Hdac2 histone deacetylase 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hdac2provided by MGI
Official Full Name: histone deacetylase 2provided by MGI
Primary source: MGI:MGI:1097691
See related: Ensembl:ENSMUSG00000019777 AllianceGenome:MGI:1097691
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: YAF1; Yy1bp; mRPD3; D10Wsu179e
Summary: Enables several functions, including DNA binding activity; Krueppel-associated box domain binding activity; and hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides. Involved in several processes, including circadian regulation of gene expression; eyelid development in camera-type eye; and negative regulation of DNA-templated transcription. Acts upstream of or within several processes, including cellular response to trichostatin A; nervous system development; and regulation of signal transduction. Located in heterochromatin; nucleus; and replication fork. Part of RNA polymerase II transcription repressor complex. Is expressed in several structures, including alimentary system; brain; early conceptus; genitourinary system; and sensory organ. Human ortholog(s) of this gene implicated in stomach cancer. Orthologous to human HDAC2 (histone deacetylase 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in CNS E11.5 (RPKM 72.6), CNS E14 (RPKM 53.5) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 19.44 cM; 10 B1

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (36850293..36877885)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (36974297..37001889)

Chromosome 10 - NC_000076.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HRD1-mediated ubiquitination of HDAC2 regulates PPARalpha-mediated autophagy and alleviates metabolic-associated fatty liver disease.
Title: HRD1-mediated ubiquitination of HDAC2 regulates PPARα-mediated autophagy and alleviates metabolic-associated fatty liver disease.
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.
HDAC1/2 and HDAC3 play distinct roles in controlling adult Meibomian gland homeostasis.
Title: HDAC1/2 and HDAC3 play distinct roles in controlling adult Meibomian gland homeostasis.
Microglial histone deacetylase 2 is dispensable for functional and histological outcomes in a mouse model of traumatic brain injury.
Title: Microglial histone deacetylase 2 is dispensable for functional and histological outcomes in a mouse model of traumatic brain injury.
Attenuation of neuronal ferroptosis in intracerebral hemorrhage by inhibiting HDAC1/2: Microglial heterogenization via the Nrf2/HO1 pathway.
Title: Attenuation of neuronal ferroptosis in intracerebral hemorrhage by inhibiting HDAC1/2: Microglial heterogenization via the Nrf2/HO1 pathway.
HDAC2 counteracts vascular calcification by activating autophagy in chronic kidney disease.
Title: HDAC2 counteracts vascular calcification by activating autophagy in chronic kidney disease.
Gut microbiota regulates hepatic ischemia-reperfusion injury-induced cognitive dysfunction via the HDAC2-ACSS2 axis in mice.
Title: Gut microbiota regulates hepatic ischemia-reperfusion injury-induced cognitive dysfunction via the HDAC2-ACSS2 axis in mice.
HDAC1/2 control mesothelium/ovarian cancer adhesive interactions impacting on Talin-1-alpha5beta1-integrin-mediated actin cytoskeleton and extracellular matrix protein remodeling.
Title: HDAC1/2 control mesothelium/ovarian cancer adhesive interactions impacting on Talin-1-α5β1-integrin-mediated actin cytoskeleton and extracellular matrix protein remodeling.
Hdac1 and Hdac2 positively regulate Notch1 gain-of-function pathogenic signaling in committed osteoblasts of male mice.
Title: Hdac1 and Hdac2 positively regulate Notch1 gain-of-function pathogenic signaling in committed osteoblasts of male mice.
Differential expression of Hdac2 in male and female mice of differing social status.
Title: Differential expression of Hdac2 in male and female mice of differing social status.

Submit: New GeneRIF Correction See all GeneRIFs (155)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (6) 1 citation
Gene trapped (1) 1 citation
Targeted (12) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Hdac2 (e-PCR), detects polymorphism
- UniSTS:516622

NoName (e-PCR)
- UniSTS:236330

D10Wsu179e (e-PCR), detects polymorphism
- UniSTS:141526

RH136178 (e-PCR)
- UniSTS:210173

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	TAS Traceable Author Statement more info	PubMed
enables Krueppel-associated box domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables NF-kappaB binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables deacetylase activity	ISO Inferred from Sequence Orthology more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables heat shock protein binding	ISO Inferred from Sequence Orthology more info
enables histone H4K16 deacetylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone binding	ISO Inferred from Sequence Orthology more info
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	IGI Inferred from Genetic Interaction more info	PubMed
enables histone deacetylase activity	ISO Inferred from Sequence Orthology more info
enables histone deacetylase activity	TAS Traceable Author Statement more info	PubMed
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables histone decrotonylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone decrotonylase activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein de-2-hydroxyisobutyrylase activity	ISO Inferred from Sequence Orthology more info
enables protein de-2-hydroxyisobutyrylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein lysine deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein lysine deacetylase activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cardiac muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to hydrogen peroxide	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to trichostatin A	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	TAS Traceable Author Statement more info	PubMed
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in dendrite development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic digit morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in epidermal cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in eyelid development in camera-type eye	IGI Inferred from Genetic Interaction more info	PubMed
involved_in fungiform papilla formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in hair follicle placode formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in heterochromatin formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hippocampus development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of intrinsic apoptotic signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of miRNA transcription	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of miRNA transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neuron projection development	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of peptidyl-lysine acetylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of stem cell population maintenance	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in odontogenesis of dentin-containing tooth	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of oligodendrocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-binding transcription factor activity	IDA Inferred from Direct Assay 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	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-1 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of male mating behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of oligodendrocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of oligodendrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of proteolysis	ISO Inferred from Sequence Orthology more info
acts_upstream_of positive regulation of signaling receptor activity	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tyrosine phosphorylation of STAT protein	ISO Inferred from Sequence Orthology more info
involved_in protein deacetylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein modification process	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell fate specification	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of protein deacetylation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of sarcomere organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of stem cell differentiation	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of ESC/E(Z) complex	ISO Inferred from Sequence Orthology more info
part_of ESC/E(Z) complex	ISS Inferred from Sequence or Structural Similarity more info
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	ISO Inferred from Sequence Orthology more info
part_of NuRD complex	ISS Inferred from Sequence or Structural Similarity more info
part_of NuRD complex	NAS Non-traceable Author Statement more info	PubMed
part_of RNA polymerase II transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed
part_of Sin3-type complex	ISO Inferred from Sequence Orthology more info
part_of Sin3-type complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
part_of histone deacetylase complex	ISO Inferred from Sequence Orthology more info
part_of histone deacetylase complex	TAS Traceable Author Statement more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
located_in replication fork	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed
part_of transcription repressor complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: histone deacetylase 2

Names: HD2; YY1 transcription factor-binding protein; protein deacylase HDAC2

NP_032255.2

EC 3.5.1.98

XP_006512618.1

EC 3.5.1.98

XP_017169295.1

EC 3.5.1.98

XP_030100750.1

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_001428519.1 → NP_001415448.1 histone deacetylase 2 isoform b

Status: VALIDATED

Source sequence(s)

AC165370
NM_001428520.1 → NP_001415449.1 histone deacetylase 2 isoform c

Status: VALIDATED

Description

Transcript Variant: This variant (3), as well as variant 4, encodes isoform c.

Source sequence(s)

AC165370
NM_001428521.1 → NP_001415450.1 histone deacetylase 2 isoform c

Status: VALIDATED

Source sequence(s)

AC165370
NM_001428522.1 → NP_001415451.1 histone deacetylase 2 isoform d

Status: VALIDATED

Source sequence(s)

AC165370
NM_008229.2 → NP_032255.2 histone deacetylase 2 isoform a

See identical proteins and their annotated locations for NP_032255.2

Status: VALIDATED

Description

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

Source sequence(s)

AB221663, AK165734, U31758

Consensus CDS

CCDS23783.1

UniProtKB/Swiss-Prot

B2RRP3, P70288

UniProtKB/TrEMBL

A0A0R4J008

Related

ENSMUSP00000019911.8, ENSMUST00000019911.14

Conserved Domains (3) summary

cd10011
Location:9 → 374

HDAC2; Histone deacetylase 2 (HDAC2)

PTZ00063
Location:9 → 398

PTZ00063; histone deacetylase; Provisional

pfam15377
Location:391 → 486

DUF4604; Domain of unknown function (DUF4604)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000076.7 Reference GRCm39 C57BL/6J

Range

36850293..36877885

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030244890.1 → XP_030100750.1 histone deacetylase 2 isoform X2

Conserved Domains (2) summary

pfam05793
Location:256 → 346

TFIIF_alpha; Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

cl17011
Location:1 → 243

Arginase_HDAC; Arginase-like and histone-like hydrolases
XM_006512555.4 → XP_006512618.1 histone deacetylase 2 isoform X1

Conserved Domains (2) summary

pfam05793
Location:357 → 458

TFIIF_alpha; Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

cl17011
Location:1 → 344

Arginase_HDAC; Arginase-like and histone-like hydrolases
XM_017313806.2 → XP_017169295.1 histone deacetylase 2 isoform X2

Conserved Domains (2) summary

pfam05793
Location:256 → 346

TFIIF_alpha; Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

cl17011
Location:1 → 243

Arginase_HDAC; Arginase-like and histone-like hydrolases