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UME1 / YPL139C Literature
All manually curated literature for the specified gene, organized by relevance to the gene and by
association with specific annotations to the gene in SGD. SGD gathers references via a PubMed search for
papers whose titles or abstracts contain “yeast” or “cerevisiae;” these papers are reviewed manually and
linked to relevant genes and literature topics by SGD curators.
- Unique References
- 159
- Aliases
-
WTM3
2
Primary Literature
Literature that either focuses on the gene or contains information about function, biological role,
cellular location, phenotype, regulation, structure, or disease homologs in other species for the gene
or gene product.
No primary literature curated.
Download References (.nbib)
- Wang C, et al. (2024) Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv 10(15):eadk7678 PMID:38598631
- Dong S, et al. (2023) Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res 33(10):790-801 PMID:37666978
- Markert JW, et al. (2023) Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex. Nat Commun 14(1):8128 PMID:38065958
- Patel AB, et al. (2023) Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Nat Commun 14(1):3061 PMID:37244892
- Camougrand N, et al. (2022) The Dep1 protein: A new regulator of mitophagy in yeast. Biochem Biophys Res Commun 635:218-226 PMID:36283334
- Tomimoto K, et al. (2019) Histone deacetylases in sake yeast affect fermentation characteristics. Biosci Biotechnol Biochem 83(8):1498-1505 PMID:30355069
- Ruan C, et al. (2016) Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex. J Biol Chem 291(10):5428-38 PMID:26747610
- Handfield LF, et al. (2015) Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images. Bioinformatics 31(6):940-7 PMID:25398614
- Tun NM, et al. (2014) Identification of aluminium transport-related genes via genome-wide phenotypic screening of Saccharomyces cerevisiae. Metallomics 6(8):1558-64 PMID:24926745
- Chen XF, et al. (2012) The Rpd3 core complex is a chromatin stabilization module. Curr Biol 22(1):56-63 PMID:22177115
- Ruiz-Roig C, et al. (2010) The Rpd3L HDAC complex is essential for the heat stress response in yeast. Mol Microbiol 76(4):1049-62 PMID:20398213
- Hontz RD, et al. (2009) Genetic identification of factors that modulate ribosomal DNA transcription in Saccharomyces cerevisiae. Genetics 182(1):105-19 PMID:19270272
- Jo WJ, et al. (2009) Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. BMC Genomics 10:130 PMID:19321002
- Sardiu ME, et al. (2009) Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One 4(10):e7310 PMID:19806189
- Yukawa M, et al. (2009) The Rpd3/HDAC complex is present at the URS1 cis-element with hyperacetylated histone H3. Biosci Biotechnol Biochem 73(2):378-84 PMID:19202282
- Zhou J, et al. (2009) Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res 37(11):3699-713 PMID:19372273
- Sertil O, et al. (2007) Direct role for the Rpd3 complex in transcriptional induction of the anaerobic DAN/TIR genes in yeast. Mol Cell Biol 27(6):2037-47 PMID:17210643
- Hancock LC, et al. (2006) Genomic analysis of the Opi- phenotype. Genetics 173(2):621-34 PMID:16582425
- Carrozza MJ, et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123(4):581-92 PMID:16286007
- Carrozza MJ, et al. (2005) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731(2):77-87; discussion 75-6 PMID:16314178
- Keogh MC, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605 PMID:16286008
- Mallory MJ and Strich R (2003) Ume1p represses meiotic gene transcription in Saccharomyces cerevisiae through interaction with the histone deacetylase Rpd3p. J Biol Chem 278(45):44727-34 PMID:12954623
- Kurdistani SK, et al. (2002) Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet 31(3):248-54 PMID:12089521
- Pemberton LF and Blobel G (1997) Characterization of the Wtm proteins, a novel family of Saccharomyces cerevisiae transcriptional modulators with roles in meiotic regulation and silencing. Mol Cell Biol 17(8):4830-41 PMID:9234739
- Strich R, et al. (1989) Identification of negative regulatory genes that govern the expression of early meiotic genes in yeast. Proc Natl Acad Sci U S A 86(24):10018-22 PMID:2690066
Related Literature
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Additional Literature
Papers that show experimental evidence for the gene or describe homologs in other species, but
for which the gene is not the paper’s principal focus.
No additional literature curated.
Download References (.nbib)
- Kumar A, et al. (2024) Dynamics of DNA damage-induced nuclear inclusions are regulated by SUMOylation of Btn2. Nat Commun 15(1):3215 PMID:38615096
- McLean S, et al. (2024) Molecular mechanisms of genotype-dependent lifespan variation mediated by caloric restriction: insight from wild yeast isolates. Front Aging 5:1408160 PMID:39055969
- Amoiradaki K, et al. (2021) The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. Int J Mol Sci 22(22) PMID:34830359
- Lanz MC, et al. (2021) In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep 22(2):e51121 PMID:33491328
- Lian J, et al. (2019) Multi-functional genome-wide CRISPR system for high throughput genotype-phenotype mapping. Nat Commun 10(1):5794 PMID:31857575
- Lee CH, et al. (2013) Chromatin remodelers fine-tune H3K36me-directed deacetylation of neighbor nucleosomes by Rpd3S. Mol Cell 52(2):255-63 PMID:24055344
- Gilmore JM, et al. (2012) Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses. Mol Cell Proteomics 11(4):M111.011544 PMID:22199229
- Grigat M, et al. (2012) Multiple histone deacetylases are recruited by corepressor Sin3 and contribute to gene repression mediated by Opi1 regulator of phospholipid biosynthesis in the yeast Saccharomyces cerevisiae. Mol Genet Genomics 287(6):461-72 PMID:22543816
- Milliman EJ, et al. (2012) Recruitment of Rpd3 to the telomere depends on the protein arginine methyltransferase Hmt1. PLoS One 7(8):e44656 PMID:22953000
- Sikorski TW, et al. (2012) Proteomic analysis demonstrates activator- and chromatin-specific recruitment to promoters. J Biol Chem 287(42):35397-35408 PMID:22902623
- Smolle M, et al. (2012) Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol 19(9):884-92 PMID:22922743
- Tao R, et al. (2011) Xbp1-mediated histone H4 deacetylation contributes to DNA double-strand break repair in yeast. Cell Res 21(11):1619-33 PMID:21467995
- Tauber E, et al. (2011) Functional gene expression profiling in yeast implicates translational dysfunction in mutant huntingtin toxicity. J Biol Chem 286(1):410-9 PMID:21044956
- Wang SS, et al. (2011) Histone H3 lysine 4 hypermethylation prevents aberrant nucleosome remodeling at the PHO5 promoter. Mol Cell Biol 31(15):3171-81 PMID:21646424
- Drouin S, et al. (2010) DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes. PLoS Genet 6(10):e1001173 PMID:21060864
- On T, et al. (2010) The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins 78(9):2075-89 PMID:20455264
- Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6:420 PMID:20959818
- Cheung V, et al. (2008) Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol 6(11):e277 PMID:18998772
- Giorgini F, et al. (2008) Histone deacetylase inhibition modulates kynurenine pathway activation in yeast, microglia, and mice expressing a mutant huntingtin fragment. J Biol Chem 283(12):7390-400 PMID:18079112
- Jani NM and Lopes JM (2008) Transcription regulation of the Saccharomyces cerevisiae PIS1 gene by inositol and the pleiotropic regulator, Ume6p. Mol Microbiol 70(6):1529-39 PMID:19019152
- Shevchenko A, et al. (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9(11):R167 PMID:19040720
- Freimoser FM, et al. (2006) Systematic screening of polyphosphate (poly P) levels in yeast mutant cells reveals strong interdependence with primary metabolism. Genome Biol 7(11):R109 PMID:17107617
- Guo X, et al. (2006) Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae. Bioinformatics 22(4):392-9 PMID:16339282
- Yu H and Gerstein M (2006) Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A 103(40):14724-31 PMID:17003135
- Ladurner AG, et al. (2003) Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol Cell 11(2):365-76 PMID:12620225
- Strich R, et al. (1994) UME6 is a key regulator of nitrogen repression and meiotic development. Genes Dev 8(7):796-810 PMID:7926768
Reviews
No reviews curated.
Download References (.nbib)
- Zhang X, et al. (2024) Research Progress on the Mechanism and Function of Histone Acetylation Regulating the Interaction between Pathogenic Fungi and Plant Hosts. J Fungi (Basel) 10(8) PMID:39194848
- Gastelum S, et al. (2023) Saccharomyces cerevisiae as a research tool for RNA-mediated human disease. Wiley Interdiscip Rev RNA e1814 PMID:37671427
- Huang C and Zhu B (2018) Roles of H3K36-specific histone methyltransferases in transcription: antagonizing silencing and safeguarding transcription fidelity. Biophys Rep 4(4):170-177 PMID:30310854
- McCauley BS and Dang W (2014) Histone methylation and aging: lessons learned from model systems. Biochim Biophys Acta 1839(12):1454-62 PMID:24859460
- Singh J (2014) Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 30:131-43 PMID:24794003
- Brückner S and Mösch HU (2012) Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae. FEMS Microbiol Rev 36(1):25-58 PMID:21521246
- Lahue RS and Frizzell A (2012) Histone deacetylase complexes as caretakers of genome stability. Epigenetics 7(8):806-10 PMID:22722985
- Morano KA, et al. (2012) The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics 190(4):1157-95 PMID:22209905
- Wagner EJ and Carpenter PB (2012) Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol 13(2):115-26 PMID:22266761
- Spain MM and Govind CK (2011) A role for phosphorylated Pol II CTD in modulating transcription coupled histone dynamics. Transcription 2(2):78-81 PMID:21468233
- Buratowski S and Kim T (2010) The role of cotranscriptional histone methylations. Cold Spring Harb Symp Quant Biol 75:95-102 PMID:21447819
- Lee JS and Shilatifard A (2007) A site to remember: H3K36 methylation a mark for histone deacetylation. Mutat Res 618(1-2):130-4 PMID:17346757
- Tabancay AP and Forsburg SL (2006) Eukaryotic DNA replication in a chromatin context. Curr Top Dev Biol 76:129-84 PMID:17118266
Gene Ontology Literature
Paper(s) associated with one or more GO (Gene Ontology) terms in SGD for the specified gene.
No gene ontology literature curated.
Download References (.nbib)
- Handfield LF, et al. (2015) Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images. Bioinformatics 31(6):940-7 PMID:25398614
- Ruiz-Roig C, et al. (2010) The Rpd3L HDAC complex is essential for the heat stress response in yeast. Mol Microbiol 76(4):1049-62 PMID:20398213
- Hontz RD, et al. (2009) Genetic identification of factors that modulate ribosomal DNA transcription in Saccharomyces cerevisiae. Genetics 182(1):105-19 PMID:19270272
- Shevchenko A, et al. (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9(11):R167 PMID:19040720
- Sertil O, et al. (2007) Direct role for the Rpd3 complex in transcriptional induction of the anaerobic DAN/TIR genes in yeast. Mol Cell Biol 27(6):2037-47 PMID:17210643
- Carrozza MJ, et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123(4):581-92 PMID:16286007
- Carrozza MJ, et al. (2005) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731(2):77-87; discussion 75-6 PMID:16314178
- Keogh MC, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605 PMID:16286008
- Pemberton LF and Blobel G (1997) Characterization of the Wtm proteins, a novel family of Saccharomyces cerevisiae transcriptional modulators with roles in meiotic regulation and silencing. Mol Cell Biol 17(8):4830-41 PMID:9234739
Phenotype Literature
Paper(s) associated with one or more pieces of classical phenotype evidence in SGD for the specified gene.
No phenotype literature curated.
Download References (.nbib)
- Camougrand N, et al. (2022) The Dep1 protein: A new regulator of mitophagy in yeast. Biochem Biophys Res Commun 635:218-226 PMID:36283334
- Amoiradaki K, et al. (2021) The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. Int J Mol Sci 22(22) PMID:34830359
- Zhao YY, et al. (2020) Genetic analysis of oxidative and endoplasmic reticulum stress responses induced by cobalt toxicity in budding yeast. Biochim Biophys Acta Gen Subj 1864(3):129516 PMID:31904504
- Jo WJ, et al. (2009) Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. BMC Genomics 10:130 PMID:19321002
- Hancock LC, et al. (2006) Genomic analysis of the Opi- phenotype. Genetics 173(2):621-34 PMID:16582425
Interaction Literature
Paper(s) associated with evidence supporting a physical or genetic interaction between the
specified gene and another gene in SGD. Currently, all interaction evidence is obtained from
BioGRID.
No interaction literature curated.
Download References (.nbib)
- Bertgen L, et al. (2024) Distinct types of intramitochondrial protein aggregates protect mitochondria against proteotoxic stress. Cell Rep 43(4):114018 PMID:38551959
- O'Brien MJ and Ansari A (2024) Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle. Biochim Biophys Acta Proteins Proteom 1872(1):140968 PMID:37863410
- Wang C, et al. (2024) Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv 10(15):eadk7678 PMID:38598631
- Carey SB, et al. (2023) A synthetic genetic array screen for interactions with the RNA helicase DED1 during cell stress in budding yeast. G3 (Bethesda) 13(1) PMID:36409020
- Caydasi AK, et al. (2023) SWR1 chromatin remodeling complex prevents mitotic slippage during spindle position checkpoint arrest. Mol Biol Cell 34(2):ar11 PMID:36542480
- Dong S, et al. (2023) Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex. Cell Res 33(10):790-801 PMID:37666978
- Guo Z, et al. (2023) Structure of a SIN3-HDAC complex from budding yeast. Nat Struct Mol Biol 30(6):753-760 PMID:37081318
- Litwin I, et al. (2023) ISW1a modulates cohesin distribution in centromeric and pericentromeric regions. Nucleic Acids Res 51(17):9101-9121 PMID:37486771
- Li X, et al. (2023) The TORC1 activates Rpd3L complex to deacetylate Ino80 and H2A.Z and repress autophagy. Sci Adv 9(10):eade8312 PMID:36888706
- Michaelis AC, et al. (2023) The social and structural architecture of the yeast protein interactome. Nature 624(7990):192-200 PMID:37968396
- Patel AB, et al. (2023) Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Nat Commun 14(1):3061 PMID:37244892
- Lamb NA, et al. (2022) Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes. Genetics 221(4) PMID:35686905
- Lehner MH, et al. (2022) Yeast Smy2 and its human homologs GIGYF1 and -2 regulate Cdc48/VCP function during transcription stress. Cell Rep 41(4):111536 PMID:36288698
- Lu PYT, et al. (2022) A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans. Genetics 222(3) PMID:36066422
- Mattingly M, et al. (2022) Mediator recruits the cohesin loader Scc2 to RNA Pol II-transcribed genes and promotes sister chromatid cohesion. Curr Biol 32(13):2884-2896.e6 PMID:35654035
- Leng H, et al. (2021) FACT interacts with Set3 HDAC and fine-tunes GAL1 transcription in response to environmental stimulation. Nucleic Acids Res 49(10):5502-5519 PMID:33963860
- Su XB, et al. (2021) SUMOylation stabilizes sister kinetochore biorientation to allow timely anaphase. J Cell Biol 220(7) PMID:33929514
- Gotor NL, et al. (2020) RNA-binding and prion domains: the Yin and Yang of phase separation. Nucleic Acids Res 48(17):9491-9504 PMID:32857852
- Gutierrez-Escribano P, et al. (2020) Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction. Mol Cell 80(6):1039-1054.e6 PMID:33301732
- Wilfling F, et al. (2020) A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits. Mol Cell 80(5):764-778.e7 PMID:33207182
- Bhalla P, et al. (2019) Interactome of the yeast RNA polymerase III transcription machinery constitutes several chromatin modifiers and regulators of the genes transcribed by RNA polymerase II. Gene 702:205-214 PMID:30593915
- Rössler I, et al. (2019) Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME. Nucleic Acids Res 47(13):6984-7002 PMID:31062022
- Miller JE, et al. (2018) Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4. G3 (Bethesda) 8(1):315-330 PMID:29158339
- Lapointe CP, et al. (2017) Architecture and dynamics of overlapped RNA regulatory networks. RNA 23(11):1636-1647 PMID:28768715
- Makrantoni V, et al. (2017) A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis. G3 (Bethesda) 7(9):3203-3215 PMID:28754723
- Shulist K, et al. (2017) Interrogation of γ-tubulin alleles using high-resolution fitness measurements reveals a distinct cytoplasmic function in spindle alignment. Sci Rep 7(1):11398 PMID:28900268
- Costanzo M, et al. (2016) A global genetic interaction network maps a wiring diagram of cellular function. Science 353(6306) PMID:27708008
- Lakshminarasimhan M, et al. (2016) Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components. Mol Cell Proteomics 15(3):960-74 PMID:26831523
- Ruan C, et al. (2016) Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex. J Biol Chem 291(10):5428-38 PMID:26747610
- Srivas R, et al. (2016) A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Mol Cell 63(3):514-25 PMID:27453043
- Steunou AL, et al. (2016) Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome. Mol Cell Biol 36(22):2768-2781 PMID:27550811
- Mattiazzi Ušaj M, et al. (2015) Yeast Saccharomyces cerevisiae adiponectin receptor homolog Izh2 is involved in the regulation of zinc, phospholipid and pH homeostasis. Metallomics 7(9):1338-51 PMID:26067383
- Elbaz-Alon Y, et al. (2014) A dynamic interface between vacuoles and mitochondria in yeast. Dev Cell 30(1):95-102 PMID:25026036
- Figley MD, et al. (2014) Profilin 1 associates with stress granules and ALS-linked mutations alter stress granule dynamics. J Neurosci 34(24):8083-97 PMID:24920614
- Kurat CF, et al. (2014) Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation. Proc Natl Acad Sci U S A 111(39):14124-9 PMID:25228766
- Aristizabal MJ, et al. (2013) High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8. PLoS Genet 9(8):e1003758 PMID:24009531
- Baker LA, et al. (2013) The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress. Mol Cell Biol 33(19):3735-48 PMID:23878396
- Van de Vosse DW, et al. (2013) A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell 152(5):969-83 PMID:23452847
- Willmund F, et al. (2013) The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis. Cell 152(1-2):196-209 PMID:23332755
- Chen XF, et al. (2012) The Rpd3 core complex is a chromatin stabilization module. Curr Biol 22(1):56-63 PMID:22177115
- Gilmore JM, et al. (2012) Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses. Mol Cell Proteomics 11(4):M111.011544 PMID:22199229
- Milliman EJ, et al. (2012) Recruitment of Rpd3 to the telomere depends on the protein arginine methyltransferase Hmt1. PLoS One 7(8):e44656 PMID:22953000
- Sharifpoor S, et al. (2012) Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res 22(4):791-801 PMID:22282571
- Smolle M, et al. (2012) Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol 19(9):884-92 PMID:22922743
- Addinall SG, et al. (2011) Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects. PLoS Genet 7(4):e1001362 PMID:21490951
- Boettner DR, et al. (2011) Clathrin light chain directs endocytosis by influencing the binding of the yeast Hip1R homologue, Sla2, to F-actin. Mol Biol Cell 22(19):3699-714 PMID:21849475
- Lee KK, et al. (2011) Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes. Mol Syst Biol 7:503 PMID:21734642
- Scherrer T, et al. (2011) Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins. Genome Biol 12(1):R3 PMID:21232131
- Tao R, et al. (2011) Xbp1-mediated histone H4 deacetylation contributes to DNA double-strand break repair in yeast. Cell Res 21(11):1619-33 PMID:21467995
- Zimmermann C, et al. (2011) A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 to cell cycle progression. Proc Natl Acad Sci U S A 108(46):18748-53 PMID:22042866
- Bandyopadhyay S, et al. (2010) Rewiring of genetic networks in response to DNA damage. Science 330(6009):1385-9 PMID:21127252
- Costanzo M, et al. (2010) The genetic landscape of a cell. Science 327(5964):425-31 PMID:20093466
- Libuda DE and Winston F (2010) Alterations in DNA replication and histone levels promote histone gene amplification in Saccharomyces cerevisiae. Genetics 184(4):985-97 PMID:20139344
- Vembar SS, et al. (2010) J domain co-chaperone specificity defines the role of BiP during protein translocation. J Biol Chem 285(29):22484-94 PMID:20430885
- Zheng J, et al. (2010) Epistatic relationships reveal the functional organization of yeast transcription factors. Mol Syst Biol 6:420 PMID:20959818
- Hannum G, et al. (2009) Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet 5(12):e1000782 PMID:20041197
- Lin YY, et al. (2009) Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136(6):1073-84 PMID:19303850
- Sardiu ME, et al. (2009) Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One 4(10):e7310 PMID:19806189
- Arnett DR, et al. (2008) A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Mol Cell Proteomics 7(11):2090-106 PMID:18596064
- Tarassov K, et al. (2008) An in vivo map of the yeast protein interactome. Science 320(5882):1465-70 PMID:18467557
- Collins SR, et al. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446(7137):806-10 PMID:17314980
- Florens L, et al. (2006) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40(4):303-11 PMID:17101441
- Gavin AC, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440(7084):631-6 PMID:16429126
- Hesselberth JR, et al. (2006) Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biol 7(4):R30 PMID:16606443
- Krogan NJ, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440(7084):637-43 PMID:16554755
- Carrozza MJ, et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123(4):581-92 PMID:16286007
- Carrozza MJ, et al. (2005) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731(2):77-87; discussion 75-6 PMID:16314178
- Keogh MC, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605 PMID:16286008
- Ptacek J, et al. (2005) Global analysis of protein phosphorylation in yeast. Nature 438(7068):679-84 PMID:16319894
- Ye P, et al. (2005) Gene function prediction from congruent synthetic lethal interactions in yeast. Mol Syst Biol 1:2005.0026 PMID:16729061
- Mallory MJ and Strich R (2003) Ume1p represses meiotic gene transcription in Saccharomyces cerevisiae through interaction with the histone deacetylase Rpd3p. J Biol Chem 278(45):44727-34 PMID:12954623
- Gavin AC, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415(6868):141-7 PMID:11805826
- Ho Y, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415(6868):180-3 PMID:11805837
- Kurdistani SK, et al. (2002) Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet 31(3):248-54 PMID:12089521
Regulation Literature
Paper(s) associated with one or more pieces of regulation evidence in SGD, as found on the
Regulation page.
No regulation literature curated.
Post-translational Modifications Literature
Paper(s) associated with one or more pieces of post-translational modifications evidence in SGD.
No post-translational modifications literature curated.
Download References (.nbib)
- Blaszczak E, et al. (2024) Dissecting Ubiquitylation and DNA Damage Response Pathways in the Yeast Saccharomyces cerevisiae Using a Proteome-Wide Approach. Mol Cell Proteomics 23(1):100695 PMID:38101750
- Leutert M, et al. (2023) The regulatory landscape of the yeast phosphoproteome. Nat Struct Mol Biol 30(11):1761-1773 PMID:37845410
- Lanz MC, et al. (2021) In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep 22(2):e51121 PMID:33491328
- Albuquerque CP, et al. (2008) A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 7(7):1389-96 PMID:18407956
High-Throughput Literature
Paper(s) associated with one or more pieces of high-throughput evidence in SGD.
No high-throughput literature curated.
Download References (.nbib)
- Li Q, et al. (2023) Genome-wide identification of resistance genes and cellular analysis of key gene knockout strain under 5-hydroxymethylfurfural stress in Saccharomyces cerevisiae. BMC Microbiol 23(1):382 PMID:38049732
- Chen X, et al. (2020) FMN reduces Amyloid-β toxicity in yeast by regulating redox status and cellular metabolism. Nat Commun 11(1):867 PMID:32054832
- Guan M, et al. (2020) Molecular fingerprints of conazoles via functional genomic profiling of Saccharomyces cerevisiae. Toxicol In Vitro 69:104998 PMID:32919014
- Helsen J, et al. (2020) Gene Loss Predictably Drives Evolutionary Adaptation. Mol Biol Evol 37(10):2989-3002 PMID:32658971
- Zhao YY, et al. (2020) Genetic analysis of oxidative and endoplasmic reticulum stress responses induced by cobalt toxicity in budding yeast. Biochim Biophys Acta Gen Subj 1864(3):129516 PMID:31904504
- Alfatah M, et al. (2019) Chemical-genetic interaction landscape of mono-(2-ethylhexyl)-phthalate using chemogenomic profiling in yeast. Chemosphere 228:219-231 PMID:31029968
- Campos SE, et al. (2018) Genomewide mechanisms of chronological longevity by dietary restriction in budding yeast. Aging Cell 17(3):e12749 PMID:29575540
- Fröhlich F, et al. (2015) The GARP complex is required for cellular sphingolipid homeostasis. Elife 4 PMID:26357016
- García R, et al. (2015) Genomic profiling of fungal cell wall-interfering compounds: identification of a common gene signature. BMC Genomics 16(1):683 PMID:26341223
- Garay E, et al. (2014) High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions. PLoS Genet 10(2):e1004168 PMID:24586198
- Gaupel AC, et al. (2014) High throughput screening identifies modulators of histone deacetylase inhibitors. BMC Genomics 15(1):528 PMID:24968945
- Hoepfner D, et al. (2014) High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions. Microbiol Res 169(2-3):107-20 PMID:24360837
- Ostrow AZ, et al. (2014) Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics. PLoS One 9(2):e87647 PMID:24504085
- VanderSluis B, et al. (2014) Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. Genome Biol 15(4):R64 PMID:24721214
- Michaillat L and Mayer A (2013) Identification of genes affecting vacuole membrane fragmentation in Saccharomyces cerevisiae. PLoS One 8(2):e54160 PMID:23383298
- Qian W, et al. (2012) The genomic landscape and evolutionary resolution of antagonistic pleiotropy in yeast. Cell Rep 2(5):1399-410 PMID:23103169
- Ratnakumar S, et al. (2011) Phenomic and transcriptomic analyses reveal that autophagy plays a major role in desiccation tolerance in Saccharomyces cerevisiae. Mol Biosyst 7(1):139-49 PMID:20963216
- Venters BJ, et al. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92 PMID:21329885
- Alamgir M, et al. (2010) Chemical-genetic profile analysis of five inhibitory compounds in yeast. BMC Chem Biol 10:6 PMID:20691087
- Kapitzky L, et al. (2010) Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. Mol Syst Biol 6:451 PMID:21179023
- Pan X, et al. (2010) Trivalent arsenic inhibits the functions of chaperonin complex. Genetics 186(2):725-34 PMID:20660648
- Ruiz-Roig C, et al. (2010) The Rpd3L HDAC complex is essential for the heat stress response in yeast. Mol Microbiol 76(4):1049-62 PMID:20398213
- Auesukaree C, et al. (2009) Genome-wide identification of genes involved in tolerance to various environmental stresses in Saccharomyces cerevisiae. J Appl Genet 50(3):301-10 PMID:19638689
- Jo WJ, et al. (2009) Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. BMC Genomics 10:130 PMID:19321002
- Breslow DK, et al. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods 5(8):711-8 PMID:18622397
- Sinha H, et al. (2008) Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics 180(3):1661-70 PMID:18780730
- Hu Z, et al. (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39(5):683-7 PMID:17417638
- Brown JA, et al. (2006) Global analysis of gene function in yeast by quantitative phenotypic profiling. Mol Syst Biol 2:2006.0001 PMID:16738548
- Freimoser FM, et al. (2006) Systematic screening of polyphosphate (poly P) levels in yeast mutant cells reveals strong interdependence with primary metabolism. Genome Biol 7(11):R109 PMID:17107617
- Dudley AM, et al. (2005) A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol 1:2005.0001 PMID:16729036
- Giorgini F, et al. (2005) A genomic screen in yeast implicates kynurenine 3-monooxygenase as a therapeutic target for Huntington disease. Nat Genet 37(5):526-31 PMID:15806102
- Xie MW, et al. (2005) Insights into TOR function and rapamycin response: chemical genomic profiling by using a high-density cell array method. Proc Natl Acad Sci U S A 102(20):7215-20 PMID:15883373
- Lum PY, et al. (2004) Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116(1):121-37 PMID:14718172
- Marston AL, et al. (2004) A genome-wide screen identifies genes required for centromeric cohesion. Science 303(5662):1367-70 PMID:14752166
- Enyenihi AH and Saunders WS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163(1):47-54 PMID:12586695
- Giaever G, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387-91 PMID:12140549
- Hanway D, et al. (2002) Previously uncharacterized genes in the UV- and MMS-induced DNA damage response in yeast. Proc Natl Acad Sci U S A 99(16):10605-10 PMID:12149442