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HDAC5 histone deacetylase 5 [ Homo sapiens (human) ]

Gene ID: 10014, updated on 2-Nov-2024

Summary

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Official Symbol
HDAC5provided by HGNC
Official Full Name
histone deacetylase 5provided by HGNC
Primary source
HGNC:HGNC:14068
See related
Ensembl:ENSG00000108840 MIM:605315; AllianceGenome:HGNC:14068
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
HD5; NY-CO-9
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 class II histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. It coimmunoprecipitates only with HDAC3 family member and might form multicomplex proteins. It also interacts with myocyte enhancer factor-2 (MEF2) proteins, resulting in repression of MEF2-dependent genes. This gene is thought to be associated with colon cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in skin (RPKM 14.0), ovary (RPKM 13.4) and 25 other tissues See more
Orthologs
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Genomic context

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See HDAC5 in Genome Data Viewer
Location:
17q21.31
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44076753..44123641, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (44929260..44976146, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42154121..42201009, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene LSM12 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8571 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42146518-42147445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42147446-42148372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12251 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42149300-42150225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42152642-42153376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42154394-42154933 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:42159496-42160695 Neighboring gene glucose-6-phosphatase catalytic subunit 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42169749-42170254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42172728-42173488 Neighboring gene Sharpr-MPRA regulatory region 9416 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42176231-42176442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42182651-42183302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42189382-42189882 Neighboring gene uncharacterized LOC105371789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42202517-42203016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42215327-42215850 Neighboring gene RNA, U6 small nuclear 131, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8576 Neighboring gene Sharpr-MPRA regulatory region 5 Neighboring gene homologous recombination factor with OB-fold Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12254

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. Role of HDAC5 Epigenetics in Chronic Craniofacial Neuropathic Pain. Hui SE, et al. Int J Mol Sci, 2024 Jun 23. PMID 38999998, Free PMC Article
  2. Neutralizing negative epigenetic regulation by HDAC5 enhances human haematopoietic stem cell homing and engraftment. Huang X, et al. Nat Commun, 2018 Jul 16. PMID 30013077, Free PMC Article
  3. Histone deacetylase 5 promotes the proliferation and invasion of lung cancer cells. Zhong L, et al. Oncol Rep, 2018 Oct. PMID 30066893
  4. HDAC5 Expression in Urothelial Carcinoma Cell Lines Inhibits Long-Term Proliferation but Can Promote Epithelial-to-Mesenchymal Transition. Jaguva Vasudevan AA, et al. Int J Mol Sci, 2019 Apr 30. PMID 31052182, Free PMC Article
  5. Abnormal methylation of histone deacetylase genes: implications on etiology and epigenetic therapy of astrocytomas. Gomes MV, et al. Anticancer Res, 2011 Apr. PMID 21508384

See all (218) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of HDAC5 Epigenetics in Chronic Craniofacial Neuropathic Pain.
    Title: Role of HDAC5 Epigenetics in Chronic Craniofacial Neuropathic Pain.
  2. Histone Trimethylations and HDAC5 Regulate Spheroid Subpopulation and Differentiation Signaling of Human Adipose-Derived Stem Cells.
    Title: Histone Trimethylations and HDAC5 Regulate Spheroid Subpopulation and Differentiation Signaling of Human Adipose-Derived Stem Cells.
  3. NFYB increases chemosensitivity in glioblastoma by promoting HDAC5-mediated transcriptional inhibition of SHMT2.
    Title: NFYB increases chemosensitivity in glioblastoma by promoting HDAC5-mediated transcriptional inhibition of SHMT2.
  4. HDAC5 Loss Enhances Phospholipid-Derived Arachidonic Acid Generation and Confers Sensitivity to cPLA2 Inhibition in Pancreatic Cancer.
    Title: HDAC5 Loss Enhances Phospholipid-Derived Arachidonic Acid Generation and Confers Sensitivity to cPLA2 Inhibition in Pancreatic Cancer.
  5. METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
    Title: METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
  6. HDAC5 inactivates CYR61-regulated CD31/mTOR axis to prevent the occurrence of preeclampsia.
    Title: HDAC5 inactivates CYR61-regulated CD31/mTOR axis to prevent the occurrence of preeclampsia.
  7. HDAC5-mediated Smad7 silencing through MEF2A is critical for fibroblast activation and hypertrophic scar formation.
    Title: HDAC5-mediated Smad7 silencing through MEF2A is critical for fibroblast activation and hypertrophic scar formation.
  8. Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients.
    Title: Epigenetic master regulators HDAC1 and HDAC5 control pathobiont Enterobacteria colonization in ileal mucosa of Crohn's disease patients.
  9. HDAC5, negatively regulated by miR-148a-3p, promotes colon cancer cell migration.
    Title: HDAC5, negatively regulated by miR-148a-3p, promotes colon cancer cell migration.
  10. HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer.
    Title: HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer.
Submit: New GeneRIF Correction See all GeneRIFs (84)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ90614

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 IPI
Inferred from Physical Interaction
more info
 PubMed 
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables histone deacetylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone deacetylase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase C binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein lysine deacetylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
contributes_to transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription corepressor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in B cell activation TAS
Traceable Author Statement
more info
 PubMed 
involved_in B cell differentiation TAS
Traceable Author Statement
more info
 PubMed 
involved_in cellular response to insulin stimulus NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
  
involved_in inflammatory response TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of cell migration involved in sprouting angiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of gene expression, epigenetic NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of myotube differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within 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 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 neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of myotube differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of protein binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to activity IEA
Inferred from Electronic Annotation
more info
  
involved_in response to cocaine IEA
Inferred from Electronic Annotation
more info
  
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
part_of histone deacetylase complex TAS
Traceable Author Statement
more info
 PubMed 
located_in nuclear speck 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 

General protein information

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Preferred Names
histone deacetylase 5
Names
antigen NY-CO-9
NP_001015053.1
NP_001369322.1
NP_005465.2
XP_011522451.1
XP_047291003.1
XP_047291004.1
XP_047291005.1
XP_047291006.1
XP_047291007.1
XP_047291008.1
XP_047291009.1
XP_047291010.1
XP_047291011.1
XP_047291012.1
XP_047291013.1
XP_054170588.1
XP_054170589.1
XP_054170590.1
XP_054170591.1
XP_054170592.1
XP_054170593.1
XP_054170594.1
XP_054170595.1
XP_054170596.1
XP_054170597.1
XP_054170598.1

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)

  1. NM_001015053.2 → NP_001015053.1  histone deacetylase 5 isoform 3

    See identical proteins and their annotated locations for NP_001015053.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
    Source sequence(s)
    AB011172, AC023855, BC051824, CN290533
    Consensus CDS
    CCDS32663.1
    UniProtKB/Swiss-Prot
    Q9UQL6
    Related
    ENSP00000225983.5, ENST00000225983.10
    Conserved Domains (2) summary
    cd10164
    Location:69 → 165
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:680 → 1096
    HDAC5; Histone deacetylase 5

  2. NM_001382393.1 → NP_001369322.1  histone deacetylase 5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AB011172, AC023855, BC051824
    Consensus CDS
    CCDS45696.1
    UniProtKB/Swiss-Prot
    C9JFV9, O60340, O60528, Q96DY4, Q9UQL6
    Related
    ENSP00000468004.1, ENST00000586802.5
    Conserved Domains (2) summary
    cd10164
    Location:68 → 164
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:679 → 1095
    HDAC5; Histone deacetylase 5

  3. NM_005474.5 → NP_005465.2  histone deacetylase 5 isoform 1

    See identical proteins and their annotated locations for NP_005465.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) uses an alternate in-frame splice site compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is 1 aa shorter compared to isoform 3.
    Source sequence(s)
    AB011172, AC023855, BC051824, BM564861
    Consensus CDS
    CCDS45696.1
    UniProtKB/Swiss-Prot
    C9JFV9, O60340, O60528, Q96DY4, Q9UQL6
    Related
    ENSP00000507606.1, ENST00000682912.1
    Conserved Domains (2) summary
    cd10164
    Location:68 → 164
    ClassIIa_HDAC5_Gln-rich-N; Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase
    cd10007
    Location:679 → 1095
    HDAC5; Histone deacetylase 5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    44076753..44123641 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435054.1 → XP_047291010.1  histone deacetylase 5 isoform X6

  2. XM_047435052.1 → XP_047291008.1  histone deacetylase 5 isoform X5

  3. XM_047435050.1 → XP_047291006.1  histone deacetylase 5 isoform X3

  4. XM_011524149.3 → XP_011522451.1  histone deacetylase 5 isoform X4

    Conserved Domains (2) summary
    cd10007
    Location:671 → 1087
    HDAC5; Histone deacetylase 5
    cl23765
    Location:69 → 156
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

  5. XM_047435048.1 → XP_047291004.1  histone deacetylase 5 isoform X2

  6. XM_047435051.1 → XP_047291007.1  histone deacetylase 5 isoform X3

  7. XM_047435049.1 → XP_047291005.1  histone deacetylase 5 isoform X2

  8. XM_047435047.1 → XP_047291003.1  histone deacetylase 5 isoform X1

  9. XM_047435053.1 → XP_047291009.1  histone deacetylase 5 isoform X9

  10. XM_047435056.1 → XP_047291012.1  histone deacetylase 5 isoform X7

  11. XM_047435055.1 → XP_047291011.1  histone deacetylase 5 isoform X7

  12. XM_047435057.1 → XP_047291013.1  histone deacetylase 5 isoform X8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    44929260..44976146 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314620.1 → XP_054170595.1  histone deacetylase 5 isoform X6

  2. XM_054314619.1 → XP_054170594.1  histone deacetylase 5 isoform X5

  3. XM_054314616.1 → XP_054170591.1  histone deacetylase 5 isoform X3

  4. XM_054314618.1 → XP_054170593.1  histone deacetylase 5 isoform X4

  5. XM_054314614.1 → XP_054170589.1  histone deacetylase 5 isoform X2

  6. XM_054314617.1 → XP_054170592.1  histone deacetylase 5 isoform X3

  7. XM_054314615.1 → XP_054170590.1  histone deacetylase 5 isoform X2

  8. XM_054314613.1 → XP_054170588.1  histone deacetylase 5 isoform X1

  9. XM_054314622.1 → XP_054170597.1  histone deacetylase 5 isoform X7

  10. XM_054314621.1 → XP_054170596.1  histone deacetylase 5 isoform X7

  11. XM_054314623.1 → XP_054170598.1  histone deacetylase 5 isoform X8

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_139205.1: Suppressed sequence

    Description
    NM_139205.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UQL6.2 GenPept UniProtKB/Swiss-Prot:Q9UQL6

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