HDAC3 histone deacetylase 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HDAC3provided by HGNC
Official Full Name: histone deacetylase 3provided by HGNC
Primary source: HGNC:HGNC:4854
See related: Ensembl:ENSG00000171720 MIM:605166; AllianceGenome:HGNC:4854
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: HD3; RPD3; KDAC3; RPD3-2
Summary: Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to the histone deacetylase/acuc/apha family. It has histone deacetylase activity and represses transcription when tethered to a promoter. It may participate in the regulation of transcription through its binding with the zinc-finger transcription factor YY1. This protein can also down-regulate p53 function and thus modulate cell growth and apoptosis. This gene is regarded as a potential tumor suppressor gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in lymph node (RPKM 21.1), adrenal (RPKM 20.9) and 25 other tissues See more
Orthologs: all
: Try the new Gene page
Try the new Transcripts and proteins table

Genomic context

Location:: 5q31.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (141620881..141636849, complement)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (142146886..142162855, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (141000448..141016416, complement)

Chromosome 5 - NC_000005.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The involvement of HDAC3 in the pathogenesis of lung injury and pulmonary fibrosis.
Title: The involvement of HDAC3 in the pathogenesis of lung injury and pulmonary fibrosis.
De novo missense variants in HDAC3 leading to epigenetic machinery dysfunction are associated with a variable neurodevelopmental disorder.
Title: De novo missense variants in HDAC3 leading to epigenetic machinery dysfunction are associated with a variable neurodevelopmental disorder.
N-Acetylgalactosamine-4-sulfatase (Arylsulfatase B) Regulates PD-L1 Expression in Melanoma by an HDAC3-Mediated Epigenetic Mechanism.
Title: N-Acetylgalactosamine-4-sulfatase (Arylsulfatase B) Regulates PD-L1 Expression in Melanoma by an HDAC3-Mediated Epigenetic Mechanism.
Matrix stiffening promotes chondrocyte senescence and the osteoarthritis development through downregulating HDAC3.
Title: Matrix stiffening promotes chondrocyte senescence and the osteoarthritis development through downregulating HDAC3.
Gut microbial metabolite targets HDAC3-FOXK1-interferon axis in fibroblast-like synoviocytes to ameliorate rheumatoid arthritis.
Title: Gut microbial metabolite targets HDAC3-FOXK1-interferon axis in fibroblast-like synoviocytes to ameliorate rheumatoid arthritis.
HDAC3 promotes Sertoli cell maturation and maintains the blood-testis barrier dynamics.
Title: HDAC3 promotes Sertoli cell maturation and maintains the blood-testis barrier dynamics.
Reduced endometrial expression of histone deacetylase 3 in women with adenomyosis who complained of heavy menstrual bleeding.
Title: Reduced endometrial expression of histone deacetylase 3 in women with adenomyosis who complained of heavy menstrual bleeding.
Pulling rank with RNA: RANKL promotes the association of PGC-1beta/RNA complexes with NCoR/HDAC3 to activate gene expression in osteoclasts.
Title: Pulling rank with RNA: RANKL promotes the association of PGC-1β/RNA complexes with NCoR/HDAC3 to activate gene expression in osteoclasts.
Hepatocyte-specific HDAC3 ablation promotes hepatocellular carcinoma in females by suppressing Foxa1/2.
Title: Hepatocyte-specific HDAC3 ablation promotes hepatocellular carcinoma in females by suppressing Foxa1/2.
Histone deacetylase 3 regulates microglial function through histone deacetylation.
Title: Histone deacetylase 3 regulates microglial function through histone deacetylation.

Submit: New GeneRIF Correction See all GeneRIFs (215)

Phenotypes

Go to the top of the page Help

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)

Interaction	Pubs
HIV-1 promoter transcription is restricted by HDAC3 in 2D10 cells as shown through shRNA knockdown or an HDAC3 specific inhibitor (BRD3308)	PubMed

Protein	Gene	Interaction	Pubs
Vif	vif	HIV-1 Vif is identified to have a physical interaction with histone deacetylase 3 (HDAC3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed
Vpr	vpr	HIV-1 Vpr depletes HDAC3 in HIV-1 latently infected J-Lat cells by targeting HDAC3 for proteasomal degradation; HDAC3 was degraded on HIV-1 LTR and resulting in recruitment of active transcription markers 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

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

SGC33638 (e-PCR)
- UniSTS:53059

SGC30748 (e-PCR)
- UniSTS:9813

A007C33 (e-PCR)
- UniSTS:56173

HDAC3_1724 (e-PCR)
- UniSTS:280749

HSC11A022 (e-PCR)
- UniSTS:78030

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor binding	TAS Traceable Author Statement more info	PubMed
enables NF-kappaB binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables cyclin binding	IPI Inferred from Physical Interaction 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
enables histone deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase activity	IEA Inferred from Electronic Annotation more info
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 activity, hydrolytic mechanism	IEA Inferred from Electronic Annotation 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
enables histone decrotonylase activity	IEA Inferred from Electronic Annotation more info
enables histone isonicotinyllysine deisonicotinylase activity	IDA Inferred from Direct Assay more info	PubMed
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 de-2-hydroxyisobutyrylase activity	IEA Inferred from Electronic Annotation more info
enables protein decrotonylase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein decrotonylase activity	IEA Inferred from Electronic Annotation more info
enables protein lysine deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein lysine deacetylase activity	IEA Inferred from Electronic Annotation more info
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 protein lysine delactylase activity	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription corepressor activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription corepressor activity	TAS Traceable Author Statement more info
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair-dependent chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to fluid shear stress	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	TAS Traceable Author Statement more info	PubMed
involved_in circadian regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in cornified envelope assembly	IEA Inferred from Electronic Annotation more info
involved_in epidermis development	IEA Inferred from Electronic Annotation more info
involved_in epigenetic regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of mitotic spindle orientation	IDA Inferred from Direct Assay more info	PubMed
involved_in establishment of skin barrier	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of JNK cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	TAS Traceable Author Statement more info	PubMed
NOT involved_in negative regulation of myotube differentiation	IMP Inferred from Mutant Phenotype 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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription initiation by RNA polymerase II	TAS Traceable Author Statement more info
involved_in positive regulation of TOR signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cold-induced thermogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of ferroptosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
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 random inactivation of X chromosome	IEA Inferred from Electronic Annotation more info
involved_in regulation of circadian rhythm	IEA Inferred from Electronic Annotation more info
involved_in regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of protein stability	IDA Inferred from Direct Assay more info	PubMed
involved_in spindle assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in chromatin	IEA Inferred from Electronic Annotation more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor 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 mitotic spindle	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	IEA Inferred from Electronic Annotation more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: histone deacetylase 3

Names: SMAP45; protein deacetylase HDAC3; protein deacylase HDAC3

NP_001341968.1

EC 3.5.1.98

NP_001341969.1

EC 3.5.1.98

NP_001341970.1

EC 3.5.1.98

NP_003874.2

EC 3.5.1.98

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_029678.2 RefSeqGene

Range

5008..20976

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001355039.2 → NP_001341968.1 histone deacetylase 3 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC008781, KC877130

Conserved Domains (1) summary

cd10005
Location:3 → 383

HDAC3; Histone deacetylase 3 (HDAC3)
NM_001355040.2 → NP_001341969.1 histone deacetylase 3 isoform 3

Status: REVIEWED

Source sequence(s)

AC008781, KC877130

UniProtKB/TrEMBL

Q9H368

Conserved Domains (1) summary

cl17011
Location:5 → 230

Arginase_HDAC; Arginase-like and histone-like hydrolases
NM_001355041.2 → NP_001341970.1 histone deacetylase 3 isoform 4

Status: REVIEWED

Source sequence(s)

AC008781, KC877130

UniProtKB/TrEMBL

Q9H368

Conserved Domains (1) summary

cl17011
Location:1 → 196

Arginase_HDAC; Arginase-like and histone-like hydrolases
NM_003883.4 → NP_003874.2 histone deacetylase 3 isoform 2

See identical proteins and their annotated locations for NP_003874.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

BC000614, BM461585, DB456387

Consensus CDS

CCDS4264.1

UniProtKB/Swiss-Prot

D3DQE1, O15379, O43268, Q9UEI5, Q9UEV0

Related

ENSP00000302967.3, ENST00000305264.8

Conserved Domains (1) summary

cd10005
Location:3 → 383

HDAC3; Histone deacetylase 3 (HDAC3)

RNA

NR_149164.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC008781, KC877130
NR_149165.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC008781, KC877130

Related

ENST00000937594.1
NR_149166.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC008781, KC877130
NR_149167.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC008781, KC877130
NR_149168.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC008781, KC877130
NR_149169.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC008781, KC877130