Browse DNMT3B

Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Nucleus
Domain PF00145 C-5 cytosine-specific DNA methylase
PF00855 PWWP domain
Function

Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1. Required for DUX4 silencing in somatic cells (PubMed:27153398).

> Gene Ontology
 
Biological Process GO:0001666 response to hypoxia
GO:0006304 DNA modification
GO:0006305 DNA alkylation
GO:0006306 DNA methylation
GO:0006479 protein methylation
GO:0006790 sulfur compound metabolic process
GO:0007584 response to nutrient
GO:0008213 protein alkylation
GO:0009116 nucleoside metabolic process
GO:0009119 ribonucleoside metabolic process
GO:0009314 response to radiation
GO:0009636 response to toxic substance
GO:0009991 response to extracellular stimulus
GO:0010212 response to ionizing radiation
GO:0010424 DNA methylation on cytosine within a CG sequence
GO:0010720 positive regulation of cell development
GO:0014074 response to purine-containing compound
GO:0014823 response to activity
GO:0016570 histone modification
GO:0016571 histone methylation
GO:0018022 peptidyl-lysine methylation
GO:0018205 peptidyl-lysine modification
GO:0031000 response to caffeine
GO:0031056 regulation of histone modification
GO:0031057 negative regulation of histone modification
GO:0031058 positive regulation of histone modification
GO:0031060 regulation of histone methylation
GO:0031061 negative regulation of histone methylation
GO:0031062 positive regulation of histone methylation
GO:0031667 response to nutrient levels
GO:0031960 response to corticosteroid
GO:0032259 methylation
GO:0032355 response to estradiol
GO:0032776 DNA methylation on cytosine
GO:0033189 response to vitamin A
GO:0033273 response to vitamin
GO:0034968 histone lysine methylation
GO:0036293 response to decreased oxygen levels
GO:0036295 cellular response to increased oxygen levels
GO:0036296 response to increased oxygen levels
GO:0040029 regulation of gene expression, epigenetic
GO:0042220 response to cocaine
GO:0042278 purine nucleoside metabolic process
GO:0042493 response to drug
GO:0043279 response to alkaloid
GO:0043414 macromolecule methylation
GO:0044728 DNA methylation or demethylation
GO:0045666 positive regulation of neuron differentiation
GO:0045814 negative regulation of gene expression, epigenetic
GO:0046128 purine ribonucleoside metabolic process
GO:0046498 S-adenosylhomocysteine metabolic process
GO:0046499 S-adenosylmethioninamine metabolic process
GO:0048545 response to steroid hormone
GO:0050769 positive regulation of neurogenesis
GO:0051384 response to glucocorticoid
GO:0051567 histone H3-K9 methylation
GO:0051568 histone H3-K4 methylation
GO:0051569 regulation of histone H3-K4 methylation
GO:0051570 regulation of histone H3-K9 methylation
GO:0051571 positive regulation of histone H3-K4 methylation
GO:0051573 negative regulation of histone H3-K9 methylation
GO:0051962 positive regulation of nervous system development
GO:0055093 response to hyperoxia
GO:0061647 histone H3-K9 modification
GO:0070482 response to oxygen levels
GO:0071383 cellular response to steroid hormone stimulus
GO:0071384 cellular response to corticosteroid stimulus
GO:0071385 cellular response to glucocorticoid stimulus
GO:0071396 cellular response to lipid
GO:0071407 cellular response to organic cyclic compound
GO:0071453 cellular response to oxygen levels
GO:0071455 cellular response to hyperoxia
GO:0071548 response to dexamethasone
GO:0071549 cellular response to dexamethasone stimulus
GO:0090116 C-5 methylation of cytosine
GO:1901605 alpha-amino acid metabolic process
GO:1901654 response to ketone
GO:1901655 cellular response to ketone
GO:1901657 glycosyl compound metabolic process
GO:1902275 regulation of chromatin organization
GO:1905268 negative regulation of chromatin organization
GO:1905269 positive regulation of chromatin organization
Molecular Function GO:0003682 chromatin binding
GO:0003714 transcription corepressor activity
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
GO:0008168 methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0009008 DNA-methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
GO:0042826 histone deacetylase binding
GO:0045322 unmethylated CpG binding
GO:0051718 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG hsa00270 Cysteine and methionine metabolism
hsa01100 Metabolic pathways
Reactome R-HSA-5334118: DNA methylation
R-HSA-212165: Epigenetic regulation of gene expression
R-HSA-74160: Gene Expression
R-HSA-5250941: Negative epigenetic regulation of rRNA expression
R-HSA-427413: NoRC negatively regulates rRNA expression
R-HSA-212300: PRC2 methylates histones and DNA
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between DNMT3B and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 
  Literatures describing the relation between DNMT3B and anti-tumor immunity in human cancer.
PMID Cancer type Relation to immunity Evidence sentences
23312906Glioma; MesotheliomaPromote immunityIn two non epithelial cancers (glioma and mesothelioma), we found that the epigenetic regulation of the NY-ESO1 gene requires the sequential recruitment of the HDAC1-mSin3a-NCOR, Dnmt3b-HDAC1-Egr1 and Dnmt1-PCNA-UHRF1-G9a complexes.The NY-ESO1 gene is a cancer/testis antigen considered to be suitable target for the immunotherapy of human malignancies.
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of DNMT3B in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of DNMT3B in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.4190.137
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-0.4540.463
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.3930.42
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.1170.735
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.2120.901
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.0030.999
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.230.458
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.4380.604
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.0870.916
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 48-0.0410.936
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 28-0.0770.913
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.2460.0891
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of DNMT3B in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27733.72.711
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27593.73.40.31
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91611.1011.10.36
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47250250.364
1329033130MelanomaallAnti-PD-1 (nivolumab) 38272.602.61
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16146.206.21
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of DNMT3B. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of DNMT3B. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by DNMT3B.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of DNMT3B. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of DNMT3B expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between DNMT3B and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolDNMT3B
NameDNA (cytosine-5-)-methyltransferase 3 beta
Aliases ICF; ICF1; M.HsaIIIB; DNA MTase HsaIIIB; DNA methyltransferase HsaIIIB; DNA (cytosine-5)-methyltransferase 3 ......
Chromosomal Location20q11.2
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting DNMT3B collected from DrugBank database.
> Drugs from DrugBank database
 

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