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

Last Reviewed on: 2002-08-20    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
contributes_to histone deacetylase activity	IMP: Inferred from Mutant Phenotype Assigned on 2006-08-08	Lechner T, et al.  (2000) Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3[middle dot]Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J Biol Chem 275(52):40961-6	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin silencing	IGI: Inferred from Genetic Interaction Assigned on 2002-08-20 IMP: Inferred from Mutant Phenotype Assigned on 2002-08-20	Lechner T, et al.  (2000) Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3[middle dot]Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J Biol Chem 275(52):40961-6	SGD
histone deacetylation	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
	IMP: Inferred from Mutant Phenotype Assigned on 2002-08-20 IPI: Inferred from Physical Interaction Assigned on 2002-08-20	Lechner T, et al.  (2000) Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3[middle dot]Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J Biol Chem 275(52):40961-6	SGD
negative regulation of chromatin silencing at rDNA	IMP: Inferred from Mutant Phenotype Assigned on 2011-07-20	Keogh MC, et al.  (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605	SGD
negative regulation of chromatin silencing at silent mating-type cassette	IMP: Inferred from Mutant Phenotype Assigned on 2011-07-20	Keogh MC, et al.  (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605	SGD
negative regulation of chromatin silencing at telomere	IMP: Inferred from Mutant Phenotype Assigned on 2011-07-20	Keogh MC, et al.  (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593-605	SGD
	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
positive regulation of transcription from RNA polymerase II promoter	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

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
Rpd3L complex	IDA: Inferred from Direct Assay 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
	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 2007-01-04	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

* 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
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: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: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)).