HCSGD entry for DNMT3A

1. General information

Official gene symbolDNMT3A
Entrez ID1788
Gene full nameDNA (cytosine-5-)-methyltransferase 3 alpha
Other gene symbolsDNMT3A2 M.HsaIIIA
Links to Entrez GeneLinks to Entrez Gene

2. Neighbors in the network

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3. Gene ontology annotation

GO ID

GO term

Evidence

Category

GO:0000122Negative regulation of transcription from RNA polymerase II promoterIEAbiological_process
GO:0000775Chromosome, centromeric regionIEAcellular_component
GO:0000791EuchromatinIDAcellular_component
GO:0003677DNA bindingIDA IEAmolecular_function
GO:0003682Chromatin bindingIEAmolecular_function
GO:0003886DNA (cytosine-5-)-methyltransferase activityIDAmolecular_function
GO:0005515Protein bindingIPImolecular_function
GO:0005634NucleusIDAcellular_component
GO:0005720Nuclear heterochromatinIEAcellular_component
GO:0005730NucleolusIDAcellular_component
GO:0005737CytoplasmIDAcellular_component
GO:0006306DNA methylationIDA IEAbiological_process
GO:0006346Methylation-dependent chromatin silencingIEAbiological_process
GO:0006349Regulation of gene expression by genetic imprintingTASbiological_process
GO:0007283SpermatogenesisIEAbiological_process
GO:0008168Methyltransferase activityIEAmolecular_function
GO:0010424DNA methylation on cytosine within a CG sequenceIEAbiological_process
GO:0016363Nuclear matrixIDAcellular_component
GO:0043045DNA methylation involved in embryo developmentIEAbiological_process
GO:0043046DNA methylation involved in gamete generationIEAbiological_process
GO:0044027Hypermethylation of CpG islandIEAbiological_process
GO:0045322Unmethylated CpG bindingIEAmolecular_function
GO:0046498S-adenosylhomocysteine metabolic processIEAbiological_process
GO:0046499S-adenosylmethioninamine metabolic processIEAbiological_process
GO:0046872Metal ion bindingIEAmolecular_function
GO:0051718DNA (cytosine-5-)-methyltransferase activity, acting on CpG substratesIEAmolecular_function
GO:0071230Cellular response to amino acid stimulusIEAbiological_process
GO:0090116C-5 methylation of cytosineIDAbiological_process
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4. Expression levels in datasets

  • Meta-analysis result

p-value upp-value downFDR upFDR down
0.27734753620.33690277350.97425123451.0000000000

  • Individual experiment result
    ( "-" represent NA in the specific microarray platform )

Data sourceUp or downLog fold change
GSE11954Down-0.0035356576
GSE13712_SHEARDown-0.2709296506
GSE13712_STATICDown-0.0309953724
GSE19018Down-0.2963234888
GSE19899_A1Up0.0434329011
GSE19899_A2Up0.5489789639
PubMed_21979375_A1Up0.5657113119
PubMed_21979375_A2Up0.5404052867
GSE35957Down-0.4599700138
GSE36640Down-1.7072559454
GSE54402Down-0.2529815282
GSE9593Down-0.3423569717
GSE43922Up0.0572972484
GSE24585Down-0.1550689003
GSE37065Down-0.1246759943
GSE28863_A1Up0.1897211389
GSE28863_A2Up0.5534801379
GSE28863_A3Down-0.0262053303
GSE28863_A4Up0.4275894969
GSE48662Up0.2319515118

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-143-3pMIMAT0000435MIRT000716qRT-PCR//Luciferase reporter assay//Western blotFunctional MTI19638978
hsa-miR-29a-3pMIMAT0000086MIRT003021Luciferase reporter assay//Western blot//qRT-PCR//Reporter assay;OtherFunctional MTI17890317
hsa-miR-29a-3pMIMAT0000086MIRT003021Immunohistochemistry//Microarray//Western blotFunctional MTI20643754
hsa-miR-29c-3pMIMAT0000681MIRT003028Luciferase reporter assay//Western blot//qRT-PCR//Reporter assay;OtherFunctional MTI17890317
hsa-miR-29c-3pMIMAT0000681MIRT003028Immunohistochemistry//Microarray//Western blotFunctional MTI20643754
hsa-miR-29c-3pMIMAT0000681MIRT003028Luciferase reporter assay//Western blotFunctional MTI23516428
hsa-miR-29b-3pMIMAT0000100MIRT003029Luciferase reporter assay//Western blot//qRT-PCR//Reporter assay;OtherFunctional MTI17890317
hsa-miR-29b-3pMIMAT0000100MIRT003029Luciferase reporter assayFunctional MTI19211935
hsa-miR-29b-3pMIMAT0000100MIRT003029Immunohistochemistry//Microarray//Western blotFunctional MTI20643754
hsa-miR-194-5pMIMAT0000460MIRT005897Luciferase reporter assay//qRT-PCR//Western blotFunctional MTI20979124
hsa-miR-369-5pMIMAT0001621MIRT005960Luciferase reporter assay//Reporter assayFunctional MTI21136442
hsa-miR-101-3pMIMAT0000099MIRT007188Immunohistochemistry//Luciferase reporter assay//qRT-PCR//Western blotFunctional MTI23124077
hsa-miR-193b-3pMIMAT0002819MIRT016379MicroarrayFunctional MTI (Weak)20304954
hsa-miR-18a-3pMIMAT0002891MIRT040898CLASHFunctional 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-29a-3pMIMAT00000861hsa-miR-29a17890317
hsa-miR-29b-3pMIMAT00001001hsa-miR-29b17890317
hsa-miR-29c-3pMIMAT00006811hsa-miR-29c17890317
hsa-miR-29b-3pMIMAT00001001hsa-miR-29b{Western blot}{overexpression by miRNA precursor transfection}19211935
hsa-miR-143-3pMIMAT00004351hsa-miR-143{Western blot}{endogenous}19638978
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6. Text-mining results about the gene

Gene occurances in abstracts of cellular senescence-associated articles: 4 abstracts the gene occurs.


PubMed ID of the article

Sentenece the gene occurs

27147278Prominent 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)
21660946Expression 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
20473858DNMT3a plays a role in switches between doxorubicin-induced senescence and apoptosis of colorectal cancer cells
20473858Here, 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
20473858The differential expression of DNMT3a and p21 in response to Dox suggests that DNMT3a may be a key factor in switches between Dox-induced senescence and apoptosis
20473858Moreover, when DNMT3a was silenced, treatment of HCT116 cells with apoptosis-inducing concentration of Dox increased the percentage of cells undergoing senescence, accompanied by upregulation of p21
20473858Surprisingly, 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
20473858Overall, these data demonstrate that DNMT3a impacts the expression of p21 and plays a role in determining the Dox-induced senescence and apoptosis in HCT116 cells
18723031The 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
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