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

Last Reviewed on: 2009-07-10    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin binding	IDA: Inferred from Direct Assay Assigned on 2009-05-15	Kanta H, et al.  (2006) Suppressor analysis of a histone defect identifies a new function for the hda1 complex in chromosome segregation. Genetics 173(1):435-50	SGD
contributes_to histone deacetylase activity	IDA: Inferred from Direct Assay Assigned on 2009-07-10	Lee JH, et al.  (2009) Structural and Functional Studies of the Yeast Class II Hda1 Histone Deacetylase Complex. J Mol Biol 391(4):744-57	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
gene silencing by RNA	IMP: Inferred from Mutant Phenotype Assigned on 2008-01-08	Camblong J, et al.  (2007) Antisense RNA Stabilization Induces Transcriptional Gene Silencing via Histone Deacetylation in S. cerevisiae. Cell 131(4):706-17	SGD
gene silencing involved in chronological cell aging	IGI: Inferred from Genetic Interaction with SGD:RRP6 Assigned on 2009-09-23 IMP: Inferred from Mutant Phenotype Assigned on 2009-09-23	Camblong J, et al.  (2007) Antisense RNA Stabilization Induces Transcriptional Gene Silencing via Histone Deacetylation in S. cerevisiae. Cell 131(4):706-17	SGD
histone deacetylation	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15 IDA: Inferred from Direct Assay Assigned on 2009-05-15	Wu J, et al.  (2001) HDA2 and HDA3 are related proteins that interact with and are essential for the activity of the yeast histone deacetylase HDA1. Proc Natl Acad Sci U S A 98(8):4391-6	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	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 involved in replicative cell aging	IGI: Inferred from Genetic Interaction with SGD:SIR3 Assigned on 2009-05-15 IMP: Inferred from Mutant Phenotype Assigned on 2003-08-20	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 transcription by transcription factor localization	IGI: Inferred from Genetic Interaction with SGD:RPD3 Assigned on 2009-05-15	Tachibana C, et al.  (2007) A poised initiation complex is activated by SNF1. J Biol Chem 282(52):37308-15	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
	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	Wu J, et al.  (2001) TUP1 utilizes histone H3/H2B-specific HDA1 deacetylase to repress gene activity in yeast. Mol Cell 7(1):117-26	SGD
positive regulation of transcription from RNA polymerase II promoter	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
regulation of chromatin silencing at telomere	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-15	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
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

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
HDA1 complex	IDA: Inferred from Direct Assay Assigned on 2009-07-22 IPI: Inferred from Physical Interaction with SGD:HDA3 Assigned on 2009-07-22	Wu J, et al.  (2001) HDA2 and HDA3 are related proteins that interact with and are essential for the activity of the yeast histone deacetylase HDA1. Proc Natl Acad Sci U S A 98(8):4391-6	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-07-22	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
	IDA: Inferred from Direct Assay Assigned on 2009-07-22	Carmen AA, et al.  (1996) HDA1 and HDA3 are components of a yeast histone deacetylase (HDA) complex. J Biol Chem 271(26):15837-44	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.

There are no High-throughput annotations for HDA1

** 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 (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 H3 deacetylation	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.	GOC
histone H4 deacetylation	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.	GOC
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)).