HCSGD entry for DNMT3B
1. General information
| Official gene symbol | DNMT3B |
|---|---|
| Entrez ID | 1789 |
| Gene full name | DNA (cytosine-5-)-methyltransferase 3 beta |
| Other gene symbols | ICF ICF1 M.HsaIIIB |
| 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 | IDA | biological_process |
| GO:0003714 | Transcription corepressor activity | IDA IMP | molecular_function |
| GO:0003886 | DNA (cytosine-5-)-methyltransferase activity | IDA NAS TAS | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005634 | Nucleus | IDA | cellular_component |
| GO:0005720 | Nuclear heterochromatin | IEA | cellular_component |
| GO:0005730 | Nucleolus | IDA | cellular_component |
| GO:0005737 | Cytoplasm | IEA | cellular_component |
| GO:0006306 | DNA methylation | NAS TAS | biological_process |
| GO:0006346 | Methylation-dependent chromatin silencing | IEA | biological_process |
| GO:0006349 | Regulation of gene expression by genetic imprinting | IEA | biological_process |
| GO:0009008 | DNA-methyltransferase activity | NAS | molecular_function |
| GO:0010212 | Response to ionizing radiation | IEA | biological_process |
| GO:0010424 | DNA methylation on cytosine within a CG sequence | IEA | biological_process |
| GO:0010628 | Positive regulation of gene expression | IMP | biological_process |
| GO:0031503 | Protein complex localization | IEA | biological_process |
| GO:0042493 | Response to drug | IEA | biological_process |
| GO:0043231 | Intracellular membrane-bounded organelle | IDA | cellular_component |
| GO:0045322 | Unmethylated CpG binding | IEA | molecular_function |
| GO:0045666 | Positive regulation of neuron differentiation | IEA | biological_process |
| GO:0046498 | S-adenosylhomocysteine metabolic process | IEA | biological_process |
| GO:0046499 | S-adenosylmethioninamine metabolic process | IEA | biological_process |
| GO:0046872 | Metal ion binding | IEA | molecular_function |
| 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:0051718 | DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates | IEA | molecular_function |
| 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 |
|---|---|---|---|
| 0.9547106265 | 0.0367389423 | 0.9999902473 | 0.3613259328 |
- 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 | -0.1565250103 |
| GSE13712_SHEAR | Down | -0.7804005110 |
| GSE13712_STATIC | Up | 0.2624314319 |
| GSE19018 | Up | 0.1625676855 |
| GSE19899_A1 | Down | -0.0954981141 |
| GSE19899_A2 | Down | -1.0104019897 |
| PubMed_21979375_A1 | Down | -0.9081859085 |
| PubMed_21979375_A2 | Down | -0.5083877407 |
| GSE35957 | Down | -0.6880832116 |
| GSE36640 | Down | -0.6186859866 |
| GSE54402 | Up | 0.0844090620 |
| GSE9593 | Down | -0.2401122098 |
| GSE43922 | Up | 0.0257082898 |
| GSE24585 | Up | 0.0166750259 |
| GSE37065 | Up | 0.0404248248 |
| GSE28863_A1 | Down | -0.1764985711 |
| GSE28863_A2 | Up | 0.1704103482 |
| GSE28863_A3 | Up | 0.1240804880 |
| GSE28863_A4 | Up | 0.1554707543 |
| GSE48662 | Down | -0.2442844202 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
Not regulated by compounds
- Drugs
Not regulated by drugs
- MicroRNAs
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-148a-3p | MIMAT0000243 | MIRT000955 | GFP reporter assay//Western blot//qRT-PCR | Functional MTI | 18367714 |
| hsa-miR-148a-3p | MIMAT0000243 | MIRT000955 | Microarray//qRT-PCR | Functional MTI (Weak) | 19435428 |
| hsa-miR-29c-3p | MIMAT0000681 | MIRT003025 | Luciferase reporter assay//Western blot//qRT-PCR//Reporter assay;Other | Functional MTI | 17890317 |
| hsa-miR-29b-3p | MIMAT0000100 | MIRT003026 | Luciferase reporter assay//Western blot//qRT-PCR//Reporter assay;Other | Functional MTI | 17890317 |
| hsa-miR-29b-3p | MIMAT0000100 | MIRT003026 | Luciferase reporter assay | Functional MTI | 18996365 |
| hsa-miR-29b-3p | MIMAT0000100 | MIRT003026 | Luciferase reporter assay | Functional MTI | 19211935 |
| hsa-miR-29a-3p | MIMAT0000086 | MIRT003027 | Luciferase reporter assay//Western blot//qRT-PCR//Reporter assay;Other | Functional MTI | 17890317 |
| hsa-miR-369-5p | MIMAT0001621 | MIRT005961 | Luciferase reporter assay//Reporter assay;Western blot;qRT-PCR | Functional MTI | 21136442 |
| hsa-miR-335-5p | MIMAT0000765 | MIRT018547 | Microarray | Functional MTI (Weak) | 18185580 |
| hsa-miR-375 | MIMAT0000728 | MIRT019897 | Microarray | Functional MTI (Weak) | 20215506 |
| hsa-miR-93-5p | MIMAT0000093 | MIRT048777 | 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} | 18367714 | |
| hsa-miR-148a-3p | MIMAT0000243 | NA | hsa-miR-148a | 18367714 | |||
| hsa-miR-148b-3p | MIMAT0000759 | 1 | hsa-miR-148b | {Western blot} | {overexpression by miRNA precursor transfection} | {GFP} | 18367714 |
| hsa-miR-29a-3p | MIMAT0000086 | 1 | hsa-miR-29a | 17890317 | |||
| hsa-miR-29a-3p | MIMAT0000086 | 2 | hsa-miR-29a | 17890317 | |||
| hsa-miR-29a-3p | MIMAT0000086 | 3 | hsa-miR-29a | 17890317 | |||
| hsa-miR-29b-3p | MIMAT0000100 | 1 | hsa-miR-29b | 17890317 | |||
| hsa-miR-29c-3p | MIMAT0000681 | 1 | hsa-miR-29c | 17890317 | |||
| hsa-miR-29b-3p | MIMAT0000100 | 1 | hsa-miR-29b | {Western blot} | {overexpression by miRNA precursor transfection} | 19211935 |
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6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 8 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 27147278 | Prominent examples include aberrations in cytokines and their signaling pathways (such as tumor necrosis factor-alpha, interferon-gamma, SMAD proteins), mutations in genes encoding the RNA splicing machinery (SF3B1, SRSF2, ZRSR2, and U2AF1 genes), mutations in genes disrupting the epigenetic machinery (TET2, DNMT3A, DNMT3B, EZH2, ASXL1) |
| 26854227 | PRMT7-deficient satellite cells express elevated levels of the CDK inhibitor p21CIP1 and low levels of its repressor, DNMT3b |
| 26854227 | Restoration of DNMT3b in PRMT7-deficient cells rescues PRMT7-mediated senescence |
| 21660946 | Expression of the de novo DNA methyltransferases DNMT3A and DNMT3B was up-regulated by transfection of miR-371 whereas expression of DNMT3A was down-regulated by miR-369-5p |
| 21502405 | The results imply that triplex-mediated targeting of DNMT3b to specific sequences may be a common pathway in epigenetic regulation |
| 18723031 | The levels of DNMT3b and methyl-CpG binding protein 2 (MeCP2) increased in both mid-aged and replicative senescent cells, while DNMT3a and MBD2 were upregulated in the mid-aged cells |
| 18723031 | Only DNMT3b was elevated in the cells in the premature senescence persistence status |
| 18332116 | Strikingly, loss of PcG complexes is accompanied by DNA methyltransferase DNMT3B dissociation and reduced DNA methylation |
| 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 |
| 11787061 | We have identified this methyltransferase as Dnmt3b which has an important role in neoplastic transformation but its role in cellular senescence and immortalization has not previously been reported |
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