SGD:DEP1

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Annotations

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	SGD_REF:S000113697 PMID:16314178^[1]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0003674	molecular function	SGD_REF:S000069584	ND: No biological Data available		F	From SGD
	GO:0005634	nucleus	SGD_REF:S000124038	IEA: Inferred from Electronic Annotation	SP_KW:KW-0539	C	From SGD
	GO:0005634	nucleus	SGD_REF:S000125578	IEA: Inferred from Electronic Annotation	SP_SL:SL-0191	C	From SGD
	GO:0005737	cytoplasm	SGD_REF:S000124038	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	From SGD
	GO:0005737	cytoplasm	SGD_REF:S000125578	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	From SGD
	GO:0006351	transcription, DNA-dependent	SGD_REF:S000124038	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	From SGD
	GO:0006355	regulation of transcription, DNA-dependent	SGD_REF:S000124038	IEA: Inferred from Electronic Annotation	SP_KW:KW-0805	P	From SGD
	GO:0006357	regulation of transcription from RNA polymerase II promoter	SGD_REF:S000055164 PMID:8056324^[2]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0006357	regulation of transcription from RNA polymerase II promoter	SGD_REF:S000145656 PMID:21646424^[3]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0006644	phospholipid metabolic process	SGD_REF:S000055164 PMID:8056324^[2]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0016568	chromatin modification	SGD_REF:S000124038	IEA: Inferred from Electronic Annotation	SP_KW:KW-0156	P	From SGD
	GO:0016575	histone deacetylation	SGD_REF:S000113697 PMID:16314178^[1]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0016575	histone deacetylation	SGD_REF:S000113735 PMID:16286007^[4]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0016575	histone deacetylation	SGD_REF:S000113736 PMID:16286008^[5]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0030174	regulation of DNA-dependent DNA replication initiation	SGD_REF:S000130224 PMID:19417103^[6]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0031939	negative regulation of chromatin silencing at telomere	SGD_REF:S000113697 PMID:16314178^[1]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0031939	negative regulation of chromatin silencing at telomere	SGD_REF:S000113736 PMID:16286008^[5]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0031939	negative regulation of chromatin silencing at telomere	SGD_REF:S000129959 PMID:19372273^[7]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0031939	negative regulation of chromatin silencing at telomere	SGD_REF:S000131064 PMID:19638198^[8]	IGI: Inferred from Genetic Interaction		P	From SGD
	GO:0031939	negative regulation of chromatin silencing at telomere	SGD_REF:S000131064 PMID:19638198^[8]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0031939	negative regulation of chromatin silencing at telomere	SGD_REF:S000133013 PMID:20133733^[9]	IDA: Inferred from Direct Assay		P	From SGD
	GO:0033698	Rpd3L complex	SGD_REF:S000113697 PMID:16314178^[1]	IDA: Inferred from Direct Assay		C	From SGD
	GO:0033698	Rpd3L complex	SGD_REF:S000113735 PMID:16286007^[4]	IDA: Inferred from Direct Assay		C	From SGD
	GO:0033698	Rpd3L complex	SGD_REF:S000113736 PMID:16286008^[5]	IDA: Inferred from Direct Assay		C	From SGD
	GO:0033698	Rpd3L complex	SGD_REF:S000128493 PMID:19040720^[10]	IDA: Inferred from Direct Assay		C	From SGD
	GO:0061186	negative regulation of chromatin silencing at silent mating-type cassette	SGD_REF:S000113736 PMID:16286008^[5]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0061188	negative regulation of chromatin silencing at rDNA	SGD_REF:S000113736 PMID:16286008^[5]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0061408	positive regulation of transcription from RNA polymerase II promoter in response to heat stress	SGD_REF:S000133875 PMID:20398213^[11]	IMP: Inferred from Mutant Phenotype		P	From SGD
	GO:0070210	Rpd3L-Expanded complex	SGD_REF:S000128493 PMID:19040720^[10]	IDA: Inferred from Direct Assay		C	From SGD
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Notes

References

See Help:References for how to manage references in GONUTS.

↑ ^1.0 ^1.1 ^1.2 ^1.3 Carrozza MJ et al. (2005) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731: 77-87; discussion 75-6 PubMed GONUTS page
↑ ^2.0 ^2.1 Lamping E et al. (1994) Isolation and characterization of a mutant of Saccharomyces cerevisiae with pleiotropic deficiencies in transcriptional activation and repression. Genetics 137: 55-65 PubMed GONUTS page
↑ Wang SS et al. (2011) Histone H3 Lysine 4 Hypermethylation Prevents Aberrant Nucleosome Remodeling at the PHO5 Promoter. Mol Cell Biol 31: 3171-81 PubMed GONUTS page
↑ ^4.0 ^4.1 Carrozza MJ et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581-92 PubMed GONUTS page
↑ ^5.0 ^5.1 ^5.2 ^5.3 ^5.4 Keogh MC et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123: 593-605 PubMed GONUTS page
↑ 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: 1077-90 PubMed GONUTS page
↑ Zhou J et al. (2009) Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res 37: 3699-713 PubMed GONUTS page
↑ ^8.0 ^8.1 Verzijlbergen KF et al. (2009) Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae. BMC Mol Biol 10: 76 PubMed GONUTS page
↑ Ehrentraut S et al. (2010) Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate. Proc Natl Acad Sci U S A 107: 5522-7 PubMed GONUTS page
↑ ^10.0 ^10.1 Shevchenko A et al. (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9: R167 PubMed GONUTS page
↑ Ruiz-Roig C et al. (2010) The Rpd3L HDAC complex is essential for the heat stress response in yeast. Mol Microbiol 76: 1049-62 PubMed GONUTS page

[PMID:16314178-0] 1.0 ^1.1 ^1.2 ^1.3 Carrozza MJ et al. (2005) Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex. Biochim Biophys Acta 1731: 77-87; discussion 75-6 PubMed GONUTS page

[PMID:8056324-1] 2.0 ^2.1 Lamping E et al. (1994) Isolation and characterization of a mutant of Saccharomyces cerevisiae with pleiotropic deficiencies in transcriptional activation and repression. Genetics 137: 55-65 PubMed GONUTS page

[PMID:21646424-2] Wang SS et al. (2011) Histone H3 Lysine 4 Hypermethylation Prevents Aberrant Nucleosome Remodeling at the PHO5 Promoter. Mol Cell Biol 31: 3171-81 PubMed GONUTS page

[PMID:16286007-3] 4.0 ^4.1 Carrozza MJ et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581-92 PubMed GONUTS page

[PMID:16286008-4] 5.0 ^5.1 ^5.2 ^5.3 ^5.4 Keogh MC et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123: 593-605 PubMed GONUTS page

[PMID:19417103-5] 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: 1077-90 PubMed GONUTS page

[PMID:19372273-6] Zhou J et al. (2009) Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res 37: 3699-713 PubMed GONUTS page

[PMID:19638198-7] 8.0 ^8.1 Verzijlbergen KF et al. (2009) Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae. BMC Mol Biol 10: 76 PubMed GONUTS page

[PMID:20133733-8] Ehrentraut S et al. (2010) Rpd3-dependent boundary formation at telomeres by removal of Sir2 substrate. Proc Natl Acad Sci U S A 107: 5522-7 PubMed GONUTS page

[PMID:19040720-9] 10.0 ^10.1 Shevchenko A et al. (2008) Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Genome Biol 9: R167 PubMed GONUTS page

[PMID:20398213-10] Ruiz-Roig C et al. (2010) The Rpd3L HDAC complex is essential for the heat stress response in yeast. Mol Microbiol 76: 1049-62 PubMed GONUTS page

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Species (Taxon ID)	Saccharomyces cerevisiae (baker's yeast) (taxon:4932)
Gene Name(s)	DEP1 ( synonyms: YAL013W, FUN54 )
Protein Name(s)	Transcriptional modulator,
External Links
SGD	S000000011

SGD:DEP1

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