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HDAC1 histone deacetylase 1 [ Homo sapiens (human) ]

Gene ID: 3065, updated on 23-Apr-2019

Summary

Official Symbol
HDAC1provided by HGNC
Official Full Name
histone deacetylase 1provided by HGNC
Primary source
HGNC:HGNC:4852
See related
Ensembl:ENSG00000116478 MIM:601241
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HD1; RPD3; KDAC1; GON-10; RPD3L1
Summary
Histone acetylation and deacetylation, catalyzed by multisubunit complexes, play a key role in the regulation of eukaryotic gene expression. The protein encoded by this gene belongs to the histone deacetylase/acuc/apha family and is a component of the histone deacetylase complex. It also interacts with retinoblastoma tumor-suppressor protein and this complex is a key element in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2, it deacetylates p53 and modulates its effect on cell growth and apoptosis. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 56.9), colon (RPKM 56.3) and 25 other tissues See more
Orthologs

Genomic context

See HDAC1 in Genome Data Viewer
Location:
1p35.2-p35.1
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (32292103..32333628)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32757708..32799227)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 167 member B Neighboring gene LCK proto-oncogene, Src family tyrosine kinase Neighboring gene MARCKS like 1 Neighboring gene uncharacterized LOC105378629

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of histone deacetylase 1 (HDAC1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat YY1 and LSF transcription factors cooperatively recruit histone deacetylase 1 (HDAC1) to the HIV-1 LTR promoter, thereby inhibiting transcription and Tat activation of the promoter PubMed
tat A compound in curry known as Curcumin inhibits HIV-1 Tat-mediated long terminal repeat transactivation by reversing Tat-induced dissociation of HDAC1 from LTR and by reducing the binding of p65/NFKappaB to LTR PubMed
tat The SIN3/HDAC complex, composed of SIN3A, SAP30, SAP18, HDAC-1 AND -2 and RbAp46/48 except SAP30, are identified to interact with HIV-1 Tat in Jurkat cell PubMed
Vpr vpr HIV-1 Vpr depletes HDAC1 in HIV-1 latently infected J-Lat cells by targeting HDAC1 for proteasomal degradation; HDAC1 was degraded on HIV-1 LTR resulting in recruitment of active transcription marks to the viral promoter and provirus activation PubMed
vpr HIV-1 Vpr binds and depletes chromatin-associated HDAC3 and HDAC1 through a VprBP-dependent mechanism resulting in hyperacetylation of histones on the HIV-1 LTR resulting in reactivation of HIV-1 promoter leading to acute infection PubMed
vpr HIV-1 Vpr depletes HDAC1, 2, 3 and 8 to overcome HIV-1 proviral latency in macrophages PubMed
vpr COUP-TF-interacting protein 2 (CTIP2) abolishes Vpr-mediated stimulation of p21 by cooperating with SUV39H1 and HDAC1/HDAC2 to silence the p21 gene transcription PubMed
integrase gag-pol KAP1 inhibits HIV-1 integration via HIV-1 IN acetylation-dependent mechanism by inducing IN/HDAC1 complex formation PubMed
gag-pol HIV-1 IN and INI1/hSNF5 bind SAP18 and selectively recruit components of Sin3a-HDAC1 complex into HIV-1 virions. HIV-1 virion-associated HDAC1 is required for efficient early post-entry events PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686H12203

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
E-box binding IEA
Inferred from Electronic Annotation
more info
 
Krueppel-associated box domain binding IEA
Inferred from Electronic Annotation
more info
 
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
NF-kappaB binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA polymerase II core promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding HDA PubMed 
contributes_to RNA polymerase II proximal promoter sequence-specific DNA binding HDA PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IGI
Inferred from Genetic Interaction
more info
PubMed 
RNA polymerase II repressing transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA polymerase II transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
activating transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
core promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone deacetylase activity TAS
Traceable Author Statement
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to nucleosomal DNA binding HDA PubMed 
p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
promoter-specific chromatin binding IEA
Inferred from Electronic Annotation
more info
 
protein N-terminus binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein deacetylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
repressing transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding TAS
Traceable Author Statement
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
ATP-dependent chromatin remodeling HDA PubMed 
beta-catenin-TCF complex assembly TAS
Traceable Author Statement
more info
 
blood coagulation TAS
Traceable Author Statement
more info
 
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
chromatin remodeling IC
Inferred by Curator
more info
PubMed 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic digit morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
endoderm development IEA
Inferred from Electronic Annotation
more info
 
epidermal cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
eyelid development in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 
fungiform papilla formation ISS
Inferred from Sequence or Structural Similarity
more info
 
hair follicle placode formation ISS
Inferred from Sequence or Structural Similarity
more info
 
hippocampus development IEA
Inferred from Electronic Annotation
more info
 
histone H3 deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H4 deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
methylation-dependent chromatin silencing IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation by host of viral transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of I-kappaB kinase/NF-kappaB signaling IEA
Inferred from Electronic Annotation
more info
 
negative regulation of androgen receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of apoptotic process TAS
Traceable Author Statement
more info
PubMed 
negative regulation of canonical Wnt signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of intrinsic apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
 
NOT negative regulation of myotube differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
odontogenesis of dentin-containing tooth ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of receptor biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
protein deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of amyloid-beta clearance IC
Inferred by Curator
more info
PubMed 
regulation of endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of megakaryocyte differentiation TAS
Traceable Author Statement
more info
 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
NuRD complex IDA
Inferred from Direct Assay
more info
PubMed 
Sin3 complex IDA
Inferred from Direct Assay
more info
PubMed 
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
heterochromatin IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase complex TAS
Traceable Author Statement
more info
PubMed 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nuclear chromatin HDA PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex HDA PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
histone deacetylase 1
Names
reduced potassium dependency, yeast homolog-like 1
NP_004955.2
XP_011539611.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_047018.1 RefSeqGene

    Range
    5001..46517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004964.3NP_004955.2  histone deacetylase 1

    See identical proteins and their annotated locations for NP_004955.2

    Status: REVIEWED

    Source sequence(s)
    AL109945
    Consensus CDS
    CCDS360.1
    UniProtKB/Swiss-Prot
    Q13547
    UniProtKB/TrEMBL
    Q6IT96
    Related
    ENSP00000362649.3, ENST00000373548.8
    Conserved Domains (1) summary
    cd10010
    Location:4374
    HDAC1; Histone deacetylase 1 (HDAC1)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    32292103..32333628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541309.2XP_011539611.1  histone deacetylase 1 isoform X1

    Conserved Domains (1) summary
    cl17011
    Location:1181
    Arginase_HDAC; Arginase-like and histone-like hydrolases
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