HDAC2 histone deacetylase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HDAC2provided by HGNC
Official Full Name: histone deacetylase 2provided by HGNC
Primary source: HGNC:HGNC:4853
See related: Ensembl:ENSG00000196591 MIM:605164
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: HD2; RPD3; YAF1; KDAC2
Summary: This gene product belongs to the histone deacetylase family. Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. Thus, it plays an important role in transcriptional regulation, cell cycle progression and developmental events. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]
Expression: Ubiquitous expression in testis (RPKM 14.8), endometrium (RPKM 10.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q21

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
109.20201120	current	GRCh38.p13 (GCF_000001405.39)	6	NC_000006.12 (113933028..113971148, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (114257320..114292359, complement)

Chromosome 6 - NC_000006.12 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?

Elevated miR-23a impairs trophoblast migration and invasiveness through HDAC2 inhibition and NF-kappaB activation.
Title: Elevated miR-23a impairs trophoblast migration and invasiveness through HDAC2 inhibition and NF-κB activation.
Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity.
Title: Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity.
The long non-coding RNA LncHDAC2 drives the self-renewal of liver cancer stem cells via activation of Hedgehog signaling.
Title: The long non-coding RNA LncHDAC2 drives the self-renewal of liver cancer stem cells via activation of Hedgehog signaling.
Ubiquitin specific peptidase 5 promotes ovarian cancer cell proliferation through deubiquitinating HDAC2.
Title: Ubiquitin specific peptidase 5 promotes ovarian cancer cell proliferation through deubiquitinating HDAC2.
Mutual Balance of Histone Deacetylases 1 and 2 and the Acetyl Reader ATAD2 Regulates the Level of Acetylation of Histone H4 on Nascent Chromatin of Human Cells.
Title: Mutual Balance of Histone Deacetylases 1 and 2 and the Acetyl Reader ATAD2 Regulates the Level of Acetylation of Histone H4 on Nascent Chromatin of Human Cells.
HDAC2-mediated upregulation of IL-6 triggers the migration of osteosarcoma cells.
Title: HDAC2-mediated upregulation of IL-6 triggers the migration of osteosarcoma cells.
HDAC2 dysregulation in the nucleus basalis of Meynert during the progression of Alzheimer's disease.
Title: HDAC2 dysregulation in the nucleus basalis of Meynert during the progression of Alzheimer's disease.
The HDAC2 could reverse the effects of miR-490-3p on growth, migration, invasion and apoptosis of prostate cancer (PCa) cells.
Title: miR-490-3p modulates the progression of prostate cancer through regulating histone deacetylase 2.
Overactivated phosphoinositide 3kinase/RACalpha serine/threonineprotein kinase/mammalian target of rapamycin (PI3K/Akt/mTOR) signaling pathway and overproduction of histone deacetylases 2 (HDAC2) have also been observed in keloid fibroblasts (KFs).
Title: CUDC‑907 reverses pathological phenotype of keloid fibroblasts in vitro and in vivo via dual inhibition of PI3K/Akt/mTOR signaling and HDAC2.
These data provide an evidence that RCHY1 negatively regulates HDAC2.
Title: E3 ligase RCHY1 negatively regulates HDAC2.

Submit: New GeneRIF Correction See all GeneRIFs (229)

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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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat induces upregulation of HDAC2 expression and downregulation of CREB and CaMKIIa expression in human neuroblastoma SK-N-MC cells	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, 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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D11S3430 (e-PCR)
- UniSTS:152671

D10S16 (e-PCR)
- UniSTS:155756

D1S1423 (e-PCR)
- UniSTS:149619

G42073 (e-PCR)
- UniSTS:93134

STS-N62138 (e-PCR)
- UniSTS:64478

Homology

Homologs of the HDAC2 gene: The HDAC2 gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, C.elegans, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 249 organisms have orthologs with human gene HDAC2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 binding	HDA more info	PubMed
RNA polymerase II repressing transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
deacetylase activity	ISS Inferred from Sequence or Structural Similarity more info
enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
heat shock protein binding	IEA Inferred from Electronic Annotation more info
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 binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to nucleosomal DNA binding	HDA more info	PubMed
promoter-specific chromatin binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein deacetylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
ATP-dependent chromatin remodeling	HDA more info	PubMed
behavioral response to ethanol	IEA Inferred from Electronic Annotation more info
blood coagulation	TAS Traceable Author Statement more info
cardiac muscle hypertrophy	IEA Inferred from Electronic Annotation more info
cellular response to dopamine	IEA Inferred from Electronic Annotation more info
cellular response to heat	IEA Inferred from Electronic Annotation more info
cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
cellular response to retinoic acid	IEA Inferred from Electronic Annotation more info
cellular response to transforming growth factor beta stimulus	IEA Inferred from Electronic Annotation more info
chromatin remodeling	IC Inferred by Curator more info	PubMed
circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
dendrite development	ISS Inferred from Sequence or Structural Similarity more info
embryonic digit morphogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
epidermal cell differentiation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
eyelid development in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info	PubMed
fungiform papilla formation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
hair follicle placode formation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
heterochromatin maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
histone H3 deacetylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone H3 deacetylation	ISS Inferred from Sequence or Structural Similarity more info
histone H4 deacetylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone H4 deacetylation	ISS Inferred from Sequence or Structural Similarity more info
histone deacetylation	IMP Inferred from Mutant Phenotype more info	PubMed
negative regulation of DNA binding	IEA Inferred from Electronic Annotation more info
negative regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
negative regulation of MHC class II biosynthetic process	IC Inferred by Curator more info	PubMed
negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
negative regulation of dendritic spine development	IEA Inferred from Electronic Annotation more info
negative regulation of neuron projection development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
negative regulation of peptidyl-lysine acetylation	IEA Inferred from Electronic Annotation more info
negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
negative regulation of transcription, DNA-templated	IC Inferred by Curator more info	PubMed
negative regulation of transcription, DNA-templated	IMP Inferred from Mutant Phenotype more info	PubMed
odontogenesis of dentin-containing tooth	ISS Inferred from Sequence or Structural Similarity more info	PubMed
positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of collagen biosynthetic process	IC Inferred by Curator more info	PubMed
positive regulation of epithelial to mesenchymal transition	IEA Inferred from Electronic Annotation more info
positive regulation of interleukin-1 production	IEA Inferred from Electronic Annotation more info
positive regulation of male mating behavior	IEA Inferred from Electronic Annotation more info
positive regulation of oligodendrocyte differentiation	IEA Inferred from Electronic Annotation more info
positive regulation of proteolysis	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of signaling receptor activity	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	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of transcription, DNA-templated	IC Inferred by Curator more info	PubMed
positive regulation of tumor necrosis factor production	IEA Inferred from Electronic Annotation more info
positive regulation of tyrosine phosphorylation of STAT protein	IEA Inferred from Electronic Annotation more info
regulation of signal transduction by p53 class mediator	TAS Traceable Author Statement more info
response to amphetamine	IEA Inferred from Electronic Annotation more info
response to caffeine	IEA Inferred from Electronic Annotation more info
response to cocaine	IEA Inferred from Electronic Annotation more info
response to drug	IEA Inferred from Electronic Annotation more info
response to hyperoxia	IEA Inferred from Electronic Annotation more info
response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
response to nicotine	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
ESC/E(Z) complex	IDA Inferred from Direct Assay more info	PubMed
NuRD complex	IDA Inferred from Direct Assay more info	PubMed
Sin3 complex	IDA Inferred from Direct Assay more info	PubMed
chromatin	HDA more info	PubMed
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
cytoplasm	TAS Traceable Author Statement more info	PubMed
histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
nucleoplasm	IDA Inferred from Direct Assay more info
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

General protein information

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Preferred Names: histone deacetylase 2

Names: YY1-associated factor 1; transcriptional regulator homolog RPD3

NP_001518.3

EC 3.5.1.98

XP_016866288.1

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.

mRNA and Protein(s)

NM_001527.4 → NP_001518.3 histone deacetylase 2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the functional protein.

Source sequence(s)

AK296856, BC031055, FO393415

Consensus CDS

CCDS43493.2

UniProtKB/Swiss-Prot

Q92769

Related

ENSP00000430432.1, ENST00000519065.6

Conserved Domains (3) summary

cd10011
Location:9 → 374

HDAC2; Histone deacetylase 2 (HDAC2)

COG4547
Location:386 → 479

CobT2; Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphorib... [Coenzyme transport and metabolism]

pfam18004
Location:436 → 488

RPN2_C; 26S proteasome regulatory subunit RPN2 C-terminal domain

RNA

NR_033441.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an additional internal exon in the 5' region, compared to variant 1. This variant is represented as non-coding due to the presence of upstream ORFs that are predicted to interfere with the translation of the longest ORF.

Source sequence(s)

AK097376, AK296856, AL590398, FO393415
NR_073443.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK092156, AL590398, FO393415

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p13 Primary Assembly

Range

113933028..113971148 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017010799.1 → XP_016866288.1 histone deacetylase 2 isoform X1

UniProtKB/Swiss-Prot

Q92769

Related

ENSP00000430008.1, ENST00000519108.5

Conserved Domains (3) summary

pfam05285
Location:362 → 438

SDA1

pfam18004
Location:406 → 458

RPN2_C; 26S proteasome regulatory subunit RPN2 C-terminal domain

cl17011
Location:1 → 344

Arginase_HDAC; Arginase-like and histone-like hydrolases