Hdac1 histone deacetylase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hdac1provided by RGD
Official Full Name: histone deacetylase 1provided by RGD
Primary source: RGD:1309799
See related: Ensembl:ENSRNOG00000009568 AllianceGenome:RGD:1309799
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables DNA-binding transcription factor binding activity; chromatin binding activity; and histone deacetylase activity. Involved in several processes, including positive regulation of cytokine production; regulation of apoptotic process; and regulation of protein modification process. Located in several cellular components, including chromatin; neuron projection; and perinuclear region of cytoplasm. Part of protein-containing complex. Biomarker of pulmonary hypertension. Orthologous to human HDAC1 (histone deacetylase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 374.0), Adrenal (RPKM 298.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (147138328..147165387, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (141853992..141881057, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (147716664..147743723, complement)

Chromosome 5 - NC_086023.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Silencing EIF3A ameliorates pulmonary arterial hypertension through HDAC1 and PTEN/PI3K/AKT pathway in vitro and in vivo.
Title: Silencing EIF3A ameliorates pulmonary arterial hypertension through HDAC1 and PTEN/PI3K/AKT pathway in vitro and in vivo.
HDAC1 overexpression promoted by METTL3-IGF2BP2 inhibits FGF21 expression in metabolic syndrome-related liver injury.
Title: HDAC1 overexpression promoted by METTL3-IGF2BP2 inhibits FGF21 expression in metabolic syndrome-related liver injury.
[(11)C]Martinostat PET analysis reveals reduced HDAC I availability in Alzheimer's disease.
Title: [(11)C]Martinostat PET analysis reveals reduced HDAC I availability in Alzheimer's disease.
Activation-induced chromatin reorganization in neurons depends on HDAC1 activity.
Title: Activation-induced chromatin reorganization in neurons depends on HDAC1 activity.
Bilateral histone deacetylase 1 and 2 activity and enrichment at unique genes following induction of long-term potentiation in vivo.
Title: Bilateral histone deacetylase 1 and 2 activity and enrichment at unique genes following induction of long-term potentiation in vivo.
HDAC1 deregulation promotes neuronal loss and deficit of motor function in stroke pathogenesis.
Title: HDAC1 deregulation promotes neuronal loss and deficit of motor function in stroke pathogenesis.
HDAC1 Expression, Histone Deacetylation, and Protective Role of Sodium Valproate in the Rat Dorsal Root Ganglia After Sciatic Nerve Transection.
Title: HDAC1 Expression, Histone Deacetylation, and Protective Role of Sodium Valproate in the Rat Dorsal Root Ganglia After Sciatic Nerve Transection.
Inhibition of Histone Deacetylase 1 Prevents the Decrease in Titin (Connectin) Content and Development of Atrophy in Rat m. soleus after 3-Day Hindlimb Unloading.
Title: Inhibition of Histone Deacetylase 1 Prevents the Decrease in Titin (Connectin) Content and Development of Atrophy in Rat m. soleus after 3-Day Hindlimb Unloading.
MiR-449 improves cardiac function by regulating HDAC1 and cTnI.
Title: MiR-449 improves cardiac function by regulating HDAC1 and cTnI.
HDAC1-mediated deacetylation of LSD1 regulates vascular calcification by promoting autophagy in chronic renal failure.
Title: HDAC1-mediated deacetylation of LSD1 regulates vascular calcification by promoting autophagy in chronic renal failure.

Submit: New GeneRIF Correction See all GeneRIFs (49)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Hdac1 (e-PCR), detects polymorphism
- UniSTS:516621

RH127908 (e-PCR)
- UniSTS:211218

BI274654 (e-PCR)
- UniSTS:249152

RH125343 (e-PCR)
- UniSTS:162165

Hdac1 (e-PCR), detects polymorphism
- UniSTS:495836

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
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 E-box binding	ISO Inferred from Sequence Orthology more info
enables Krueppel-associated box domain binding	ISO Inferred from Sequence Orthology more info
enables NF-kappaB binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II core promoter sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables core promoter sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables deacetylase activity	IDA Inferred from Direct Assay more info	PubMed
enables enzyme 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	IEA Inferred from Electronic Annotation more info
enables histone deacetylase activity	ISO Inferred from Sequence Orthology more info
enables histone deacetylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables histone decrotonylase activity	ISO Inferred from Sequence Orthology more info
enables histone decrotonylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables p53 binding	ISO Inferred from Sequence Orthology 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 lysine deacetylase activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription corepressor activity	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to oxidative stress	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to platelet-derived growth factor stimulus	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to tumor necrosis factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in circadian regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in embryonic digit morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endoderm development	ISO Inferred from Sequence Orthology more info
involved_in epidermal cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in eyelid development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in fungiform papilla formation	ISO Inferred from Sequence Orthology more info
involved_in hair follicle placode formation	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within hippocampus development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of androgen receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of insulin secretion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of intrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
NOT involved_in negative regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of peptidyl-lysine acetylation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in odontogenesis of dentin-containing tooth	ISO Inferred from Sequence Orthology more info
acts_upstream_of oligodendrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of chemokine (C-X-C motif) ligand 2 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of interleukin-1 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of oligodendrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of oligodendrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of smooth muscle cell proliferation	IGI Inferred from Genetic Interaction 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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of type B pancreatic cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of tyrosine phosphorylation of STAT protein	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to amphetamine	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to caffeine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hyperoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to lipopolysaccharide	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
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 Sin3-type complex	ISO Inferred from Sequence Orthology more info
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of heterochromatin	ISO Inferred from Sequence Orthology more info
part_of histone deacetylase complex	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
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 perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone deacetylase 1

Names: HD1; protein deacetylase HDAC1; protein decrotonylase HDAC1

NP_001020580.1

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.