HDAC1 histone deacetylase 1 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 1p35.2-p35.1

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (32292083..32333626)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (32150000..32191544)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (32757684..32799227)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia.
Title: HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia.
HDAC1 mediates epithelial-mesenchymal transition and promotes cancer cell invasion in glioblastoma.
Title: HDAC1 mediates epithelial-mesenchymal transition and promotes cancer cell invasion in glioblastoma.
Proteomics-based trapping with single or multiple inactive mutants reproducibly profiles histone deacetylase 1 substrates.
Title: Proteomics-based trapping with single or multiple inactive mutants reproducibly profiles histone deacetylase 1 substrates.
Regulation of osteogenesis in bone marrow-derived mesenchymal stem cells via histone deacetylase 1 and 2 co-cultured with human gingival fibroblasts and periodontal ligament cells.
Title: Regulation of osteogenesis in bone marrow-derived mesenchymal stem cells via histone deacetylase 1 and 2 co-cultured with human gingival fibroblasts and periodontal ligament cells.
Histone deacetylase 1, Sirtuin 1, and Sirtuin 3 single-nucleotide polymorphisms and the risk of endometriosis in South Indian women.
Title: Histone deacetylase 1, Sirtuin 1, and Sirtuin 3 single-nucleotide polymorphisms and the risk of endometriosis in South Indian women.
Histone deacetylases 1 and 2 target gene regulatory networks of nephron progenitors to control nephrogenesis.
Title: Histone deacetylases 1 and 2 target gene regulatory networks of nephron progenitors to control nephrogenesis.
HDAC1/3-dependent moderate liquid-liquid phase separation of YY1 promotes METTL3 expression and AML cell proliferation.
Title: HDAC1/3-dependent moderate liquid-liquid phase separation of YY1 promotes METTL3 expression and AML cell proliferation.
The emerging role of histone deacetylase 1 in allergic diseases.
Title: The emerging role of histone deacetylase 1 in allergic diseases.
Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients.
Title: Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients.
LncRNA SNHG1 regulates neuroblastoma cell fate via interactions with HDAC1/2.
Title: LncRNA SNHG1 regulates neuroblastoma cell fate via interactions with HDAC1/2.

Submit: New GeneRIF Correction See all GeneRIFs (426)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48422 (e-PCR)
- UniSTS:38186

RH77985 (e-PCR)
- UniSTS:37215

WI-8367 (e-PCR)
- UniSTS:146569

RH70655 (e-PCR)
- UniSTS:68258

RH80765 (e-PCR)
- UniSTS:87751

RH64844 (e-PCR)
- UniSTS:90583

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription factor binding	TAS Traceable Author Statement more info	PubMed
enables E-box binding	IEA Inferred from Electronic Annotation more info
enables Krueppel-associated box domain binding	IEA Inferred from Electronic Annotation more info
enables NF-kappaB binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IGI Inferred from Genetic Interaction more info	PubMed
enables RNA polymerase II core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone deacetylase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables histone deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone deacetylase activity	TAS Traceable Author Statement more info	PubMed
enables histone deacetylase binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone decrotonylase activity	IDA Inferred from Direct Assay more info	PubMed
contributes_to nucleosomal DNA binding	HDA more info	PubMed
enables p53 binding	IPI Inferred from Physical Interaction more info	PubMed
enables promoter-specific chromatin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein lysine deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein lysine deacetylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein lysine deacetylase activity	TAS Traceable Author Statement more info
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent heterochromatin formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to platelet-derived growth factor stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin organization	TAS Traceable Author Statement more info	PubMed
involved_in chromatin remodeling	HDA more info	PubMed
involved_in chromatin remodeling	IC Inferred by Curator more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic digit morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoderm development	IEA Inferred from Electronic Annotation more info
involved_in epidermal cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in eyelid development in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in fungiform papilla formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in hair follicle placode formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in hippocampus development	IEA Inferred from Electronic Annotation more info
involved_in histone deacetylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation by host of viral transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of androgen receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of negative regulation of apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of canonical Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of cell migration	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of intrinsic apoptotic signaling pathway	IEA Inferred from Electronic Annotation more info
NOT involved_in negative regulation of myotube differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay 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	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in odontogenesis of dentin-containing tooth	ISS Inferred from Sequence or Structural Similarity more info
involved_in oligodendrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of oligodendrocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of positive regulation of signaling receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deacetylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of amyloid-beta clearance	IC Inferred by Curator more info	PubMed
involved_in regulation of cell fate specification	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of stem cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of NuRD complex	IDA Inferred from Direct Assay more info	PubMed
part_of NuRD complex	NAS Non-traceable Author Statement more info	PubMed
part_of Sin3 complex	IDA Inferred from Direct Assay more info	PubMed
part_of Sin3 complex	NAS Non-traceable Author Statement more info	PubMed
part_of chromatin	HDA more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
part_of heterochromatin	IEA Inferred from Electronic Annotation more info
part_of histone deacetylase complex	IDA Inferred from Direct Assay more info	PubMed
part_of histone deacetylase complex	TAS Traceable Author Statement more info	PubMed
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of protein-containing complex	HDA more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription repressor complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: histone deacetylase 1

Names: protein deacetylase HDAC1; protein decrotonylase HDAC1; reduced potassium dependency, yeast homolog-like 1

NP_004955.2

EC 3.5.1.98

XP_011539611.1

EC 3.5.1.98

XP_054192178.1

EC 3.5.1.98

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

NG_047018.1 RefSeqGene

Range

4977..46520

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_004964.3 → NP_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:4 → 374

HDAC1; Histone deacetylase 1 (HDAC1)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

32292083..32333626

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DRG0

Conserved Domains (1) summary

cl17011
Location:1 → 181

Arginase_HDAC; Arginase-like and histone-like hydrolases