HCSGD entry for HDAC1
1. General information
| Official gene symbol | HDAC1 |
|---|---|
| Entrez ID | 3065 |
| Gene full name | histone deacetylase 1 |
| Other gene symbols | GON-10 HD1 RPD3 RPD3L1 |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0000118 | Histone deacetylase complex | TAS | cellular_component |
| GO:0000122 | Negative regulation of transcription from RNA polymerase II promoter | IDA IMP TAS | biological_process |
| GO:0000278 | Mitotic cell cycle | TAS | biological_process |
| GO:0000790 | Nuclear chromatin | IDA | cellular_component |
| GO:0001047 | Core promoter binding | IDA | molecular_function |
| GO:0001103 | RNA polymerase II repressing transcription factor binding | IPI | molecular_function |
| GO:0001106 | RNA polymerase II transcription corepressor activity | IDA | molecular_function |
| GO:0003700 | Sequence-specific DNA binding transcription factor activity | TAS | molecular_function |
| GO:0004407 | Histone deacetylase activity | IDA IEA IMP TAS | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005634 | Nucleus | IDA | cellular_component |
| GO:0005654 | Nucleoplasm | IDA TAS | cellular_component |
| GO:0005730 | Nucleolus | IDA | cellular_component |
| GO:0005737 | Cytoplasm | TAS | cellular_component |
| GO:0005829 | Cytosol | IDA | cellular_component |
| GO:0006338 | Chromatin remodeling | IC | biological_process |
| GO:0006351 | Transcription, DNA-templated | TAS | biological_process |
| GO:0006367 | Transcription initiation from RNA polymerase II promoter | TAS | biological_process |
| GO:0006476 | Protein deacetylation | IDA | biological_process |
| GO:0007179 | Transforming growth factor beta receptor signaling pathway | TAS | biological_process |
| GO:0007219 | Notch signaling pathway | TAS | biological_process |
| GO:0007596 | Blood coagulation | TAS | biological_process |
| GO:0008134 | Transcription factor binding | IPI TAS | molecular_function |
| GO:0008284 | Positive regulation of cell proliferation | IMP | biological_process |
| GO:0009913 | Epidermal cell differentiation | ISS | biological_process |
| GO:0010467 | Gene expression | TAS | biological_process |
| GO:0010832 | Negative regulation of myotube differentiation | IMP | biological_process |
| GO:0010870 | Positive regulation of receptor biosynthetic process | IMP | biological_process |
| GO:0016032 | Viral process | IEA | biological_process |
| GO:0016568 | Chromatin modification | TAS | biological_process |
| GO:0016575 | Histone deacetylation | IMP | biological_process |
| GO:0016580 | Sin3 complex | IDA | cellular_component |
| GO:0016581 | NuRD complex | IDA | cellular_component |
| GO:0019899 | Enzyme binding | IPI | molecular_function |
| GO:0032041 | NAD-dependent histone deacetylase activity (H3-K14 specific) | IEA | molecular_function |
| GO:0033558 | Protein deacetylase activity | IDA IMP | molecular_function |
| GO:0033613 | Activating transcription factor binding | IPI | molecular_function |
| GO:0042475 | Odontogenesis of dentin-containing tooth | ISS | biological_process |
| GO:0042733 | Embryonic digit morphogenesis | ISS | biological_process |
| GO:0042826 | Histone deacetylase binding | IPI | molecular_function |
| GO:0043066 | Negative regulation of apoptotic process | ISS | biological_process |
| GO:0043922 | Negative regulation by host of viral transcription | IMP | biological_process |
| GO:0045786 | Negative regulation of cell cycle | TAS | biological_process |
| GO:0045892 | Negative regulation of transcription, DNA-templated | IMP | biological_process |
| GO:0045893 | Positive regulation of transcription, DNA-templated | IDA | biological_process |
| GO:0045944 | Positive regulation of transcription from RNA polymerase II promoter | IDA | 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:0048011 | Neurotrophin TRK receptor signaling pathway | TAS | biological_process |
| GO:0060766 | Negative regulation of androgen receptor signaling pathway | IDA | biological_process |
| GO:0060789 | Hair follicle placode formation | ISS | biological_process |
| GO:0061029 | Eyelid development in camera-type eye | ISS | biological_process |
| GO:0061198 | Fungiform papilla formation | ISS | 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 |
|---|---|---|---|
| 0.9782574750 | 0.0299308689 | 0.9999902473 | 0.3268783492 |
- 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 | -0.1209915488 |
| GSE13712_SHEAR | Down | -0.0383664879 |
| GSE13712_STATIC | Up | 0.0051361941 |
| GSE19018 | Down | -0.3731563868 |
| GSE19899_A1 | Down | -0.3012173856 |
| GSE19899_A2 | Down | -0.2532707428 |
| PubMed_21979375_A1 | Down | -0.7411268338 |
| PubMed_21979375_A2 | Down | -0.1045577495 |
| GSE35957 | Down | -0.3150577313 |
| GSE36640 | Down | -0.6125842618 |
| GSE54402 | Up | 0.1240741608 |
| GSE9593 | Down | -0.3605810784 |
| GSE43922 | Down | -0.0657405479 |
| GSE24585 | Up | 0.2744680444 |
| GSE37065 | Down | -0.0963505049 |
| GSE28863_A1 | Down | -0.0081031414 |
| GSE28863_A2 | Up | 0.3601469687 |
| GSE28863_A3 | Down | -0.1491746517 |
| GSE28863_A4 | Down | -0.5576643421 |
| GSE48662 | Down | -0.2609809476 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
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- Drugs
Name | Drug | Accession number |
|---|---|---|
| Vorinostat | DB02546 | EXPT02902 |
| SB939 | DB05223 | - |
| MGCD-0103 | DB05651 | - |
| CRA-024781 | DB05921 | - |
| Romidepsin | DB06176 | - |
| Panobinostat | DB06603 | - |
- MicroRNAs
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-449b-5p | MIMAT0003327 | MIRT006353 | Luciferase reporter assay//Western blot | Functional MTI | 21418558 |
| hsa-miR-449a | MIMAT0001541 | MIRT003760 | Luciferase reporter assay//qRT-PCR//Western blot//Reporter assay;Other | Functional MTI | 19252524 |
| hsa-miR-449a | MIMAT0001541 | MIRT003760 | Immunoblot | Functional MTI (Weak) | 20948989 |
| hsa-miR-449a | MIMAT0001541 | MIRT003760 | Luciferase reporter assay//Western blot | Functional MTI | 21418558 |
| hsa-miR-34a-5p | MIMAT0000255 | MIRT025557 | Reporter assay;Proteomics | Functional MTI | 21566225 |
| hsa-miR-24-3p | MIMAT0000080 | MIRT030619 | Sequencing | Functional MTI (Weak) | 20371350 |
| hsa-miR-671-5p | MIMAT0003880 | MIRT039285 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-615-3p | MIMAT0003283 | MIRT039704 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-92a-3p | MIMAT0000092 | MIRT049098 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-30a-5p | MIMAT0000087 | MIRT049948 | CLASH | Functional MTI (Weak) | 23622248 |
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- mirRecord
No target information from mirRecord
6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 22 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 27311997 | The results showed that a repressor complex composed of NFX1-91, mSin3A and histone deacetylase 1 was involved in the PKC-delta-induced repression of the hTERT promoter, which resulted in the repression of hTERT transcription |
| 26824319 | As parthenolide reduces MITF-M transcript level and HDAC1 protein level, parthenolide-activated depletion of MITF-M protein may be considered as a result of transcriptional regulation, however, the influence of parthenolide on other elements of a dynamic control over MITF-M cannot be ruled out |
| 26824319 | Our data suggest that parthenolide can be developed as a drug used in combination therapy against melanoma when simultaneous inhibition of MITF-M, NF-kappaB and HDAC1 is needed |
| 25672483 | Further investigation of the underlying mechanism indicated that down-regulation of ING2 significantly increased expression of p21, whilst decreasing expression of HDAC1 |
| 24218884 | Comparative Q-PCR was utilized to investigate target gene (P66SHC, EP300, HDAC1) expressions respectively in H2O2 treated groups and normal cell groups |
| 24218884 | CONCLUSION: P66SHC, EP300 and HDAC1 probably play a role in cellular replicative senescence and oxidative-stress inducing premature senescence |
| 22731250 | SPRR2A enhances p53 deacetylation through HDAC1 and down regulates p21 promoter activity |
| 22731250 | The p300 CH3 domain is essential for both the autoacetylation of p300 and transference of the acetyl group to p53 and HDAC1 is a component of several non-p300 complexes that enhance p53 deacetylation, ubiquitination, and proteosomal degradation |
| 22731250 | HDAC1 can also bind the p300-CH3 domain, regulating p300 acetylation and interfering with p300 mediated p53 acetylation |
| 22731250 | The importance of this pathway is illustrated by showing complete restoration of p53 acetylation and partial restoration of p300 acetylation by treating SPRR2A expressing cells with HDAC1 siRNA |
| 22731250 | CONCLUSION: Up-regulation of SPRR2A, similar to that seen during barrier epithelia wound repair responses reduces p53 acetylation by interfering with p300-p53 interactions and by increasing HDAC1 expression |
| 21420382 | In addition, HDAC1 overexpression led to senescence through both an accumulation of hypophosphorylated active retinoblastoma protein (pRb) and an increase in the protein level of protein phosphatase 2A catalytic subunit (PP2Ac) |
| 21383005 | EZH2 depletion removes histone deacetylase 1 (HDAC1) from the CDKN1A transcriptional start site and downstream region, enhancing histone 3 acetylation globally and at CDKN1A |
| 21124965 | The arrested spermatocytes in Ing2(-/-) testes were characterized by lack of specific HDAC1 accumulation and deregulated chromatin acetylation |
| 21124965 | This study establishes ING2 as a novel regulator of spermatogenesis functioning through both p53- and chromatin-mediated mechanisms, suggests that an HDAC1/ING2/H3K4me3-regulated, stage-specific coordination of chromatin modifications is essential to normal spermatogenesis, and provides an animal model to study idiopathic and iatrogenic infertility in men |
| 20948989 | We also reveal that miR-449a suppresses Rb phosphorylation through the knockdown of Cyclin D1 and previously validated target HDAC1 |
| 20473858 | Surprisingly, no changes in DNA methylation status at p21 promoter were detected at either ranges of Dox, although DNMT3a and HDAC1 were recruited to p21 promoter at apoptosis-inducing Dox concentration, where they were present in the same complex |
| 19818845 | Role of HDAC1 in senescence, aging, and cancer |
| 19818845 | HDAC1 is a member of the class I of histone deacetylases that also includes HDAC2, -3 and -8 |
| 19818845 | Although HDAC1 has been mostly studied in the context of cancer, recent evidence strongly suggests that it plays critical roles in cellular senescence, aging of the liver, myelination, and adult neurogenesis |
| 19818845 | Here we review such roles and discuss the entangled relationships between HDAC1 with histone acetyltransferases and other HDACs including SIRT1 |
| 18691180 | Gene expression appears to be altered by targeting of HDAC complexes to gene promoters since INGla associates with several-fold higher levels of HDAC1 in senescent, compared to replication-competent cells and ING1 is found on the PCNA promoter by chromatin immunoprecipitation analysis |
| 18193082 | In vitro and in vivo binding studies indicated that the p33(ING1b) and p33(ING2) subunits of the mSIN3A/HDAC1 complex are responsible for the recruitment of SIRT1 to the R2 domain |
| 18193082 | Explicitly, SIRT1 is recruited by ING proteins and inhibits R2-associated mSIN3A/HDAC1 transcriptional repression activity |
| 17578512 | This senescence response is likely due to chromatin modifications because RB complexes from senescent melanocytes contain increased levels of histone deacetylase (HDAC) activity and tethered HDAC1 |
| 17578512 | Here we show that HDAC1 is prominently detected in p16(INK4a)-positive, senescent intradermal melanocytic nevi but not in proliferating, recurrent nevus cells that localize to the epidermal/dermal junction |
| 17578512 | To assess the role of HDAC1 in the senescence of melanocytes and nevi, we used tetracycline-based inducible expression systems in cultured melanocytic cells |
| 17578512 | These results provide new insights into the role of the RB pathway in regulating cellular senescence and implicate HDAC1 as a likely mediator of early chromatin remodeling events |
| 17316622 | Oct-1 specifically interacts with this binding site in vitro and in vivo and SMRT and HDAC1 are present in the p15(INK4b) proximal promoter region |
| 16516887 | Relocalization occurs concomitantly with interaction with a subset of nuclear proteins, including PCNA, p53 and several regulators of acetylation such as the p300/CBP and PCAF histone acetyltransferases (HATs), as well as the histone deacetylases HDAC1 and hSir2 |
| 16250917 | We also found that HDAC1 levels decline during normal replicative senescence |
| 16250917 | Reduced HDAC1 expression levels in senescent cells may be an important event in mediating the transition to a senescent phenotype |
| 15781639 | We show here that Tbx2 is overexpressed in melanoma cell lines and that Tbx2 targets histone deacetylase 1 to the p21Cip1 (CDKN1A) initiator |
| 15781639 | Strikingly, expression of an inducible dominant-negative Tbx2 (dnTbx2) leads to displacement of histone deacetylase 1, up-regulation of p21(Cip1) expression, and the induction of replicative senescence in CDKN2A-null B16 melanoma cells |
| 15171255 | PID/MTA2 is a p53-interacting protein that induces p53 deacetylation by recruiting the HDAC1 complex |
| 15171255 | We present data indicating that both HDAC1 and Sir2alpha are critical for p53-dependent stress response |
| 15171255 | Finally, we propose a model regarding the differential roles of HDAC1 and Sir2alpha in the regulation of p53 function |
| 14522900 | Both ING1 and p53 were able to suppress AFP transcription and cause p21 induction; hSIR2, a negative regulator of the p53 protein, showed the opposite effects on the AFP promoter and, like HDAC1, repressed p21 promoter activity |
| 11418121 | By Northern blot and Western blot, we found a significant decrease in the abundance of HDAC-1 in senescent cells |
| 11418121 | While by anion exchange chromatography we found a single peak of activity in extracts from young cells, which coincided with the elution of both HDAC-1 and HDAC-2, in senescent cells a second peak of activity was found |
| 11418121 | This second peak of activity is associated with HDAC-2 but does not contain HDAC-1 |
| 11257101 | The failure to deacetylate and thus repress transcription by the Class I histone deacetylases HDAC1 and HDAC2 due to disruption of the Rb family of proteins has been firmly established as a mechanism leading to increases in growth rate and cellular proliferation |
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