40S ribosomal gene product S6B (S10B) (rp9) (YS4) YBR182C SMP1 Probable DNA-binding transcription factor, Homolog to SRF /SL-2 YBR183W YPC1 alkaline ceramidase with reverse activity YBR184W MEL1 alpha-galactosidase YBR185C MBA1 involved in assembly of mitochondrial respiratory complexes YBR186W PCH2 Putative ATPase YBR187W probable membrane protein YBR188C NTC20 splicing factor YBR189W RPS9B Ribosomal protein S9B (S13) (rp21) (YS11) YBR190W questionable ORF YBR191W RPL21A Ribosomal protein L21A YBR192W RIM2 Probable carrier protein, mitochondrial YBR193C MED8 Stoichiometric member of mediator complex YBR194W hypothetical protein YBR195C MSI1 p50 subunit of the yeast omatin Assembly Factor-I (CAF-I) negative regulator of ras-mediated camp induction ; homologous to beta subunit of GTP-binding proteins YBR196C PGI1 Glucose-6-phosphate isomerase YBR197C YBR198C TAF90 Probable transcription-associated factor protein, probable -transducin type YBR200W BEM1 contains two SH3 domains YBR201W DER1 involved in degradation in the ER YBR203W hypothetical protein YBR204C Probable serine-active lipase, peroxisomal (EX ) YBR205W KTR3 Putative alpha-1,2-mannosyltransferase YBR206W questionable ORF YBR207W FTH1 probable membrane protein YBR208C DUR1,2 Urea amidolyase (contains urea carboxylase and allophanate hydrolase) YBR209W hypothetical protein YBR210W strong similarity to D.melanogaster cornichon protein YBR211C AME1 regulator of microtubule stability YBR212W NGR1 negative growth regulatory protein YBR213W MET8 Effector in the expression of PAPS reductase and sulfite reductase YBR214W SDS24 nuclear protein similar to pombe sds23 YBR215W HPC2 highly charged, basic protein YBR216C strong similarity to hypothetical protein YGL060w YBR217W APG12 involved in autophagy YBR218C PYC2 pyruvate carboxylase YBR219C YBR220C similarity to human acetyl-coenzyme A transporter YBR221C PDB1 beta subunit of pyruvate dehydrogenase (E1 beta) YBR222C FAT2 Probable AMP-binding protein YBR223C hypothetical protein YBR224W questionable ORF YBR225W hypothetical protein YBR226C questionable ORF YBR227C MCX1 Mitochondrial ATP-binding protein, similar to ClpX YBR228W similarity to hypothetical A.thaliana protein YBR229C ROT2 Glucosidase II YBR230C hypothetical protein YBR231C AOR1 Actin Overexpression Resistant YBR232C questionable ORF YBR233W PBP2 Homolog to human hnrnp complex K protein YBR234C ARC40 component of Arp2 /Arp3 protein complex YBR235W similarity to bumetanide-sensitive Na-K-Cl cotransport protein YBR236C ABD1 RNA (guanine-7-)methyltransferase (cap methyltransferase) YBR237W PRP5 RNA helicase homolog YBR238C strong similarity to general chromatin factor Spt16p YBR239C Probable Zn-finger protein YBR240C THI2 Probable Zn-finger protein YBR241C Probable sugar transport protein YBR242W Probable ATP /GTP-binding protein YBR243C ALG7 UDP-N-acetyl-glucosamine-1-P transferase (GPT) YBR244W GPX2 Probable glutathione peroxidase (EC ) YBR245C ISW1 ATPase component of a four subunit chromatin remodeling complex YBR246W hypothetical protein YBR247C ENP1 Putative 57 kda protein with an apparent MW of 70 kda by SDS-PAGE YBR248C HIS7 glutamine amidotransferase:cyclase, also called imidazole glycerol phosphate synthase YBR249C ARO4 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YBR250W hypothetical protein YBR251W MRPS5 Probable mitochondrial ribosomal protein S5 YBR252W DUT1 dutp pyrophosphatase (dutpase) YBR253W SRB6 transcription factor, part of Srb /Mediator complex