hdac1 histone deacetylase 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hdac1provided by ZNC
Official Full Name: histone deacetylase 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-020419-32
See related: Ensembl:ENSDARG00000015427 AllianceGenome:ZFIN:ZDB-GENE-020419-32
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: hdac-1; chunp6919; zgc:65818; wu:fb19h11; wu:fi06f03; zgc:101582; mp:zf637-2-001987
Summary: Enables transcription corepressor activity. Involved in negative regulation of transcription by RNA polymerase II. Acts upstream of or within with a positive effect on secondary heart field specification. Acts upstream of or within several processes, including cardiac muscle cell proliferation; digestive system development; and nervous system development. Predicted to be located in cytoplasm and nucleus. Predicted to be part of NuRD complex. Is expressed in immature eye; nervous system; pectoral fin; and pharyngeal arch. Orthologous to human HDAC1 (histone deacetylase 1). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 19

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	19	NC_133194.1 (32277852..32287811)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	19	NC_007130.7 (29808700..29818648)

Chromosome 19 - NC_133194.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hdac1-deficiency affects the cell cycle axis Cdc25-Cdk1 causing impaired G2/M phase progression and reduced cardiomyocyte proliferation in zebrafish.
Title: Hdac1-deficiency affects the cell cycle axis Cdc25-Cdk1 causing impaired G2/M phase progression and reduced cardiomyocyte proliferation in zebrafish.
A unique macrophage subpopulation signals directly to progenitor cells to promote regenerative neurogenesis in the zebrafish spinal cord.
Title: A unique macrophage subpopulation signals directly to progenitor cells to promote regenerative neurogenesis in the zebrafish spinal cord.
Hdac1 regulates differentiation of liver progenitor cells into hepatocytes via Sox9b and differentiation of LPCs into biliary epithelial cells via Cdk8, Fbxw7, and Notch3 in zebrafish with severe hepatocyte loss.
Title: Hdac1 Regulates Differentiation of Bipotent Liver Progenitor Cells During Regeneration via Sox9b and Cdk8.
rbbp4 is required for survival of postmitotic precursors, and hdac1 maintains proliferation of the neural stem cell/progenitor pool.
Title: Epigenetic regulators Rbbp4 and Hdac1 are overexpressed in a zebrafish model of RB1 embryonal brain tumor, and are required for neural progenitor survival and proliferation.
data represent a step towards the comprehension of HDAC1 regulation by its PTM code, with important implications in unravelling its roles both in physiology and pathology
Title: Dynamic phosphorylation of Histone Deacetylase 1 by Aurora kinases during mitosis regulates zebrafish embryos development.
results indicate that HDAC1 plays an important role in otic vesicle formation.
Title: Histone deacetylase 1 is required for the development of the zebrafish inner ear.
HDAC activity is necessary for control of cell proliferation and migration of posterior lateral line primordium and hair cell differentiation during early stages of its development in zebrafish.
Title: Histone deacetylase activity is required for embryonic posterior lateral line development.
This study reveals distinct functional and temporal requirements for zebrafish hdac1 during neural crest-derived craniofacial and peripheral neuron development.
Title: Distinct functional and temporal requirements for zebrafish Hdac1 during neural crest-derived craniofacial and peripheral neuron development.
Hdac1 is required for expression of erm and fgf20a in rhombomeres; Hdac1-dependent expression of these two genes is attenuated in rhombomere boundary regions by Notch signalling activity
Title: Opposing actions of histone deacetylase 1 and Notch signalling restrict expression of erm and fgf20a to hindbrain rhombomere centres during zebrafish neurogenesis.
HDAC1 is required for pancreatic epithelial proliferation in development and cancer.
Title: Histone deacetylase 1 is required for exocrine pancreatic epithelial proliferation in development and cancer.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

fb19h11.x1 (e-PCR)
- UniSTS:203041

z46730 (e-PCR), detects polymorphism
- UniSTS:238484

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables histone acetyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
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, hydrolytic mechanism	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	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

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within Wnt signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within convergent extension involved in axis elongation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of dorsal identity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within digestive tract development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within exocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within facial nucleus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hematopoietic stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within liver development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within melanocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within oligodendrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within osteoblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rostrocaudal neural tube patterning	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect secondary heart field specification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: histone deacetylase 1

Names: col; colgate

NP_775343.1

EC 3.5.1.98

XP_005159649.1

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_173236.1 → NP_775343.1 histone deacetylase 1

See identical proteins and their annotated locations for NP_775343.1

Status: PROVISIONAL

Source sequence(s)

AF506201

UniProtKB/TrEMBL

Q8JIY7

Related

ENSDARP00000051798.4, ENSDART00000051799.6

Conserved Domains (2) summary

cd10010
Location:5 → 375

HDAC1; Histone deacetylase 1 (HDAC1)

PTZ00063
Location:8 → 406

PTZ00063; histone deacetylase; Provisional

RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

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

Reference GRCz12tu Primary Assembly

Genomic

NC_133194.1 Reference GRCz12tu Primary Assembly

Range

32277852..32287811

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005159592.6 → XP_005159649.1 histone deacetylase 1 isoform X1

UniProtKB/TrEMBL

A0A2R8QIW0, A0A8M2B6N2

Related

ENSDARP00000155165.1

Conserved Domains (2) summary

cd10010
Location:5 → 375

HDAC1; Histone deacetylase 1 (HDAC1)

PTZ00063
Location:8 → 406

PTZ00063; histone deacetylase; Provisional