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DEP1 Rpd3L histone deacetylase complex subunit DEP1 [ Saccharomyces cerevisiae S288C ]

Gene ID: 851220, updated on 14-Nov-2024

Summary

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Official Symbol
DEP1
Official Full Name
Rpd3L histone deacetylase complex subunit DEP1
Primary source
SGD:S000000011
Locus tag
YAL013W
See related
AllianceGenome:SGD:S000000011; FungiDB:YAL013W; VEuPathDB:YAL013W
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
FUN54
Summary
Predicted to enable histone deacetylase binding activity. Involved in several processes, including regulation of gene expression; regulation of inositol biosynthetic process; and regulation of phospholipid biosynthetic process. Located in mitochondrion and nucleus. Part of Rpd3L complex. [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See DEP1 in Genome Data Viewer
Location:
chromosome: I
Exon count:
1
Sequence:
Chromosome: I; NC_001133.9 (129270..130487)

Chromosome I - NC_001133.9Genomic Context describing neighboring genes Neighboring gene bifunctional N-glycosylase/AP lyase NTG1 Neighboring gene syntaxin Neighboring gene cystathionine gamma-lyase CYS3 Neighboring gene Swc3p

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_001133.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The Dep1 protein: A new regulator of mitophagy in yeast. Camougrand N, et al. Biochem Biophys Res Commun, 2022 Dec 20. PMID 36283334
  2. Isolation and characterization of a mutant of Saccharomyces cerevisiae with pleiotropic deficiencies in transcriptional activation and repression. Lamping E, et al. Genetics, 1994 May. PMID 8056324, Free PMC Article
  3. Rpd3- and spt16-mediated nucleosome assembly and transcriptional regulation on yeast ribosomal DNA genes. Johnson JM, et al. Mol Cell Biol, 2013 Jul. PMID 23689130, Free PMC Article
  4. The roles of the catalytic and noncatalytic activities of Rpd3L and Rpd3S in the regulation of gene transcription in yeast. Yeheskely-Hayon D, et al. PLoS One, 2013. PMID 24358376, Free PMC Article
  5. 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. Knott SR, et al. Genes Dev, 2009 May 1. PMID 19417103, Free PMC Article

See all (111) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Dep1 protein: A new regulator of mitophagy in yeast.
    Title: The Dep1 protein: A new regulator of mitophagy in yeast.
Submit: New GeneRIF Correction

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

Gene Ontology Provided by SGD

Function Evidence Code Pubs
enables histone deacetylase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in cellular response to heat IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of inositol biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of phosphatidylcholine biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of phosphatidylserine biosynthetic process 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 silent mating-type cassette heterochromatin formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of inositol biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of phosphatidylcholine biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of phosphatidylserine biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated DNA replication initiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Rpd3L complex HDA PubMed 
part_of Rpd3L complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Rpd3L-Expanded complex HDA PubMed 
part_of Sin3-type complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus 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
Rpd3L histone deacetylase complex subunit DEP1
NP_009389.3
  • Component of the Rpd3L histone deacetylase complex; required for diauxic shift-induced histone H2B deposition onto rDNA genes; transcriptional modulator involved in regulation of structural phospholipid biosynthesis genes and metabolically unrelated genes, as well as maintenance of telomeres, mating efficiency, and sporulation; localizes to both the nucleus and mitochondria where it may play a role in mitophagy

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

  1. NC_001133.9 Reference assembly

    Range
    129270..130487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001178158.2 → NP_009389.3  TPA: Rpd3L histone deacetylase complex subunit DEP1 [Saccharomyces cerevisiae S288C]

    See identical proteins and their annotated locations for NP_009389.3

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    D6VPK5, P31385, Q86ZS5
    UniProtKB/TrEMBL
    A7A0F6, G2W8L9, N1P932
    Conserved Domains (1) summary
    pfam08598
    Location:182 → 402
    Sds3; Sds3-like
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P31385.3

Gene LinkOut

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