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
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

Genomic context

Location:: 1p35.2-p35.1

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
109.20191205	current	GRCh38.p13 (GCF_000001405.39)	1	NC_000001.11 (32292083..32333628)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (32757708..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?

Collectively, these data indicate that HDAC1/2 containing complexes are critical regulators of histone crotonylation in vivo.
Title: Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo.
High HDAC1 expression is associated with Intrahepatic Cholangiocarcinoma.
Title: Carbohydrate Antigen 19-9 Is a Prognostic Factor Which Correlates With HDAC1 and HIF-1α for Intrahepatic Cholangiocarcinoma.
HDAC1 promotes glycolysis in gastric cancer and affects HIF-1alpha activity in tumor progression and metastasis. HDAC1(High) expression was also an independent adverse prognostic factor for overall survival and disease-free survival
Title: Histone deacetylase-1 as a prognostic factor and mediator of gastric cancer progression by enhancing glycolysis.
This tag-mediated reprogramming of the HDAC1/2 protein interaction network suggests a mechanism whereby HDAC1 is first loaded into the CCT complex.
Title: Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly.
Sox6 as a regulator of pancreatic cancer development was shown to interact with the promoter of Twist1, a helix-loop-helix transcription factor involved in the induction of EMT, and to modulate the expression of Twist1 by recruiting HDAC1 to the promoter of the Twist1 gene.
Title: Identification of Sox6 as a regulator of pancreatic cancer development.
Authors confirmed that high expression of HDAC1 in CLL patients with TP53 mutation, which is closely related to poor prognosis and drug-resistance.
Title: Entinostat combined with Fludarabine synergistically enhances the induction of apoptosis in TP53 mutated CLL cells via the HDAC1/HO-1 pathway.
NLK boosts cell proliferation and E2F1 activity and controls the cell cycle switch by releasing HDAC1 from the E2F1 complex, us priming colorectal cancer progression
Title: Nemo-like kinase (NLK) primes colorectal cancer progression by releasing the E2F1 complex from HDAC1.
Combined inhibition of HDAC1/2 and Brd4 resolved the aberrant ISG expression detected in cells derived from patients with two inherited interferonopathies, ISG15 and USP18 deficiencies, defining a novel therapeutic approach to ISG-associated autoimmune diseases.
Title: HDAC stimulates gene expression through BRD4 availability in response to IFN and in interferonopathies.
sing CRISPR/Cas9 genomic editing, we found that HDAC1 and HDAC2 knockout cells significantly induced cell apoptosis, indicating that the regulation of HDAC1 and HDAC2 is extremely important in maintaining K562 cell survival.
Title: HDAC1,2 Knock-Out and HDACi Induced Cell Apoptosis in Imatinib-Resistant K562 Cells.
Results reveal a prominent role for transcriptional regulator SIN3A (SIN3A) in the transcriptional response to hypoxia, and suggesting a model where modulation of the associated histone deacetylase 1/2 activity, rather than its recruitment, determines the transcriptional output.
Title: The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia.

Submit: New GeneRIF Correction See all GeneRIFs (342)

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

Homology

Homologs of the HDAC1 gene: The HDAC1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 235 organisms have orthologs with human gene HDAC1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 more info	PubMed
contributes_to RNA polymerase II proximal promoter sequence-specific DNA binding	HDA more info	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	IBA Inferred from Biological aspect of Ancestor 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 more info	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 more info	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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone H3 deacetylation	IDA Inferred from Direct Assay more info	PubMed
histone H4 deacetylation	IBA Inferred from Biological aspect of Ancestor 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	IBA Inferred from Biological aspect of Ancestor 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
Sin3-type complex	IBA Inferred from Biological aspect of Ancestor 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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone deacetylase complex	TAS Traceable Author Statement more info	PubMed
neuronal cell body	IEA Inferred from Electronic Annotation more info
nuclear chromatin	HDA more info	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 more info	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

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Preferred Names: histone deacetylase 1

Names: reduced potassium dependency, yeast homolog-like 1

NP_004955.2

EC 3.5.1.98

XP_011539611.1

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

Download

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

UniProtKB/TrEMBL

Q6IT96

Related

ENSP00000362649.3, ENST00000373548.8

Conserved Domains (1) summary

cd10010
Location:4 → 374

HDAC1; Histone deacetylase 1 (HDAC1)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p13 Primary Assembly

Range

32292083..32333628

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

cl17011
Location:1 → 181

Arginase_HDAC; Arginase-like and histone-like hydrolases