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HDAC8 histone deacetylase 8 [ Homo sapiens (human) ]

Gene ID: 55869, updated on 15-Apr-2019

Summary

Official Symbol
HDAC8provided by HGNC
Official Full Name
histone deacetylase 8provided by HGNC
Primary source
HGNC:HGNC:13315
See related
Ensembl:ENSG00000147099 MIM:300269
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
HD8; WTS; RPD3; CDA07; CDLS5; KDAC8; MRXS6; HDACL1
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 class I of the histone deacetylase family. It catalyzes the deacetylation of lysine residues in the histone N-terminal tails and represses transcription in large multiprotein complexes with transcriptional co-repressors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
Expression
Ubiquitous expression in adrenal (RPKM 3.9), thyroid (RPKM 3.1) and 25 other tissues See more
Orthologs

Genomic context

See HDAC8 in Genome Data Viewer
Location:
Xq13.1
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (72329516..72573103, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (71549366..71792953, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373250 Neighboring gene ribosomal protein S4 X-linked Neighboring gene Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 Neighboring gene RNA, U2 small nuclear 68, pseudogene Neighboring gene phosphorylase kinase regulatory subunit alpha 1 Neighboring gene matrin 3 pseudogene Neighboring gene PHKA1 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Cornelia de Lange syndrome 5
MedGen: C3550903 OMIM: 300882 GeneReviews: Cornelia de Lange Syndrome
Compare labs
De Lange syndrome
MedGen: C0270972 GeneReviews: Cornelia de Lange Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-03-28)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2018-03-28)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr depletes HDAC1, 2, 3 and 8 to overcome HIV-1 proviral latency in macrophages PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Alcoholism, organism-specific biosystem (from KEGG)
    Alcoholism, organism-specific biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Alcoholism, conserved biosystem (from KEGG)
    Alcoholism, conserved biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Cell Cycle, organism-specific biosystem (from WikiPathways)
    Cell Cycle, organism-specific biosystemThe cell cycle is the series of events that takes place in a cell leading to its division and duplication (replication). Regulation of the cell cycle involves processes crucial to the survival of a c...
  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
    Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants, organism-specific biosystem (from REACTOME)
    Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants, organism-specific biosystemWhen found in cis, HD and PEST domain mutations act synergistically, increasing NOTCH1 transcriptional activity up to ~40-fold, compared with up to ~10-fold and up to ~2-fold increase with HD mutatio...
  • Constitutive Signaling by NOTCH1 PEST Domain Mutants, organism-specific biosystem (from REACTOME)
    Constitutive Signaling by NOTCH1 PEST Domain Mutants, organism-specific biosystemAs NOTCH1 PEST domain is intracellular, NOTCH1 PEST domain mutants are expected to behave as the wild-type NOTCH1 with respect to ligand binding and proteolytic cleavage mediated activation of signal...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
    Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
  • HDACs deacetylate histones, organism-specific biosystem (from REACTOME)
    HDACs deacetylate histones, organism-specific biosystemLysine deacetylases (KDACs), historically referred to as histone deacetylases (HDACs), are divided into the Rpd3/Hda1 metal-dependent 'classical HDAC family' (de Ruijter et al. 2003, Verdin et al. 2...
  • Initiation of transcription and translation elongation at the HIV-1 LTR, organism-specific biosystem (from WikiPathways)
    Initiation of transcription and translation elongation at the HIV-1 LTR, organism-specific biosystemFollowing cellular activation or drug treatment, NFAT and NF-kB translocate to the nucleus and bind sites at the HIV-1 LTR. NFAT and NF-kB recruit p300/CBP to the LTR, resulting in acetylation of his...
  • Integrated Pancreatic Cancer Pathway, organism-specific biosystem (from WikiPathways)
    Integrated Pancreatic Cancer Pathway, organism-specific biosystemAn integrated pathway model which displays the protein-protein interactions (PPIs) among the relevant proteins for pancreatic cancer. This pathway is a collection of different mechanistic protein pat...
  • M Phase, organism-specific biosystem (from REACTOME)
    M Phase, organism-specific biosystemMitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Fin...
  • Mitotic Anaphase, organism-specific biosystem (from REACTOME)
    Mitotic Anaphase, organism-specific biosystemIn anaphase, the paired chromosomes separate at the centromeres, and move to the opposite sides of the cell. The movement of the chromosomes is facilitated by a combination of kinetochore movement al...
  • Mitotic Metaphase and Anaphase, organism-specific biosystem (from REACTOME)
    Mitotic Metaphase and Anaphase, organism-specific biosystemMetaphase is marked by the formation of the metaphase plate. The metaphase plate is formed when the spindle fibers align the chromosomes along the middle of the cell. Such an organization helps to ...
  • Mitotic Prometaphase, organism-specific biosystem (from REACTOME)
    Mitotic Prometaphase, organism-specific biosystemThe dissolution of the nuclear membrane marks the beginning of the prometaphase. Kinetochores are created when proteins attach to the centromeres. Microtubules then attach at the kinetochores, and th...
  • NOTCH1 Intracellular Domain Regulates Transcription, organism-specific biosystem (from REACTOME)
    NOTCH1 Intracellular Domain Regulates Transcription, organism-specific biosystemNICD1 produced by activation of NOTCH1 in response to Delta and Jagged ligands (DLL/JAG) presented in trans, traffics to the nucleus where it acts as a transcription regulator. In the nucleus, NICD1 ...
  • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
    Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
  • Resolution of Sister Chromatid Cohesion, organism-specific biosystem (from REACTOME)
    Resolution of Sister Chromatid Cohesion, organism-specific biosystemThe resolution of sister chromatids in mitotic prometaphase involves removal of cohesin complexes from chromosomal arms, with preservation of cohesion at centromeres (Losada et al. 1998, Hauf et al. ...
  • Separation of Sister Chromatids, organism-specific biosystem (from REACTOME)
    Separation of Sister Chromatids, organism-specific biosystemWhile sister chromatids resolve in prometaphase, separating along chromosomal arms, the cohesion of sister centromeres persists until anaphase. At the anaphase onset, the anaphase promoting complex/c...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by NOTCH, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH, organism-specific biosystemThe Notch Signaling Pathway (NSP) is a highly conserved pathway for cell-cell communication. NSP is involved in the regulation of cellular differentiation, proliferation, and specification. For exam...
  • Signaling by NOTCH1, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1, organism-specific biosystemNOTCH1 functions as both a transmembrane receptor presented on the cell surface and as a transcriptional regulator in the nucleus.NOTCH1 receptor presented on the plasma membrane is activated by a me...
  • Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer, organism-specific biosystemMutations in the heterodimerization domain (HD) and PEST domain of NOTCH1 are frequently found in cis in T-cell acute lymphoblastic leukemia. While HD mutations alone result in up to ~10-fold increas...
  • Signaling by NOTCH1 PEST Domain Mutants in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 PEST Domain Mutants in Cancer, organism-specific biosystemNOTCH1 PEST domain mutations are frequently found in T-cell acute lymphoblastic leukemia (T-ALL). PEST domain mutations interfere with ubiquitination-mediated NOTCH1 downregulation and result in prol...
  • Signaling by NOTCH1 in Cancer, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH1 in Cancer, organism-specific biosystemHuman NOTCH1 was cloned as a chromosome 9 gene, translocated to the T-cell beta receptor (TCBR) promoter on chromosome 7 in T-cell acute lymphoblastic leukemia (T-ALL) (Ellisen et al. 1991). This tra...
  • Signaling events mediated by HDAC Class I, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events mediated by HDAC Class I, organism-specific biosystem
    Signaling events mediated by HDAC Class I
  • Viral carcinogenesis, organism-specific biosystem (from KEGG)
    Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
  • Viral carcinogenesis, conserved biosystem (from KEGG)
    Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Hsp70 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Hsp90 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylase activity TAS
Traceable Author Statement
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
chromatin assembly or disassembly TAS
Traceable Author Statement
more info
PubMed 
chromatin organization TAS
Traceable Author Statement
more info
PubMed 
histone H3 deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H4 deacetylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cohesin loading IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein stability IDA
Inferred from Direct Assay
more info
PubMed 
regulation of telomere maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
sister chromatid cohesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deacetylase complex TAS
Traceable Author Statement
more info
PubMed 
nuclear chromosome TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
nucleus TAS
Traceable Author Statement
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
histone deacetylase 8
Names
histone deacetylase-like 1
NP_001159890.1
NP_001159891.1
NP_001159892.1
NP_001159894.1
NP_001159920.1
NP_060956.1
XP_011529288.3
XP_016885129.2
XP_016885130.2
XP_016885131.1
XP_016885132.1
XP_016885133.1
XP_016885134.1
XP_016885135.1
XP_016885136.2
XP_024308173.1

NCBI Reference Sequences (RefSeq)

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

  1. NG_015851.1 RefSeqGene

    Range
    5001..248588
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166418.1NP_001159890.1  histone deacetylase 8 isoform 2

    See identical proteins and their annotated locations for NP_001159890.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate exons in the 5' coding region, compared to variant 1, resulting in a protein (isoform 2) that maintains the reading frame but is shorter, compared to isoform 1.
    Source sequence(s)
    AK296641, BC050433, BP229332, DC352390
    Consensus CDS
    CCDS55449.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362691.4, ENST00000373589.9
    Conserved Domains (1) summary
    cl17011
    Location:16286
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  2. NM_001166419.1NP_001159891.1  histone deacetylase 8 isoform 3

    See identical proteins and their annotated locations for NP_001159891.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several alternate 3' exons and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (3) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK074326, BP229332, DC352390
    Consensus CDS
    CCDS55451.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000414486.2, ENST00000439122.7
    Conserved Domains (1) summary
    cl17011
    Location:16246
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  3. NM_001166420.1NP_001159892.1  histone deacetylase 8 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks a large portion of the 3' coding region and has a distinct 3' UTR, compared to variant 1. The encoded isoform (5) has a shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AI651236, BF514915, BP229332, BQ189619, DC352390
    Consensus CDS
    CCDS55450.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362655.1, ENST00000373554.6
    Conserved Domains (1) summary
    cl17011
    Location:16146
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  4. NM_001166422.1NP_001159894.1  histone deacetylase 8 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks multiple alternate 3' exons and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (5) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI651236, AI916593, BP229332, DC352390
    Consensus CDS
    CCDS55452.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362657.3, ENST00000373556.8
    Conserved Domains (1) summary
    cl17011
    Location:16147
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  5. NM_001166448.1NP_001159920.1  histone deacetylase 8 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks multiple alternate coding exons and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (3) maintains the reading frame, but is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK074326, BP229332, BQ632790, DC352390
    Consensus CDS
    CCDS55448.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362660.4, ENST00000373559.8
    Conserved Domains (1) summary
    cl17011
    Location:16129
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  6. NM_018486.3NP_060956.1  histone deacetylase 8 isoform 1

    See identical proteins and their annotated locations for NP_060956.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AJ277724, BC050433, BP229332
    Consensus CDS
    CCDS14420.1
    UniProtKB/Swiss-Prot
    Q9BY41
    Related
    ENSP00000362674.3, ENST00000373573.9
    Conserved Domains (1) summary
    cd10000
    Location:16377
    HDAC8; Histone deacetylase 8 (HDAC8)

RNA

  1. NR_051952.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK298767, BC050433, BP229332, DC352390

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    72329516..72573103 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029644.2XP_016885133.1  histone deacetylase 8 isoform X6

  2. XM_017029642.1XP_016885131.1  histone deacetylase 8 isoform X4

    Related
    ENSP00000497568.1, ENST00000647654.1
  3. XM_017029643.2XP_016885132.1  histone deacetylase 8 isoform X5

  4. XM_017029641.2XP_016885130.2  histone deacetylase 8 isoform X3

    Related
    ENSP00000362685.2, ENST00000373583.6
    Conserved Domains (1) summary
    cd10000
    Location:16351
    HDAC8; Histone deacetylase 8 (HDAC8)
  5. XM_017029640.2XP_016885129.2  histone deacetylase 8 isoform X2

    Conserved Domains (1) summary
    cd10000
    Location:16345
    HDAC8; Histone deacetylase 8 (HDAC8)
  6. XM_011530986.3XP_011529288.3  histone deacetylase 8 isoform X1

    Related
    ENSP00000497188.1, ENST00000647886.1
    Conserved Domains (1) summary
    cd10000
    Location:16371
    HDAC8; Histone deacetylase 8 (HDAC8)
  7. XM_024452405.1XP_024308173.1  histone deacetylase 8 isoform X10

    Conserved Domains (1) summary
    cl17011
    Location:1176
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  8. XM_017029646.1XP_016885135.1  histone deacetylase 8 isoform X8

  9. XM_017029645.2XP_016885134.1  histone deacetylase 8 isoform X7

  10. XM_017029647.2XP_016885136.2  histone deacetylase 8 isoform X9

    Related
    ENSP00000498144.1, ENST00000650126.1
    Conserved Domains (1) summary
    cl17011
    Location:16220
    Arginase_HDAC; Arginase-like and histone-like hydrolases

RNA

  1. XR_938402.3 RNA Sequence

    Related
    ENST00000647594.1
  2. XR_001755711.2 RNA Sequence

    Related
    ENST00000648855.1
  3. XR_002958780.1 RNA Sequence

    Related
    ENST00000648939.1
  4. XR_002958781.1 RNA Sequence

    Related
    ENST00000648504.1
  5. XR_002958783.1 RNA Sequence

  6. XR_002958779.1 RNA Sequence

  7. XR_002958782.1 RNA Sequence

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