RPD3 histone deacetylase RPD3 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: RPD3
Official Full Name: histone deacetylase RPD3
Primary source: SGD:S000005274
Locus tag: YNL330C
See related: AllianceGenome:SGD:S000005274; FungiDB:YNL330C; VEuPathDB:YNL330C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: MOF6; REC3; SDI2; SDS6
Summary: Enables histone deacetylase activity; transcription coactivator activity; and transcription corepressor activity. Involved in several processes, including mitotic cell cycle phase transition; nucleolus organization; and regulation of gene expression. Located in nuclear periphery. Part of Rpd3L complex and Rpd3S complex. Human ortholog(s) of this gene implicated in stomach cancer. Orthologous to human HDAC1 (histone deacetylase 1) and HDAC2 (histone deacetylase 2). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See RPD3 in Genome Data Viewer

Location:: chromosome: XIV

Exon count:: 1

Sequence:: Chromosome: XIV; NC_001146.8 (18001..19302, complement)

Chromosome XIV - NC_001146.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001146.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Histone Deacetylases Hst1 and Rpd3 Integrate De Novo NAD[+] Metabolism with Phosphate Sensing in Saccharomyces cerevisiae.
Title: The Histone Deacetylases Hst1 and Rpd3 Integrate De Novo NAD(+) Metabolism with Phosphate Sensing in Saccharomyces cerevisiae.
The histone deacetylases Rpd3 and Hst1 antagonistically regulate de novo NAD(+) metabolism in the budding yeast Saccharomyces cerevisiae.
Title: The histone deacetylases Rpd3 and Hst1 antagonistically regulate de novo NAD(+) metabolism in the budding yeast Saccharomyces cerevisiae.
RPD3 and UME6 are involved in the activation of PDR5 transcription and pleiotropic drug resistance in rho(0) cells of Saccharomyces cerevisiae.
Title: RPD3 and UME6 are involved in the activation of PDR5 transcription and pleiotropic drug resistance in ρ(0) cells of Saccharomyces cerevisiae.
Genetic screen for suppressors of increased silencing in rpd3 mutants in Saccharomyces cerevisiae identifies a potential role for H3K4 methylation.
Title: Genetic screen for suppressors of increased silencing in rpd3 mutants in Saccharomyces cerevisiae identifies a potential role for H3K4 methylation.
The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast.
Title: The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast.
NuA3 HAT antagonizes the Rpd3S and Rpd3L HDACs to optimize mRNA and lncRNA expression dynamics.
Title: NuA3 HAT antagonizes the Rpd3S and Rpd3L HDACs to optimize mRNA and lncRNA expression dynamics.
Gcn5 and Rpd3 have a limited role in the regulation of cell cycle transcripts during the G1 and S phases in Saccharomyces cerevisiae.
Title: Gcn5 and Rpd3 have a limited role in the regulation of cell cycle transcripts during the G1 and S phases in Saccharomyces cerevisiae.
Rpd3L and Hda1 histone deacetylase complexes contribute to the repair of replication-born double strand breaks by facilitating cohesin loading.
Title: Rpd3L and Hda1 histone deacetylases facilitate repair of broken forks by promoting sister chromatid cohesion.
Data sugget that an active mark, H3K4me3 enriched at active promoters, instructs histone deacetylase RPD3 (Rpd3L HDAC) to induce histone deacetylation and termed transcriptional repression memory (TREM).
Title: Rpd3L HDAC links H3K4me3 to transcriptional repression memory.
Our findings present the first evidence that H3K4me and H3K36me act combinatorially to control Rpd3S.
Title: Combinatorial Genetic Control of Rpd3S Through Histone H3K4 and H3K36 Methylation in Budding Yeast.

Submit: New GeneRIF Correction See all GeneRIFs (53)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables histone H3K14 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H3K4 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H3K9 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K12 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K16 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K5 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K8 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone deacetylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	IEA Inferred from Electronic Annotation more info
enables histone deacetylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription coactivator activity	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription corepressor activity	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in G1/S transition of mitotic cell cycle	IGI Inferred from Genetic Interaction more info	PubMed
involved_in G1/S transition of mitotic cell cycle	IPI Inferred from Physical Interaction more info	PubMed
involved_in G2/M transition of mitotic cell cycle	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to heat	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to nitrogen starvation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in meiotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of rDNA heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of reciprocal meiotic recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of silent mating-type cassette heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase I	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IPI Inferred from Physical Interaction more info	PubMed
involved_in nucleophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of macroautophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to nucleolar rDNA repeats	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rDNA chromatin condensation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated DNA replication initiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of DNA-templated DNA replication initiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IPI Inferred from Physical Interaction more info	PubMed
involved_in transcription elongation by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of Rpd3L complex	HDA more info	PubMed
part_of Rpd3L complex	IDA Inferred from Direct Assay more info	PubMed
part_of Rpd3L-Expanded complex	HDA more info	PubMed
part_of Rpd3L-Expanded complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Rpd3S complex	IDA Inferred from Direct Assay more info	PubMed
part_of Sin3-type complex	IDA Inferred from Direct Assay more info	PubMed
part_of Snt2C complex	HDA more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
part_of histone deacetylase complex	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear periphery	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: histone deacetylase RPD3

NP_014069.1

EC 3.5.1.98

Histone deacetylase, component of both Rpd3S and Rpd3L complexes; regulates transcription, silencing, autophagy and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members; Rpd3(L) recruitment to the subtelomeric region is regulated by interaction with the Hmt1p methyltransferase; delays late firing of single copy origins by opposing the Fkh1/2 origin activation pathway

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001146.8 Reference assembly

Range

18001..19302 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183168.1 → NP_014069.1 TPA: histone deacetylase RPD3 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014069.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W0L7, P32561

UniProtKB/TrEMBL

A6ZSF2, B3LPG2, C7GWS5, C8ZGJ5, G2WLE1, N1NWJ8

Conserved Domains (1) summary

cd10004
Location:18 → 392

RPD3-like; reduced potassium dependency-3 (RPD3)-like