HCSGD entry for HDAC4
1. General information
| Official gene symbol | HDAC4 |
|---|---|
| Entrez ID | 9759 |
| Gene full name | histone deacetylase 4 |
| Other gene symbols | AHO3 BDMR HA6116 HD4 HDAC-4 HDAC-A HDACA |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
This gene isn't in PPI subnetwork.
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0000118 | Histone deacetylase complex | IDA | cellular_component |
| GO:0000122 | Negative regulation of transcription from RNA polymerase II promoter | IDA IEA IMP | biological_process |
| GO:0001047 | Core promoter binding | IEA | molecular_function |
| GO:0001501 | Skeletal system development | IEA | biological_process |
| GO:0002076 | Osteoblast development | IEA | biological_process |
| GO:0003714 | Transcription corepressor activity | IEA | molecular_function |
| GO:0004407 | Histone deacetylase activity | IDA IEA | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005634 | Nucleus | IDA IEA | cellular_component |
| GO:0005737 | Cytoplasm | IDA | cellular_component |
| GO:0005829 | Cytosol | IEA | cellular_component |
| GO:0006338 | Chromatin remodeling | IDA | biological_process |
| GO:0006351 | Transcription, DNA-templated | IEA | biological_process |
| GO:0006954 | Inflammatory response | TAS | biological_process |
| GO:0007399 | Nervous system development | TAS | biological_process |
| GO:0008134 | Transcription factor binding | IEA IPI | molecular_function |
| GO:0008270 | Zinc ion binding | IDA | molecular_function |
| GO:0008284 | Positive regulation of cell proliferation | IMP | biological_process |
| GO:0008285 | Negative regulation of cell proliferation | IEA | biological_process |
| GO:0010832 | Negative regulation of myotube differentiation | IMP | biological_process |
| GO:0010882 | Regulation of cardiac muscle contraction by calcium ion signaling | IEA | biological_process |
| GO:0014894 | Response to denervation involved in regulation of muscle adaptation | IEA ISS | biological_process |
| GO:0014898 | Cardiac muscle hypertrophy in response to stress | TAS | biological_process |
| GO:0016575 | Histone deacetylation | IDA IMP | biological_process |
| GO:0016787 | Hydrolase activity | IEA | molecular_function |
| GO:0017053 | Transcriptional repressor complex | IDA | cellular_component |
| GO:0019901 | Protein kinase binding | IEA | molecular_function |
| GO:0030018 | Z disc | IEA | cellular_component |
| GO:0030183 | B cell differentiation | TAS | biological_process |
| GO:0030955 | Potassium ion binding | IDA | molecular_function |
| GO:0031594 | Neuromuscular junction | IEA | cellular_component |
| GO:0031672 | A band | IEA | cellular_component |
| GO:0032041 | NAD-dependent histone deacetylase activity (H3-K14 specific) | IEA | molecular_function |
| GO:0033235 | Positive regulation of protein sumoylation | IDA | biological_process |
| GO:0033558 | Protein deacetylase activity | IDA | molecular_function |
| GO:0033613 | Activating transcription factor binding | IPI | molecular_function |
| GO:0034983 | Peptidyl-lysine deacetylation | IDA | biological_process |
| GO:0042113 | B cell activation | TAS | biological_process |
| GO:0042493 | Response to drug | IEA | biological_process |
| GO:0042641 | Actomyosin | IEA | cellular_component |
| GO:0042826 | Histone deacetylase binding | IPI | molecular_function |
| GO:0043234 | Protein complex | IEA | cellular_component |
| GO:0043393 | Regulation of protein binding | IMP | biological_process |
| GO:0043433 | Negative regulation of sequence-specific DNA binding transcription factor activity | IMP | biological_process |
| GO:0043565 | Sequence-specific DNA binding | IDA | molecular_function |
| GO:0044212 | Transcription regulatory region DNA binding | IDA | molecular_function |
| GO:0045668 | Negative regulation of osteoblast differentiation | IEA | biological_process |
| GO:0045820 | Negative regulation of glycolysis | IEA ISS | biological_process |
| GO:0045892 | Negative regulation of transcription, DNA-templated | IDA IMP | biological_process |
| GO:0045893 | Positive regulation of transcription, DNA-templated | ISS | biological_process |
| GO:0045944 | Positive regulation of transcription from RNA polymerase II promoter | IEA IMP ISS | biological_process |
| GO:0046969 | NAD-dependent histone deacetylase activity (H3-K9 specific) | IEA | molecular_function |
| GO:0046970 | NAD-dependent histone deacetylase activity (H4-K16 specific) | IEA | molecular_function |
| GO:0048742 | Regulation of skeletal muscle fiber development | IEA | biological_process |
| GO:0051091 | Positive regulation of sequence-specific DNA binding transcription factor activity | IMP | biological_process |
| GO:0070491 | Repressing transcription factor binding | IPI | molecular_function |
| GO:0070555 | Response to interleukin-1 | IMP | biological_process |
| GO:0070932 | Histone H3 deacetylation | IDA | biological_process |
| GO:0070933 | Histone H4 deacetylation | IDA | biological_process |
| GO:0097372 | NAD-dependent histone deacetylase activity (H3-K18 specific) | IEA | molecular_function |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.9737474298 | 0.0557133202 | 0.9999902473 | 0.4441036644 |
- Individual experiment result
( "-" represent NA in the specific microarray platform )
( "-" represent NA in the specific microarray platform )
| Data source | Up or down | Log fold change |
|---|---|---|
| GSE11954 | Down | -0.2136007404 |
| GSE13712_SHEAR | Down | -0.1583831110 |
| GSE13712_STATIC | Down | -0.2845209495 |
| GSE19018 | Down | -0.5875717961 |
| GSE19899_A1 | Down | -0.3370822272 |
| GSE19899_A2 | Down | -0.9668724428 |
| PubMed_21979375_A1 | Down | -0.5250034841 |
| PubMed_21979375_A2 | Up | 0.0274108228 |
| GSE35957 | Down | -0.0813514905 |
| GSE36640 | Up | 0.0139548028 |
| GSE54402 | Down | -0.3007059214 |
| GSE9593 | Down | -0.4723560661 |
| GSE43922 | Up | 0.0401170530 |
| GSE24585 | Down | -0.0407047476 |
| GSE37065 | Down | -0.0407415399 |
| GSE28863_A1 | Up | 0.0328405460 |
| GSE28863_A2 | Up | 0.0679189316 |
| GSE28863_A3 | Up | 0.1391606409 |
| GSE28863_A4 | Down | -0.0022847295 |
| GSE48662 | Down | -0.0835147674 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
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- Drugs
Name | Drug | Accession number |
|---|---|---|
| Romidepsin | DB06176 | - |
| Panobinostat | DB06603 | - |
| N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide | DB07879 | - |
| 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL | DB08613 | - |
- MicroRNAs
- mirTarBase
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-29b-3p | MIMAT0000100 | MIRT000096 | Luciferase reporter assay | Functional MTI | 23478036 |
| hsa-miR-140-5p | MIMAT0000431 | MIRT000693 | qRT-PCR//Western blot//Luciferase reporter assay | Functional MTI | 19734943 |
| hsa-miR-1 | MIMAT0000416 | MIRT001053 | Western blot//Luciferase reporter assay | Functional MTI | 18818206 |
| hsa-miR-1 | MIMAT0000416 | MIRT001053 | Western blot | Functional MTI | 18593903 |
| hsa-miR-22-3p | MIMAT0000077 | MIRT004035 | Luciferase reporter assay//qRT-PCR//Western blot | Functional MTI | 20842113 |
| hsa-miR-22-3p | MIMAT0000077 | MIRT004035 | Luciferase reporter assay | Functional MTI | 23349832 |
| hsa-miR-30c-5p | MIMAT0000244 | MIRT007109 | qRT-PCR//Western blot | Functional MTI | 23469762 |
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- mirRecord
- mirRecord
MicroRNA name | mirBase ID | Target site number | MiRNA mature ID | Test method inter | MiRNA regulation site | Reporter target site | Pubmed ID |
|---|---|---|---|---|---|---|---|
| hsa-miR-1 | MIMAT0000416 | NA | hsa-miR-1 | {Western blot} | {overexpression by miRNA precursor transfection} | 18818206 | |
| hsa-miR-140-5p | MIMAT0000431 | NA | hsa-miR-140-5p | {Western blot} | {overexpression} | 19734943 | |
| hsa-miR-365a-3p | MIMAT0000710 | 1 | hsa-miR-365 | {Western blot} | {overexpression by miRNA mimics tranfection} | 21856783 |
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6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 5 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 26414199 | HDAC4 stabilizes SIRT1 via sumoylation SIRT1 to delay cellular senescence |
| 26414199 | This study shows that the expression patterns of HDAC4 and Sirtuin 1 (SIRT1; the mammalian homolog of Sir2) are positively correlated during cellular senescence |
| 26414199 | Moreover, the overexpression of HDAC4 delays senescence, whereas the knockdown of HDAC4 leads to premature senescence in human fibroblasts |
| 26414199 | Furthermore, it is demonstrated that HDAC4 increases endogenous SIRT1 expression by enhancing its sumoylation modification levels, thereby stabilizing its protein levels |
| 26324717 | The deltaB isoform of CaMKII is the predominant nuclear splice variant in the adult heart and regulates cardiomyocyte hypertrophic gene expression by signaling to the histone deacetylase HDAC4 |
| 19583777 | We also show that histone deacetylase (HDAC) 3 and HDAC4 inhibited p16(INK4a) promoter activity in a dose-dependent manner |
| 19583777 | These data suggest that ZBP-89 and HDAC3, but not HDAC4, can work coordinately to restrain cell senescence by downregulating p16(INK4a) expression through an epigenetic modification of histones |
| 18558095 | Specifically, HDAC3 and HDAC4 inhibited the p16(INK4a) promoter activity |
| 18558095 | The chromatin immunoprecipitation (ChIP) assays verified that HDAC3 and HDAC4 were recruited to p16(INK4a) promoter by YY1 |
| 11257101 | This inappropriate deacetylation by HDAC4, HDAC5 and HDAC6 follows their relocalization from the cytoplasm to the nucleus |
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