HCSGD entry for DNMT1
1. General information
| Official gene symbol | DNMT1 |
|---|---|
| Entrez ID | 1786 |
| Gene full name | DNA (cytosine-5-)-methyltransferase 1 |
| Other gene symbols | AIM CXXC9 DNMT HSN1E MCMT |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0000122 | Negative regulation of transcription from RNA polymerase II promoter | IEA | biological_process |
| GO:0003677 | DNA binding | IDA IEA | molecular_function |
| GO:0003723 | RNA binding | IEA | molecular_function |
| GO:0003886 | DNA (cytosine-5-)-methyltransferase activity | IDA IEA | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005634 | Nucleus | IEA | cellular_component |
| GO:0005657 | Replication fork | IEA | cellular_component |
| GO:0005721 | Centromeric heterochromatin | IEA | cellular_component |
| GO:0006306 | DNA methylation | IEA TAS | biological_process |
| GO:0006351 | Transcription, DNA-templated | IEA | biological_process |
| GO:0008134 | Transcription factor binding | IEA | molecular_function |
| GO:0008168 | Methyltransferase activity | IEA | molecular_function |
| GO:0008270 | Zinc ion binding | IEA | molecular_function |
| GO:0008327 | Methyl-CpG binding | IEA | molecular_function |
| GO:0009008 | DNA-methyltransferase activity | IDA | molecular_function |
| GO:0010216 | Maintenance of DNA methylation | IDA IEA | biological_process |
| GO:0010628 | Positive regulation of gene expression | IMP | biological_process |
| GO:0016458 | Gene silencing | IEA | biological_process |
| GO:0016568 | Chromatin modification | IEA | biological_process |
| GO:0042127 | Regulation of cell proliferation | IEA | biological_process |
| GO:0051571 | Positive regulation of histone H3-K4 methylation | IMP | biological_process |
| GO:0051573 | Negative regulation of histone H3-K9 methylation | IMP | biological_process |
| GO:0071230 | Cellular response to amino acid stimulus | IEA | biological_process |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.9631887960 | 0.0088500627 | 0.9999902473 | 0.1868023256 |
- 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 | -0.3615116854 |
| GSE13712_SHEAR | Up | 0.0598389523 |
| GSE13712_STATIC | Down | -0.1123918822 |
| GSE19018 | Down | -0.3523463698 |
| GSE19899_A1 | Down | -0.8198262242 |
| GSE19899_A2 | Down | -0.9837824362 |
| PubMed_21979375_A1 | Up | 0.1701842098 |
| PubMed_21979375_A2 | Down | -0.7022100068 |
| GSE35957 | Down | -1.0271061410 |
| GSE36640 | Down | -1.6111145700 |
| GSE54402 | Up | 0.1755827403 |
| GSE9593 | Down | -1.1505611041 |
| GSE43922 | Down | -0.2255927900 |
| GSE24585 | Up | 0.0776769926 |
| GSE37065 | Down | -0.2567590780 |
| GSE28863_A1 | Up | 0.2310940245 |
| GSE28863_A2 | Up | 0.2022494643 |
| GSE28863_A3 | Up | 0.0989946897 |
| GSE28863_A4 | Down | -0.0175554198 |
| GSE48662 | Down | -0.5898375663 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
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- Drugs
Name | Drug | Accession number |
|---|---|---|
| Azacitidine | DB00928 | APRD00809 |
| Procainamide | DB01035 | APRD00509 |
| Flucytosine | DB01099 | APRD00299 |
| Decitabine | DB01262 | - |
- MicroRNAs
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-148a-3p | MIMAT0000243 | MIRT000020 | Luciferase reporter assay | Functional MTI | 20146264 |
| hsa-miR-148a-3p | MIMAT0000243 | MIRT000020 | qRT-PCR//Luciferase reporter assay//Western blot | Functional MTI | 20483747 |
| hsa-miR-148a-3p | MIMAT0000243 | MIRT000020 | Flow//qRT-PCR//Western blot | Functional MTI | 22167392 |
| hsa-miR-29b-3p | MIMAT0000100 | MIRT003661 | immunoblot//Luciferase reporter assay//qRT-PCR | Non-Functional MTI | 19211935 |
| hsa-miR-152-3p | MIMAT0000438 | MIRT004456 | Luciferase reporter assay | Functional MTI | 20146264 |
| hsa-miR-152-3p | MIMAT0000438 | MIRT004456 | Luciferase reporter assay//Microarray//qRT-PCR//Western blot | Functional MTI | 20841484 |
| hsa-miR-152-3p | MIMAT0000438 | MIRT004456 | Luciferase reporter assay//qRT-PCR//Western blot//Reporter assay;Western blot;qRT-PCR | Functional MTI | 20578129 |
| hsa-miR-152-3p | MIMAT0000438 | MIRT004456 | Immunoblot//Immunoprecipitaion//Luciferase reporter assay//qRT-PCR//Western blot | Functional MTI | 23125218 |
| hsa-miR-301b | MIMAT0004958 | MIRT004598 | Luciferase reporter assay | Non-Functional MTI | 20146264 |
| hsa-miR-126-3p | MIMAT0000445 | MIRT005729 | Flow//Luciferase reporter assay//Microarray//qRT-PCR//Western blot | Functional MTI | 21165896 |
| hsa-miR-126-3p | MIMAT0000445 | MIRT005729 | Flow//Luciferase reporter assay//qRT-PCR//Western blot | Functional MTI | 21538319 |
| hsa-miR-342-3p | MIMAT0000753 | MIRT006443 | Luciferase reporter assay//qRT-PCR//Western blot | Functional MTI | 21565830 |
| hsa-miR-185-5p | MIMAT0000455 | MIRT006696 | Immunoprecipitaion//Luciferase reporter assay//Microarray//Quantitative proteomic approach//Western blot | Functional MTI | 21962230 |
| hsa-miR-140-5p | MIMAT0000431 | MIRT006890 | Immunohistochemistry//Luciferase reporter assay//Microarray//qRT-PCR//Western blot | Functional MTI | 22898998 |
| hsa-miR-193b-3p | MIMAT0002819 | MIRT016347 | Microarray | Functional MTI (Weak) | 20304954 |
| hsa-miR-148b-3p | MIMAT0000759 | MIRT019396 | Microarray | Functional MTI (Weak) | 17612493 |
| hsa-miR-155-5p | MIMAT0000646 | MIRT020737 | Proteomics | Functional MTI (Weak) | 18668040 |
| hsa-miR-877-3p | MIMAT0004950 | MIRT037038 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-484 | MIMAT0002174 | MIRT041763 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-149-5p | MIMAT0000450 | MIRT045615 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-30b-5p | MIMAT0000420 | MIRT046163 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-100-5p | MIMAT0000098 | MIRT048504 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-26a-5p | MIMAT0000082 | MIRT050072 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-1260b | MIMAT0015041 | MIRT052671 | CLASH | Functional MTI (Weak) | 23622248 |
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- mirRecord
MicroRNA name | mirBase ID | Target site number | MiRNA mature ID | Test method inter | MiRNA regulation site | Reporter target site | Pubmed ID |
|---|---|---|---|---|---|---|---|
| hsa-miR-148a-3p | MIMAT0000243 | 1 | hsa-miR-148a | {Western blot} | {overexpression by miRNA precursor transfection} | 20146264 | |
| hsa-miR-148b-3p | MIMAT0000759 | NA | hsa-miR-148b | 21205300 | |||
| hsa-miR-342-3p | MIMAT0000753 | 1 | hsa-miR-342 | {Western blot} | {overexpression} | 21565830 |
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6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 15 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 27206849 | Further, CDK inhibition with palbociclib promoted autophagy-dependent degradation of the DNA methyltransferase DNMT1 |
| 27206849 | Lastly, we found that CDK4 interacted with and phosphorylated DNMT1 in vitro, suggesting that CDK activity is required for its stabilization |
| 25512341 | Instead, lincRNA-p21 associates with the H3K9 methyltransferase SETDB1 and the maintenance DNA methyltransferase DNMT1, which is facilitated by the RNA-binding protein HNRNPK |
| 25355277 | MSCs were treated with high glucose (HG) in order to induce senescence, which was markedly attenuated by pre-treatment with isosorbide dinitrate (ISDN), a commonly used nitrate, as indicated by senescence-associated galactosidase (SA-beta-gal) activity, p21 expression, as well as by the mRNA levels of DNA methyltransferase 1 (DNMT1) and differentiated embryo chondrocyte expressed gene 1 (DEC1), which are senescence-related biomarkers |
| 24804545 | Mechanically, PRIMA-1 induced global DNA demethylation in these cells mainly through inhibiting the expression of DNA methyltransferase (DNMT) 1, 3a and 3b, and upregulating the expression of GADD45a |
| 23249948 | HBP1-mediated transcriptional regulation of DNA methyltransferase 1 and its impact on cell senescence |
| 23249948 | The activity of DNA methyltransferase 1 (DNMT1) is associated with diverse biological activities, including cell proliferation, senescence, and cancer development |
| 23249948 | In this study, we demonstrated that the HMG box-containing protein 1 (HBP1) transcription factor is a new repressor of DNMT1 in a complex mechanism during senescence |
| 23249948 | The DNMT1 gene contains an HBP1-binding site at bp -115 to -134 from the transcriptional start site |
| 23249948 | HBP1 repressed the endogenous DNMT1 gene through sequence-specific binding, resulting in both gene-specific (e |
| 23249948 | The HBP1-mediated repression by DNMT1 contributed to replicative and premature senescence, the latter of which could be induced by Ras and HBP1 itself |
| 23249948 | HBP1 both repressed the DNMT1 gene and activated the p16 gene in premature senescence |
| 23249948 | While intricate, the reciprocal partnership between HBP1 and DNMT1 has exceptional importance, since its abrogation compromises senescence and promotes tumorigenesis |
| 22606351 | It can be further aided by the transcriptional repression of proliferation-associated genes by the action of HP1gamma, HMGA, and DNMT proteins to produce a repressive chromatin environment |
| 21572997 | Here we show that inhibition of DNA methyltransferases (DNMTs) with 5-azacytidine (5-AzaC) or with specific small interfering RNA (siRNA) against DNMT1 and 3b induced the cellular senescence of human umbilical cord blood-derived multipotent stem cells (hUCB-MSCs) and increased p16(INK4A) and p21(CIP1/WAF1) expression |
| 21572997 | DNMT inhibition changed histone marks into the active forms and decreased the methylation of CpG islands in the p16(INK4A) and p21(CIP1/WAF1) promoter regions |
| 21572997 | We found that DNMT inhibition decreased expression levels of Polycomb-group (PcG) proteins and increased expression of microRNAs (miRNAs), which target PcG proteins |
| 20969773 | In addition, DNMT1 is upregulated in BME65Cs |
| 20473858 | Here, we report that the DNA methyltransferase (DNMT) DNMT3a was upregulated by Dox especially at concentrations that induced apoptosis in HCT116 colorectal cancer cells, and this process was regulated by p53 |
| 18723031 | The genome methylation level decreased gradually during the premature as well as replicative senescence, which was associated with the reduction in the expression of DNMT1, reflecting global hypomethylation as a distinct feature of senescent cells |
| 17634574 | A method to detect DNA methyltransferase I gene transcription in vitro in aging systems |
| 17634574 | DNA methyltransferase 1 (DNMT1) is thought to play an important role in maintaining already established methylation patterns during DNA replication and catalyzes the transfer of a methyl moiety from S-adenosyl-L-methionine (SAM) to the 5-position of cytosines in the CpG dinucleotide |
| 17634574 | Several studies illustrate changes in activity and transcription of DNMT1 during aging and here we show a comprehensive method of detection of DNMT1 mRNA transcription from senescing cells in culture |
| 17070654 | In this paper, a molecular model of in vitro cellular aging is presented in which changes in DNA methylation, in particular, global hypomethylation related to methyltransferase Dnmt1 downregulation, and specific hypermethylation related to methyltransferase Dnmt3b upregulation as seen during cellular aging, could be responsible for the inactivation of replication origins or foci and the subsequent documented reduction in DNA replication capacity and increased mutations that are observed in senescent cells |
| 16960018 | A cellular senescence-like phenotype can be induced in immortal LFS cells by treating them with the DNA methyltransferase (DNMT) inhibitor 5-aza-deoxycytidine |
| 12821946 | Treatment of spontaneously immortal Li-Fraumeni fibroblasts with 5-aza-2'-deoxycytidine (5AZA-dC), an inhibitor of DNA methyltransferase (DNMT), induces a senescence-like state |
| 11787061 | We resolved three Dnmt fractions, one of which was the major maintenance methyltransferase, Dnmt1, which declined steadily in activity with cellular senescence and immortalization |
| 11787061 | However, a more basic Dnmt, which has significant de novo methylating activity, increased markedly in activity in aging and immortalized cells |
| 11787061 | An acidic Dnmt we isolated also had increased de novo methylating activity in senescent and immortalized WI-38 cells |
| 11787061 | These studies indicate that reduced genome-wide methylation in aging cells may be attributed to attenuated Dnmt1 activity but that regional or gene-localized hypermethylation in aging and immortalized cells may be linked to increased de novo methylation by Dnmts other than the maintenance methyltransferase |
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