Gene description for HDAC6
Gene name histone deacetylase 6
Gene symbol HDAC6
Other names/aliases CPBHM
HD6
JM21
PPP1R90
Species Homo sapiens
 Database cross references - HDAC6
ExoCarta ExoCarta_10013
Vesiclepedia VP_10013
Entrez Gene 10013
HGNC 14064
MIM 300272
UniProt Q9UBN7  
 HDAC6 identified in exosomes derived from the following tissue/cell type
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Thymus 23844026    
 Gene ontology annotations for HDAC6
Molecular Function
    misfolded protein binding GO:0051787 EXP
    beta-catenin binding GO:0008013 IPI
    tubulin deacetylase activity GO:0042903 ISS
    core promoter binding GO:0001047 IDA
    actin binding GO:0003779 IEA
    alpha-tubulin binding GO:0043014 IDA
    ubiquitin protein ligase binding GO:0031625 IPI
    enzyme binding GO:0019899 ISS
    dynein complex binding GO:0070840 IDA
    histone deacetylase activity GO:0004407 IMP
    polyubiquitin binding GO:0031593 IDA
    beta-tubulin binding GO:0048487 IEA
    NAD-dependent histone deacetylase activity (H3-K18 specific) GO:0097372 IEA
    microtubule binding GO:0008017 ISS
    NAD-dependent histone deacetylase activity (H4-K16 specific) GO:0046970 IEA
    zinc ion binding GO:0008270 IEA
    Hsp90 protein binding GO:0051879 IDA
    protein binding GO:0005515 IPI
    tau protein binding GO:0048156 IDA
    NAD-dependent histone deacetylase activity (H3-K14 specific) GO:0032041 IEA
    histone deacetylase binding GO:0042826 IPI
    NAD-dependent histone deacetylase activity (H3-K9 specific) GO:0046969 IEA
Biological Process
    response to misfolded protein GO:0051788 IMP
    histone H4 deacetylation GO:0070933 IEA
    histone H3-K9 deacetylation GO:1990619 IEA
    cellular response to heat GO:0034605 TAS
    polyubiquitinated misfolded protein transport GO:0070845 IMP
    negative regulation of protein complex disassembly GO:0043242 IMP
    positive regulation of hydrogen peroxide-mediated programmed cell death GO:1901300 IDA
    regulation of gene expression, epigenetic GO:0040029 IMP
    positive regulation of signal transduction GO:0009967 IMP
    regulation of fat cell differentiation GO:0045598 IEA
    response to toxic substance GO:0009636 IMP
    regulation of microtubule-based movement GO:0060632 IC
    transcription, DNA-templated GO:0006351 IEA
    misfolded or incompletely synthesized protein catabolic process GO:0006515 IMP
    positive regulation of epithelial cell migration GO:0010634 IMP
    intracellular protein transport GO:0006886 IMP
    response to growth factor GO:0070848 IMP
    negative regulation of transcription, DNA-templated GO:0045892 ISS
    aggresome assembly GO:0070842 IMP
    organelle organization GO:0006996 TAS
    positive regulation of chaperone-mediated protein complex assembly GO:0090035 IMP
    cellular response to misfolded protein GO:0071218 IEA
    positive regulation of receptor biosynthetic process GO:0010870 IMP
    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway GO:0043162 IEA
    lysosome localization GO:0032418 IMP
    regulation of receptor activity GO:0010469 IMP
    negative regulation of oxidoreductase activity GO:0051354 IC
    peptidyl-lysine deacetylation GO:0034983 IMP
    Hsp90 deacetylation GO:0070846 IMP
    negative regulation of hydrogen peroxide metabolic process GO:0010727 IC
    cellular response to hydrogen peroxide GO:0070301 IMP
    negative regulation of proteolysis GO:0045861 IMP
    protein polyubiquitination GO:0000209 IEA
    regulation of androgen receptor signaling pathway GO:0060765 TAS
    protein deacetylation GO:0006476 IMP
    histone H3-K9 modification GO:0061647 IEA
    macroautophagy GO:0016236 IMP
    regulation of establishment of protein localization GO:0070201 IEA
    protein complex disassembly GO:0043241 IEA
    tubulin deacetylation GO:0090042 ISS
    response to organic substance GO:0010033 IMP
    histone deacetylation GO:0016575 ISS
    negative regulation of microtubule depolymerization GO:0007026 IEA
    cellular response to topologically incorrect protein GO:0035967 IMP
Subcellular Localization
    caveola GO:0005901 IDA
    inclusion body GO:0016234 IDA
    axon GO:0030424 ISS
    perinuclear region of cytoplasm GO:0048471 IDA
    nucleus GO:0005634 ISS
    microtubule GO:0005874 IDA
    cell leading edge GO:0031252 IDA
    nucleoplasm GO:0005654 IDA
    dynein complex GO:0030286 IDA
    microtubule associated complex GO:0005875 IDA
    histone deacetylase complex GO:0000118 IDA
    perikaryon GO:0043204 ISS
    aggresome GO:0016235 IDA
    cytoplasmic microtubule GO:0005881 IEA
    cytoplasm GO:0005737 ISS
    dendrite GO:0030425 ISS
    cytosol GO:0005829 TAS
 Experiment description of studies that identified HDAC6 in exosomes
1
Experiment ID 489
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 6
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
2
Experiment ID 490
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 7
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
3
Experiment ID 491
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 8
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
4
Experiment ID 492
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 9
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
5
Experiment ID 217
MISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|CD81|CD9|CD63
EV Enriched markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23844026    
Organism Homo sapiens
Experiment description Characterization of human thymic exosomes.
Authors Skogberg G, Gudmundsdottir J, van der Post S, Sandstrom K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O.
Journal name PLoS One
Publication year 2013
Sample Thymus
Sample name Normal-Thymus
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for HDAC6
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 SIRT2 22933
Affinity Capture-MS Homo sapiens
2 RUNX2  
Affinity Capture-Western Homo sapiens
3 PLAA 9373
Affinity Capture-MS Homo sapiens
4 CBFA2T3  
Affinity Capture-Western Homo sapiens
5 ZBTB16  
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
6 HDAC11  
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
7 RELB  
Affinity Capture-MS Homo sapiens
8 BCOR  
Affinity Capture-Western Homo sapiens
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