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HDAC6 histone deacetylase 6 [ Homo sapiens (human) ]

Gene ID: 10013, updated on 20-Sep-2020

Summary

Official Symbol
HDAC6provided by HGNC
Official Full Name
histone deacetylase 6provided by HGNC
Primary source
HGNC:HGNC:14064
See related
Ensembl:ENSG00000094631 MIM:300272
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
HD6; JM21; CPBHM; PPP1R90
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 II of the histone deacetylase/acuc/apha family. It contains an internal duplication of two catalytic domains which appear to function independently of each other. This protein possesses histone deacetylase activity and represses transcription. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in kidney (RPKM 18.6), testis (RPKM 15.9) and 25 other tissues See more
Orthologs

Genomic context

See HDAC6 in Genome Data Viewer
Location:
Xp11.23
Exon count:
32
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (48801398..48824982)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48660086..48683408)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chrX.952 Neighboring gene GATA binding protein 1 Neighboring gene ES cell expressed Ras Neighboring gene proprotein convertase subtilisin/kexin type 1 inhibitor

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 Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 infectivity is decreased by HDAC6 overexpression in the virus producing cells (HEK293T) PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env The binding of HIV-1 gp120 to CD4+-permissive cells increases the level of acetylated alpha-tubulin in a CD4-dependent manner; overexpression of Histone Deacetylase 6 (HDAC6) inhibits the acetylation of alpha-tubulin and prevents HIV-1-cell fusion PubMed
Envelope transmembrane glycoprotein gp41 env Overexpression of Histone Deacetylase 6 (HDAC6) inhibits the acetylation of alpha-tubulin and remarkably prevents HIV-1 gp120/41-dependent cell fusion PubMed
Tat tat HIV-1 Tat-induced phosphorylation of CHUK (IKKalpha), IKBKB (IKKbeta), and RELA (p65) and NFKBI (IkappaBalpha) degradation are enhanced by HDAC6 in CRT-MG human astroglioma cells suggesting that HDAC6 is responsible for HIV-1 Tat-induced NF-kB activation PubMed
tat HIV-1 Tat-induced JUN (AP1) DNA binding activity is enhanced by HDAC6 in CRT-MG human astroglioma cells PubMed
tat HIV-1 Tat-induced phosphorylation of JUN (AP1) is enhanced by HDAC6 in CRT-MG human astroglioma cells suggesting that HDAC6 participates in HIV-1 Tat-induced regulation of JUN (AP1) signaling cascades PubMed
tat HIV-1 Tat-induced phosphorylation of MAPK1, MAPK3, MAPK14 and MAPK8 proteins is enhanced by HDAC6 in CRT-MG human astroglioma cells suggesting that HDAC6 is responsible for HIV-1 Tat-induced activation of MAPKs PubMed
tat HIV-1 Tat-induced increase in expression of ICAM1 is enhanced by HDAC6 in CRT-MG human astroglioma cells PubMed
tat HIV-1 Tat-induced increase in expression of CCL2, CXCL8 and CXCL10 is enhanced by HDAC6 in CRT-MG human astroglioma cells PubMed
tat HIV-1 Tat increases HDAC6 mRNA and protein expression levels in time- and dose-dependent manner and correlates with a reduced level of acetylated alpha-tubulin in CRT-MG human astroglioma cells PubMed
tat HIV-1 Tat and HDAC6 interact in the cytoplasm in a microtubule-dependent manner, which leads to deacetylate Tat at position Lys28 and to inhibit Tat-mediated transactivation PubMed
Vif vif HIV-1 Vif interacts with endogeneous non-degraded APOBEC3G (and HDAC6) when overexpressed in CEM.NKR.CCR5 cells as demonstrated by co-IP using cell lysates treated with Rnase A (suggesting interaction is direct protein-protein and not tethered by RNA) PubMed
vif HIV-1 degradation is mediated by HDAC6 overexpression in HEK293T cells and is independent of the APOBEC3G-Vif interaction PubMed
vif HIV-1 Vif-mediated APOBEC3G ubiquitination and proteasome degradation is inhibited by HDAC6 PubMed
vif HIV-1 Vif complexes with HDAC6 and APOBEC3G to form a ternary complex as demonstrated by co-IP assay using HEK293T cells lysates PubMed
vif HIV-1 Vif binds HDAC6 as demonstrated by GST-Vif, HA-HDAC6 pull-down assay PubMed
vif HIV-1 Vif protein expression is decreased by overexpression of HDAC6 in HEK293T cells without affecting endogeneous CBFB protein levels and this decrease is dependent on the C-terminal Buz domain of HDAC6 protein PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ16239

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Hsp90 protein binding IDA
Inferred from Direct Assay
more info
PubMed 
NAD-dependent histone deacetylase activity (H3-K14 specific) IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
NOT acetylspermidine deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
actin binding IEA
Inferred from Electronic Annotation
more info
 
alpha-tubulin binding IDA
Inferred from Direct Assay
more info
PubMed 
beta-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
beta-tubulin binding IEA
Inferred from Electronic Annotation
more info
 
dynein complex binding IDA
Inferred from Direct Assay
more info
PubMed 
enzyme binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone deacetylase binding IPI
Inferred from Physical Interaction
more info
PubMed 
microtubule binding IDA
Inferred from Direct Assay
more info
PubMed 
microtubule binding ISS
Inferred from Sequence or Structural Similarity
more info
 
misfolded protein binding EXP
Inferred from Experiment
more info
PubMed 
polyubiquitin modification-dependent protein binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
tau protein binding IDA
Inferred from Direct Assay
more info
PubMed 
tau protein binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
tau protein binding NAS
Non-traceable Author Statement
more info
PubMed 
tau protein binding TAS
Traceable Author Statement
more info
PubMed 
tubulin deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
tubulin deacetylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
tubulin deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
tubulin deacetylase activity TAS
Traceable Author Statement
more info
PubMed 
ubiquitin binding IEA
Inferred from Electronic Annotation
more info
 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Hsp90 deacetylation IEA
Inferred from Electronic Annotation
more info
 
aggresome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
autophagy IEA
Inferred from Electronic Annotation
more info
 
cellular response to hydrogen peroxide IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to misfolded protein IEA
Inferred from Electronic Annotation
more info
 
cellular response to topologically incorrect protein IMP
Inferred from Mutant Phenotype
more info
PubMed 
cilium assembly TAS
Traceable Author Statement
more info
 
collateral sprouting IEA
Inferred from Electronic Annotation
more info
 
dendritic spine morphogenesis IEA
Inferred from Electronic Annotation
more info
 
histone H3 deacetylation IEA
Inferred from Electronic Annotation
more info
 
histone deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
intracellular protein transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosome localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
mitochondrion localization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of hydrogen peroxide metabolic process IC
Inferred by Curator
more info
PubMed 
negative regulation of microtubule depolymerization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of oxidoreductase activity IC
Inferred by Curator
more info
PubMed 
negative regulation of protein complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein complex disassembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of proteolysis IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization IGI
Inferred from Genetic Interaction
more info
PubMed 
peptidyl-lysine deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT polyamine deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
polyubiquitinated misfolded protein transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of epithelial cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of hydrogen peroxide-mediated programmed cell death IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of peptidyl-serine phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of receptor biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
protein deacetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deacetylation TAS
Traceable Author Statement
more info
PubMed 
protein destabilization IEA
Inferred from Electronic Annotation
more info
 
protein polyubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein quality control for misfolded or incompletely synthesized proteins IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein-containing complex disassembly IEA
Inferred from Electronic Annotation
more info
 
regulation of androgen receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
regulation of autophagy TAS
Traceable Author Statement
more info
PubMed 
regulation of autophagy of mitochondrion TAS
Traceable Author Statement
more info
PubMed 
regulation of establishment of protein localization IEA
Inferred from Electronic Annotation
more info
 
regulation of fat cell differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of macroautophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of microtubule-based movement IC
Inferred by Curator
more info
PubMed 
regulation of protein stability IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to growth factor IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to misfolded protein IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT spermidine deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
tubulin deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
tubulin deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
tubulin deacetylation TAS
Traceable Author Statement
more info
PubMed 
ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
aggresome IDA
Inferred from Direct Assay
more info
PubMed 
aggresome TAS
Traceable Author Statement
more info
PubMed 
axon ISS
Inferred from Sequence or Structural Similarity
more info
 
caveola IDA
Inferred from Direct Assay
more info
PubMed 
cell leading edge IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytoplasmic microtubule IEA
Inferred from Electronic Annotation
more info
 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with dynein complex IDA
Inferred from Direct Assay
more info
PubMed 
histone deacetylase complex IDA
Inferred from Direct Assay
more info
PubMed 
inclusion body IDA
Inferred from Direct Assay
more info
PubMed 
microtubule IDA
Inferred from Direct Assay
more info
PubMed 
microtubule associated complex IDA
Inferred from Direct Assay
more info
PubMed 
multivesicular body TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
perikaryon ISS
Inferred from Sequence or Structural Similarity
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone deacetylase 6
Names
protein phosphatase 1, regulatory subunit 90
tubulin-lysine deacetylase HDAC6
NP_001308154.1
NP_001308155.1
NP_001308156.1
NP_001308157.1
NP_001308158.1
NP_001308159.1
NP_001308160.1
NP_006035.2
XP_016884676.1

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_012560.1 RefSeqGene

    Range
    4988..27900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001321225.2NP_001308154.1  histone deacetylase 6 isoform a

    Status: REVIEWED

    Source sequence(s)
    AK302926, AL137696, DC402494
    UniProtKB/TrEMBL
    B4DZH6, Q9NSW6
    Conserved Domains (3) summary
    cd10003
    Location:499849
    HDAC6-dom2; Histone deacetylase 6, domain 2
    cd11682
    Location:113449
    HDAC6-dom1; Histone deacetylase 6, domain 1
    pfam02148
    Location:11471209
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  2. NM_001321226.2NP_001308155.1  histone deacetylase 6 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC231533
    Consensus CDS
    CCDS14306.1
    UniProtKB/Swiss-Prot
    Q9UBN7
    UniProtKB/TrEMBL
    A0A024QZ26
    Conserved Domains (3) summary
    cd10003
    Location:485835
    HDAC6-dom2; Histone deacetylase 6, domain 2
    cd11682
    Location:99435
    HDAC6-dom1; Histone deacetylase 6, domain 1
    pfam02148
    Location:11331195
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  3. NM_001321227.2NP_001308156.1  histone deacetylase 6 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC231533
    Consensus CDS
    CCDS14306.1
    UniProtKB/Swiss-Prot
    Q9UBN7
    UniProtKB/TrEMBL
    A0A024QZ26
    Related
    ENSP00000496013.1, ENST00000644068.1
    Conserved Domains (3) summary
    cd10003
    Location:485835
    HDAC6-dom2; Histone deacetylase 6, domain 2
    cd11682
    Location:99435
    HDAC6-dom1; Histone deacetylase 6, domain 1
    pfam02148
    Location:11331195
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  4. NM_001321228.2NP_001308157.1  histone deacetylase 6 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC231533
    Consensus CDS
    CCDS14306.1
    UniProtKB/Swiss-Prot
    Q9UBN7
    UniProtKB/TrEMBL
    A0A024QZ26
    Related
    ENSP00000496046.1, ENST00000643374.1
    Conserved Domains (3) summary
    cd10003
    Location:485835
    HDAC6-dom2; Histone deacetylase 6, domain 2
    cd11682
    Location:99435
    HDAC6-dom1; Histone deacetylase 6, domain 1
    pfam02148
    Location:11331195
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  5. NM_001321229.1NP_001308158.1  histone deacetylase 6 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC231533
    Consensus CDS
    CCDS14306.1
    UniProtKB/Swiss-Prot
    Q9UBN7
    UniProtKB/TrEMBL
    A0A024QZ26
    Conserved Domains (3) summary
    cd10003
    Location:485835
    HDAC6-dom2; Histone deacetylase 6, domain 2
    cd11682
    Location:99435
    HDAC6-dom1; Histone deacetylase 6, domain 1
    pfam02148
    Location:11331195
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  6. NM_001321230.2NP_001308159.1  histone deacetylase 6 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC231533, BC005872, BC011498
    Consensus CDS
    CCDS87740.1
    UniProtKB/TrEMBL
    Q9BRX7
    Related
    ENSP00000496727.1, ENST00000462730.5
    Conserved Domains (1) summary
    cl17011
    Location:99145
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  7. NM_001321231.2NP_001308160.1  histone deacetylase 6 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC231533, BC005872
    Consensus CDS
    CCDS87740.1
    UniProtKB/TrEMBL
    Q9BRX7
    Related
    ENSP00000494447.1, ENST00000465269.5
    Conserved Domains (1) summary
    cl17011
    Location:99145
    Arginase_HDAC; Arginase-like and histone-like hydrolases
  8. NM_006044.4NP_006035.2  histone deacetylase 6 isoform b

    See identical proteins and their annotated locations for NP_006035.2

    Status: REVIEWED

    Source sequence(s)
    AC231533, AJ011972, AL137696, DC377684
    Consensus CDS
    CCDS14306.1
    UniProtKB/Swiss-Prot
    Q9UBN7
    UniProtKB/TrEMBL
    A0A024QZ26, Q9NSW6
    Related
    ENSP00000334061.5, ENST00000334136.11
    Conserved Domains (3) summary
    cd10003
    Location:485835
    HDAC6-dom2; Histone deacetylase 6, domain 2
    cd11682
    Location:99435
    HDAC6-dom1; Histone deacetylase 6, domain 1
    pfam02148
    Location:11331195
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

RNA

  1. NR_135591.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC231533
    Related
    ENST00000647398.1
  2. NR_135592.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC231533, AK295884, BC005872
  3. NR_135593.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC231533, BC005872, DA191923

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    48801398..48824982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029187.1XP_016884676.1  histone deacetylase 6 isoform X1

RNA

  1. XR_246712.2 RNA Sequence

  2. XR_002958755.1 RNA Sequence

  3. XR_002958756.1 RNA Sequence

  4. XR_002958757.1 RNA Sequence

  5. XR_001755632.2 RNA Sequence

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