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

Genomic context

Location:: 6q21

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
109.20191205	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

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HDAC2 and GR-alpha expression in lung tissues are potential biomarkers for predicting corticosteroid sensitivity.
Title: Expression of GR-α and HDAC2 in steroid-Sensitive and steroid-Insensitive interstitial lung disease.
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.
AC-miR-95-5p-Exos may act as an HDAC2/8 inhibitor and exhibit potential as a disease-modifying osteoarthritis drug.
Title: Exosomal miR-95-5p regulates chondrogenesis and cartilage degradation via histone deacetylase 2/8.
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.
Our data suggest that disruption of the Tip60 HAT/HDAC2 balance is a critical initial step in Alzheimer's disease
Title: Restoring Tip60 HAT/HDAC2 Balance in the Neurodegenerative Brain Relieves Epigenetic Transcriptional Repression and Reinstates Cognition.
Hutchinson-Gilford progeria cells show impaired lamin A/C-HDAC2 interplay and accumulation of p21 upon stress recovery.
Title: Altered modulation of lamin A/C-HDAC2 interaction and p21 expression during oxidative stress response in HGPS.
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.
in hISMC from resected Crohn's strictures, we observed a significantly reduced contractile phenotype compared with patient-matched intrinsic controls that was associated with increased patient-specific expression of DNA methyltransferase 1, HDAC2, and HDAC5.
Title: Epigenetic modification of intestinal smooth muscle cell phenotype during proliferation.

Submit: New GeneRIF Correction See all GeneRIFs (212)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

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

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

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: 264 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
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 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
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
maintenance of chromatin silencing	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 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 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	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 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
Sin3-type complex	IBA Inferred from Biological aspect of Ancestor 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
nuclear chromatin	HDA 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

Go to the top of the page Help

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)

Go to the top of the page Help

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

Q92769

Related

ENSP00000430432.1, ENST00000519065.6

Conserved Domains (2) summary

cd10011
Location:9 → 374

HDAC2; Histone deacetylase 2 (HDAC2)

pfam14797
Location:393 → 487

SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex

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_073443.1 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, FO393415

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_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 (2) summary

pfam14797
Location:363 → 457

SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex

cl17011
Location:1 → 344

Arginase_HDAC; Arginase-like and histone-like hydrolases