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; AllianceGenome:HGNC:4853
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
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (113933028..113971148, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (115116117..115154233, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (114254192..114292312, 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?

HDAC2 promotes autophagy-associated HCC malignant progression by transcriptionally activating LAPTM4B.
Title: HDAC2 promotes autophagy-associated HCC malignant progression by transcriptionally activating LAPTM4B.
ACAP3 negatively regulated by HDAC2 inhibits the malignant development of papillary thyroid carcinoma cells.
Title: ACAP3 negatively regulated by HDAC2 inhibits the malignant development of papillary thyroid carcinoma cells.
HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair.
Title: HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair.
Inhibition of HDAC2 sensitises antitumour therapy by promoting NLRP3/GSDMD-mediated pyroptosis in colorectal cancer.
Title: Inhibition of HDAC2 sensitises antitumour therapy by promoting NLRP3/GSDMD-mediated pyroptosis in colorectal cancer.
The Epigenetic Modifiers HDAC2 and HDAC7 Inversely Associate with Cancer Stemness and Immunity in Solid Tumors.
Title: The Epigenetic Modifiers HDAC2 and HDAC7 Inversely Associate with Cancer Stemness and Immunity in Solid Tumors.
Inhibition of endothelial histone deacetylase 2 shifts endothelial-mesenchymal transitions in cerebral arteriovenous malformation models.
Title: Inhibition of endothelial histone deacetylase 2 shifts endothelial-mesenchymal transitions in cerebral arteriovenous malformation models.
Short communication: TNF-alpha and IGF-1 regulates epigenetic mechanisms of HDAC2 and HDAC10.
Title: Short communication: TNF-α and IGF-1 regulates epigenetic mechanisms of HDAC2 and HDAC10.
SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2.
Title: SARS-CoV-2 NSP5 antagonizes MHC II expression by subverting histone deacetylase 2.
SOX4/HDAC2 Axis Enhances Cell Survivability and Reduces Apoptosis by Activating AKT/MAPK Signaling in Colorectal Cancer.
Title: SOX4/HDAC2 Axis Enhances Cell Survivability and Reduces Apoptosis by Activating AKT/MAPK Signaling in Colorectal Cancer.
HDAC2 counteracts vascular calcification by activating autophagy in chronic kidney disease.
Title: HDAC2 counteracts vascular calcification by activating autophagy in chronic kidney disease.

Submit: New GeneRIF Correction See all GeneRIFs (283)

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

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables NF-kappaB binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables heat shock protein binding	IEA Inferred from Electronic Annotation more info
enables histone H3K14 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H3K4 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H3K9 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K12 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K16 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K5 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone H4K8 deacetylase activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	ISS Inferred from Sequence or Structural Similarity more info
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 promoter-specific chromatin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein de-2-hydroxyisobutyrylase 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 protein lysine delactylase activity	IDA Inferred from Direct Assay more info	PubMed
enables tubulin deacetylase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in behavioral response to ethanol	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle hypertrophy	IEA Inferred from Electronic Annotation more info
involved_in cellular response to dopamine	IEA Inferred from Electronic Annotation more info
involved_in cellular response to heat	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to retinoic acid	IEA Inferred from Electronic Annotation more info
involved_in cellular response to transforming growth factor beta stimulus	IEA Inferred from Electronic Annotation more info
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 dendrite development	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic digit morphogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in epidermal cell differentiation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in eyelid development in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in fungiform papilla formation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in hair follicle placode formation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IC Inferred by Curator more info	PubMed
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of MHC class II biosynthetic process	IC Inferred by Curator more info	PubMed
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of cell migration	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of dendritic spine development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron projection development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of peptidyl-lysine acetylation	IEA Inferred from Electronic Annotation more info
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	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 transcription by competitive promoter binding	IMP Inferred from Mutant Phenotype 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 odontogenesis of dentin-containing tooth	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of DNA-templated transcription	IC Inferred by Curator 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 collagen biosynthetic process	IC Inferred by Curator more info	PubMed
involved_in positive regulation of epithelial to mesenchymal transition	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of interleukin-1 production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of male mating behavior	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of oligodendrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of proteolysis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of positive regulation of signaling receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of tumor necrosis factor production	IEA Inferred from Electronic Annotation more info
involved_in protein modification process	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell fate specification	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of stem cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in response to amphetamine	IEA Inferred from Electronic Annotation more info
involved_in response to amyloid-beta	IEA Inferred from Electronic Annotation more info
involved_in response to caffeine	IEA Inferred from Electronic Annotation more info
involved_in response to cocaine	IEA Inferred from Electronic Annotation more info
involved_in response to hyperoxia	IEA Inferred from Electronic Annotation more info
involved_in response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in response to nicotine	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of ESC/E(Z) complex	IDA Inferred from Direct Assay more info	PubMed
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
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-type complex	IDA Inferred from Direct Assay more info	PubMed
part_of Sin3-type complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	HDA more info	PubMed
located_in chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
part_of histone deacetylase complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
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

General protein information

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Preferred Names: histone deacetylase 2

Names: YY1-associated factor 1; protein deacylase HDAC2; transcriptional regulator homolog RPD3

NP_001518.3

EC 3.5.1.98

XP_047274648.1

EC 3.5.1.98

XP_054211242.1

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

See identical proteins and their annotated locations for NP_001518.3

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

B3KRS5, B4DL58, E1P561, Q5SRI8, Q5SZ86, Q8NEH4, Q92769

UniProtKB/TrEMBL

B3KUJ5

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