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

Last Reviewed on: 2006-08-11    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
transcription coactivator activity	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-08	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:UME6 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
double-strand break repair via nonhomologous end joining	IMP: Inferred from Mutant Phenotype Assigned on 2005-02-24	Jazayeri A, et al.  (2004) Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair. Proc Natl Acad Sci U S A 101(6):1644-9	SGD
histone deacetylation	IMP: Inferred from Mutant Phenotype Assigned on 2011-07-20	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
	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-11	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
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
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
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
	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 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
negative regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-11	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	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-11	Bernstein BE, et al.  (2000) Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci U S A 97(25):13708-13	SGD
positive regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-11	De Nadal E, et al.  (2004) The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature 427(6972):370-4	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-11	Bernstein BE, et al.  (2000) Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci U S A 97(25):13708-13	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
regulation of DNA-dependent DNA replication initiation	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
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

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
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

** 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.

Biological Process | Cellular Component

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
cell cycle	IEA: Inferred from Electronic Annotation with EBI:KW-0131 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
cell division	IEA: Inferred from Electronic Annotation with EBI:KW-0132 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
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
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:IPR003822 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	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
nucleus	IEA: Inferred from Electronic Annotation with EBI:IPR003822 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	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)).