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HDAC1 histone deacetylase 1 [ Homo sapiens (human) ]

Gene ID: 3065, updated on 5-Jan-2025

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; AllianceGenome:HGNC:4852
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
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Genomic context

See HDAC1 in Genome Data Viewer
Location:
1p35.2-p35.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32292083..32333626)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32150000..32191544)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32757684..32799227)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 587 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 588 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 684 Neighboring gene family with sequence similarity 167 member B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 590 Neighboring gene LCK proto-oncogene, Src family tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32758549-32759123 Neighboring gene MPRA-validated peak162 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 592 Neighboring gene uncharacterized LOC124903949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32801487-32802056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 686 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32803079-32803207 Neighboring gene MARCKS like 1 Neighboring gene uncharacterized LOC105378629 Neighboring gene Sharpr-MPRA regulatory region 14076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 596 Neighboring gene uncharacterized LOC124903933

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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 PubChem

Interactions

General gene information

Clone Names

  • DKFZp686H12203

Gene Ontology Provided by GOA

Items 1 - 25 of 36
Function Evidence Code Pubs
enables DNA-binding transcription factor binding PubMed 
enables DNA-binding transcription factor binding PubMed 
enables E-box binding  
enables Krueppel-associated box domain binding  
enables NF-kappaB binding PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding PubMed 
enables RNA polymerase II core promoter sequence-specific DNA binding PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding PubMed 
enables core promoter sequence-specific DNA binding PubMed 
enables enzyme binding PubMed 
enables histone H3K14 deacetylase activity, hydrolytic mechanism  
enables histone H3K4 deacetylase activity, hydrolytic mechanism  
enables histone H3K9 deacetylase activity, hydrolytic mechanism  
enables histone H4K12 deacetylase activity, hydrolytic mechanism  
enables histone H4K16 deacetylase activity, hydrolytic mechanism  
enables histone H4K5 deacetylase activity, hydrolytic mechanism  
enables histone H4K8 deacetylase activity, hydrolytic mechanism  
enables histone deacetylase activity  
enables histone deacetylase activity PubMed 
enables histone deacetylase activity PubMed 
enables histone deacetylase activity PubMed 
enables histone deacetylase binding PubMed 
enables histone decrotonylase activity PubMed 
enables metal ion binding  
contributes_to nucleosomal DNA binding PubMed 
enables p53 binding PubMed 
enables promoter-specific chromatin binding  
enables protein binding PubMed 
enables protein binding PubMed 
enables protein lysine deacetylase activity PubMed 
enables protein lysine deacetylase activity PubMed 
enables protein lysine deacetylase activity  
enables protein lysine delactylase activity PubMed 
enables transcription corepressor activity PubMed 
enables transcription corepressor binding PubMed 
enables tubulin deacetylase activity  
Items 1 - 25 of 36
Items 1 - 25 of 51
Process Evidence Code Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation PubMed 
involved_in cellular response to platelet-derived growth factor stimulus  
involved_in chromatin organization PubMed 
involved_in chromatin remodeling PubMed 
involved_in chromatin remodeling PubMed 
involved_in chromatin remodeling PubMed 
involved_in circadian regulation of gene expression  
involved_in embryonic digit morphogenesis  
involved_in endoderm development  
involved_in epidermal cell differentiation  
involved_in eyelid development in camera-type eye  
involved_in fungiform papilla formation  
involved_in hair follicle placode formation  
involved_in heterochromatin formation  
involved_in hippocampus development  
involved_in negative regulation by host of viral transcription PubMed 
involved_in negative regulation of DNA-templated transcription PubMed 
involved_in negative regulation of DNA-templated transcription  
involved_in negative regulation of DNA-templated transcription PubMed 
involved_in negative regulation of androgen receptor signaling pathway PubMed 
involved_in negative regulation of apoptotic process  
acts_upstream_of negative regulation of apoptotic process PubMed 
involved_in negative regulation of canonical NF-kappaB signal transduction  
involved_in negative regulation of canonical Wnt signaling pathway PubMed 
involved_in negative regulation of cell migration PubMed 
involved_in negative regulation of gene expression PubMed 
involved_in negative regulation of gene expression, epigenetic PubMed 
involved_in negative regulation of intrinsic apoptotic signaling pathway  
NOT involved_in negative regulation of myotube differentiation PubMed 
involved_in negative regulation of stem cell population maintenance PubMed 
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in negative regulation of transcription by RNA polymerase II PubMed 
involved_in negative regulation of transforming growth factor beta receptor signaling pathway PubMed 
involved_in neuron differentiation  
involved_in odontogenesis of dentin-containing tooth  
involved_in oligodendrocyte differentiation  
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of DNA-templated transcription PubMed 
involved_in positive regulation of cell population proliferation PubMed 
involved_in positive regulation of gene expression  
involved_in positive regulation of oligodendrocyte differentiation  
acts_upstream_of positive regulation of signaling receptor activity PubMed 
involved_in positive regulation of smooth muscle cell proliferation  
involved_in positive regulation of stem cell population maintenance PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in protein deacetylation PubMed 
involved_in regulation of cell fate specification PubMed 
involved_in regulation of stem cell differentiation PubMed 
involved_in regulation of transcription by RNA polymerase II PubMed 
Items 1 - 25 of 51
Component Evidence Code Pubs
part_of NuRD complex  
part_of NuRD complex PubMed 
part_of NuRD complex PubMed 
part_of Sin3-type complex PubMed 
part_of Sin3-type complex PubMed 
located_in chromatin PubMed 
located_in chromatin PubMed 
located_in cytoplasm PubMed 
located_in cytosol PubMed 
located_in heterochromatin  
part_of histone deacetylase complex PubMed 
part_of histone deacetylase complex PubMed 
located_in neuronal cell body  
located_in nucleoplasm PubMed 
located_in nucleoplasm  
located_in nucleus PubMed 
located_in nucleus PubMed 
part_of protein-containing complex PubMed 
part_of protein-containing complex PubMed 
part_of transcription repressor complex  

General protein information

Preferred Names
histone deacetylase 1
Names
protein deacetylase HDAC1
protein deacylase HDAC1
protein decrotonylase HDAC1
reduced potassium dependency, yeast homolog-like 1
NP_004955.2
XP_011539611.1
XP_054192178.1

NCBI Reference Sequences (RefSeq)

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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
    4977..46520
    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, Q92534
    UniProtKB/TrEMBL
    B5BU61, D3DPP9, Q6IT96
    Related
    ENSP00000362649.3, ENST00000373548.8
    Conserved Domains (1) summary
    cd10010
    Location:4374
    HDAC1; Histone deacetylase 1 (HDAC1)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    32292083..32333626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541309.3XP_011539611.1  histone deacetylase 1 isoform X1

    UniProtKB/TrEMBL
    B4DRG0
    Conserved Domains (1) summary
    cl17011
    Location:1181
    Arginase_HDAC; Arginase-like and histone-like hydrolases

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    32150000..32191544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336203.1XP_054192178.1  histone deacetylase 1 isoform X1

    UniProtKB/TrEMBL
    B4DRG0
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