This page displays GO annotations in different sections according to the annotation method used to add that annotation to SGD.

Last Reviewed on: 2010-07-20    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
histone deacetylase activity	IMP: Inferred from Mutant Phenotype Assigned on 2009-09-14	Rundlett SE, et al.  (1998) Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392(6678):831-5	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2001-01-18	Rundlett SE, et al.  (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A 93(25):14503-8	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-09-14 IDA: Inferred from Direct Assay Assigned on 2009-09-14	Adachi N, et al.  (2002) A conserved motif common to the histone acetyltransferase Esa1 and the histone deacetylase Rpd3. J Biol Chem 277(38):35688-95	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-09-14	Kadosh D and Struhl K  (1998) Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes Dev 12(6):797-805	SGD
transcription coactivator activity	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-08 IPI: Inferred from Physical Interaction with SGD:HMF1 Assigned on 2010-05-24	De Nadal E, et al.  (2004) The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature 427(6972):370-4	SGD
transcription corepressor activity	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-08 IPI: Inferred from Physical Interaction with SGD:SIN3 Assigned on 2009-09-14	Kadosh D and Struhl K  (1997) Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89(3):365-71	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
histone H3 deacetylation	IMP: Inferred from Mutant Phenotype Assigned on 2010-05-24	Rundlett SE, et al.  (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A 93(25):14503-8	SGD
histone H4 deacetylation	IMP: Inferred from Mutant Phenotype Assigned on 2010-05-24	Rundlett SE, et al.  (1998) Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392(6678):831-5	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-05-24	Rundlett SE, et al.  (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A 93(25):14503-8	SGD
negative regulation of chromatin silencing at rDNA	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-20	Sun ZW and Hampsey M  (1999) A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152(3):921-32	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-20	Smith JS, et al.  (1999) A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 19(4):3184-97	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-20	Kim S, et al.  (1999) Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol Biol Cell 10(10):3125-36	SGD
negative regulation of chromatin silencing at silent mating-type cassette	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-20	Sun ZW and Hampsey M  (1999) A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152(3):921-32	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-20	Kim S, et al.  (1999) Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol Biol Cell 10(10):3125-36	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-20	Zhou J, et al.  (2009) Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res 37(11):3699-713	SGD
negative regulation of chromatin silencing at telomere	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Sun ZW and Hampsey M  (1999) A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152(3):921-32	SGD
	IDA: Inferred from Direct Assay Assigned on 2011-07-20	Ehrentraut S, et al.  (2010) Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate. Proc Natl Acad Sci U S A 107(12):5522-7	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Kim S, et al.  (1999) Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol Biol Cell 10(10):3125-36	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Zhou J, et al.  (2009) Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res 37(11):3699-713	SGD
negative regulation of reciprocal meiotic recombination	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Merker JD, et al.  (2008) The histone methylase Set2p and the histone deacetylase Rpd3p repress meiotic recombination at the HIS4 meiotic recombination hotspot in Saccharomyces cerevisiae. DNA Repair (Amst) 7(8):1298-308	SGD
negative regulation of transcription during meiosis	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Inai T, et al.  (2007) Interplay between chromatin and trans-acting factors on the IME2 promoter upon induction of the gene at the onset of meiosis. Mol Cell Biol 27(4):1254-63	SGD
negative regulation of transcription from RNA polymerase I promoter	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Hontz RD, et al.  (2009) Genetic Identification of Factors That Modulate Ribosomal DNA Transcription in Saccharomyces cerevisiae. Genetics 182(1):105-19	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Tsang CK, et al.  (2003) Chromatin-mediated regulation of nucleolar structure and RNA Pol I localization by TOR. EMBO J 22(22):6045-56	SGD
negative regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Agricola E, et al.  (2006) H4 acetylation does not replace H3 acetylation in chromatin remodelling and transcription activation of Adr1-dependent genes. Mol Microbiol 62(5):1433-46	SGD
	IGI: Inferred from Genetic Interaction with SGD:HOS2, SGD:HOS1 Assigned on 2010-07-12 IPI: Inferred from Physical Interaction with SGD:CYC8 Assigned on 2010-07-12	Watson AD, et al.  (2000) Ssn6-Tup1 interacts with class I histone deacetylases required for repression. Genes Dev 14(21):2737-44	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Schroder M, et al.  (2004) The unfolded protein response represses differentiation through the RPD3-SIN3 histone deacetylase. EMBO J 23(11):2281-92	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-07-20	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	SGD
positive regulation of macroautophagy	IMP: Inferred from Mutant Phenotype Assigned on 2013-03-05	Yi C, et al.  (2012) Function and molecular mechanism of acetylation in autophagy regulation. Science 336(6080):474-7	SGD
positive regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Zhang Z and Reese JC  (2004) Redundant mechanisms are used by Ssn6-Tup1 in repressing chromosomal gene transcription in Saccharomyces cerevisiae. J Biol Chem 279(38):39240-50	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	Xin X, et al.  (2007) Regulation of the HAP1 gene involves positive actions of histone deacetylases. Biochem Biophys Res Commun 362(1):120-5	SGD
	IGI: Inferred from Genetic Interaction with SGD:HOS2 Assigned on 2010-07-12 IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Sharma VM, et al.  (2007) Histone deacetylases RPD3 and HOS2 regulate the transcriptional activation of DNA damage-inducible genes. Mol Cell Biol 27(8):3199-210	SGD
	IGI: Inferred from Genetic Interaction with SGD:MOT3 Assigned on 2010-07-12 IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	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	SGD
positive regulation of transcription from RNA polymerase II promoter in response to heat stress	IMP: Inferred from Mutant Phenotype Assigned on 2012-01-25	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	SGD
protein localization to nucleolar rDNA repeats	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Tsang CK, et al.  (2007) Nutrient starvation promotes condensin loading to maintain rDNA stability. EMBO J 26(2):448-58	SGD
regulation of DNA-dependent DNA replication initiation	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Vogelauer M, et al.  (2002) Histone acetylation regulates the time of replication origin firing. Mol Cell 10(5):1223-33	SGD
	IGI: Inferred from Genetic Interaction with SGD:CLB5 Assigned on 2010-07-12 IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Aparicio JG, et al.  (2004) The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol 24(11):4769-80	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-13	Knott SR, et al.  (2009) Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. Genes Dev 23(9):1077-90	SGD
regulation of transcription by chromatin organization	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	Verdone L, et al.  (2002) Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. EMBO J 21(5):1101-11	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Kadosh D and Struhl K  (1998) Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol Cell Biol 18(9):5121-7	SGD
regulation of transcription involved in G1/S phase of mitotic cell cycle	IGI: Inferred from Genetic Interaction with SGD:HOS3, SGD:CLN3 Assigned on 2009-10-19 IPI: Inferred from Physical Interaction with SGD:WHI5 Assigned on 2010-07-12	Huang D, et al.  (2009) Dual regulation by pairs of cyclin-dependent protein kinases and histone deacetylases controls G1 transcription in budding yeast. PLoS Biol 7(9):e1000188	SGD
regulation of transcription involved in G2/M-phase of mitotic cell cycle	IGI: Inferred from Genetic Interaction with SGD:NDD1 Assigned on 2010-07-12	Veis J, et al.  (2007) Activation of the G2/M-Specific Gene CLB2 Requires Multiple Cell Cycle Signals. Mol Cell Biol 27(23):8364-8373	SGD
regulation of transcription involved in S phase of mitotic cell cycle	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Nishizawa M, et al.  (2008) Transcriptional repression by the Pho4 transcription factor controls the timing of SNZ1 expression. Eukaryot Cell 7(6):949-57	SGD
replicative cell aging	IMP: Inferred from Mutant Phenotype Assigned on 2010-07-12	Kim S, et al.  (1999) Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Mol Biol Cell 10(10):3125-36	SGD
transcription elongation from RNA polymerase II promoter	IGI: Inferred from Genetic Interaction with SGD:SPT5 Assigned on 2010-07-13	Quan TK and Hartzog GA  (2010) Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4-Spt5 in Transcription. Genetics 184(2):321-34	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
histone deacetylase complex	IDA: Inferred from Direct Assay Assigned on 2001-01-18	Rundlett SE, et al.  (1996) HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A 93(25):14503-8	SGD
Rpd3L complex	IDA: Inferred from Direct Assay Assigned on 2007-01-04	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	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-05-20	Keogh MC, et al.  (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-05-18	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	SGD
Rpd3S complex	IDA: Inferred from Direct Assay Assigned on 2007-01-04	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	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-05-20	Keogh MC, et al.  (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605	SGD
Sin3-type complex	IDA: Inferred from Direct Assay Assigned on 2009-07-22	Kasten MM, et al.  (1997) A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators. Mol Cell Biol 17(8):4852-8	SGD

* Manually curated GO annotations reflect our best understanding of the basic molecular function, biological process, and cellular component for this gene product. Manually curated annotations are assigned by SGD curators based on published papers when available, or by curatorial statements if necessary. Curators periodically review all Manually curated GO annotations for accuracy and completeness. The "Last Reviewed on:" date at the top of this section indicates when these annotations were last reviewed.

Cellular Component

High-throughput Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
Rpd3L complex	IDA: Inferred from Direct Assay Assigned on 2009-01-08	Shevchenko A, et al.  (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9(11):R167	SGD
Rpd3L-Expanded complex	IDA: Inferred from Direct Assay Assigned on 2009-01-08	Shevchenko A, et al.  (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9(11):R167	SGD
Snt2C complex	IDA: Inferred from Direct Assay Assigned on 2009-01-08	Shevchenko A, et al.  (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9(11):R167	SGD

** GO annotations from High-throughput experiments are made based on a variety of large scale high-throughput experiments, including genome-wide experiments. Many of these annotations are made based on GO annotations (or mappings to GO annotations) assigned by the authors, rather than SGD curators. While SGD curators read these publications and often work closely with authors to incorporate the information, each individual annotation may not necessarily be reviewed by a curator. GO Annotations from high-throughput experiments will be assigned only when this type of data is available, and thus may not be assigned in all three aspects of the Gene Ontologies.

Molecular Function | Biological Process | Cellular Component

Computational Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
histone deacetylase activity	IEA: Inferred from Electronic Annotation with EBI:IPR003084 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
histone deacetylase activity (H3-K14 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
histone deacetylase activity (H3-K9 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
histone deacetylase activity (H4-K16 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
hydrolase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0378 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
NAD-dependent histone deacetylase activity (H3-K14 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
NAD-dependent histone deacetylase activity (H3-K18 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
NAD-dependent histone deacetylase activity (H3-K9 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
NAD-dependent histone deacetylase activity (H4-K16 specific)	IEA: Inferred from Electronic Annotation with IUBMB:3.5.1.98 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin modification	IEA: Inferred from Electronic Annotation with EBI:KW-0156 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
histone deacetylation	IEA: Inferred from Electronic Annotation with EBI:IPR003084 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0805 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:KW-0804 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

Computational Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
cytoplasm	IEA: Inferred from Electronic Annotation with EBI:SL-0086 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
	IEA: Inferred from Electronic Annotation with EBI:KW-0963 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleus	IEA: Inferred from Electronic Annotation with EBI:SL-0191 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
	IEA: Inferred from Electronic Annotation with EBI:KW-0539 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

*** Computational GO Annotations are predictions. These annotations are NOT reviewed by a curator. Currently, all computational GO annotations for S. cerevisiae are assigned by an external source (for example, the Gene Ontology Annotation (GOA) project of the European Bioinformatics Institute (EBI)).