DNMT3B

DNMT3B
Available structures
PDB	Ortholog search: PDBe RCSB
List of PDB id codes
	3QKJ, 3FLG, 5CIU
Identifiers
Aliases	DNMT3B, ICF, ICF1, M.HsaIIIB, DNA (cytosine-5-)-methyltransferase 3 beta, DNA methyltransferase 3 beta, FSHD4
External IDs	OMIM: 602900; MGI: 1261819; HomoloGene: 56000; GeneCards: DNMT3B; OMA:DNMT3B - orthologs
Gene location (Human)
Chr.	Chromosome 20 (human)
End	32,809,356 bp
Gene location (Mouse)
Chr.	Chromosome 2 (mouse)
End	153,529,650 bp
RNA expression pattern
	Top expressed in
	secondary oocyte; ; hair follicle; ; sperm; ; embryo; ; gonad; ; testicle; ; ganglionic eminence; ; body of pancreas; ; ventricular zone; ; corpus epididymis;
	Top expressed in
	epiblast; ; primitive streak; ; embryo; ; pelvic part of vagina; ; paramesonephric duct; ; epithelium of vagina; ; ejaculatory duct; ; tail of embryo; ; abdominal wall; ; embryo;
	More reference expression data
	More reference expression data
Gene ontology
Molecular function	methyltransferase activity; transferase activity; DNA binding; transcription corepressor activity; DNA-methyltransferase activity; chromatin binding; metal ion binding; protein binding; DNA (cytosine-5-)-methyltransferase activity; DNA-binding transcription factor activity, RNA polymerase II-specific; histone deacetylase binding;
Cellular component	cytoplasm; intracellular membrane-bounded organelle; nucleoplasm; nucleus;
Biological process	response to ionizing radiation; C-5 methylation of cytosine; response to estradiol; response to hypoxia; cellular response to hyperoxia; negative regulation of transcription by RNA polymerase II; response to activity; cellular response to dexamethasone stimulus; response to vitamin A; DNA methylation; methylation; positive regulation of gene expression; negative regulation of gene expression, epigenetic; positive regulation of histone H3-K4 methylation; positive regulation of neuron differentiation; negative regulation of histone H3-K9 methylation; regulation of gene expression; response to caffeine; response to toxic substance; response to cocaine;
	Sources:Amigo / QuickGO
Orthologs
	1789
	13436
	ENSG00000088305
	ENSMUSG00000027478
	Q9UBC3
	O88509
NM_001207055; NM_001207056; NM_006892; NM_175848; NM_175849;
	NM_175850
NM_001003960; NM_001003961; NM_001003963; NM_001122997; NM_001271744;
	NM_001271745; NM_001271746; NM_001271747; NM_010068
NP_001193984; NP_001193985; NP_008823; NP_787044; NP_787045;
	NP_787046
NP_001003960; NP_001003961; NP_001003963; NP_001116469; NP_001258673;
	NP_001258674; NP_001258675; NP_001258676; NP_034198
	Wikidata
View/Edit Human	View/Edit Mouse

DNA (cytosine-5)-methyltransferase 3 beta, is an enzyme that in humans in encoded by the DNMT3B gene.^[5] Mutation in this gene are associated with immunodeficiency, centromere instability and facial anomalies syndrome.^[6]

Function

CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase which is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes primarily to the nucleus and its expression is developmentally regulated. Eight alternatively spliced transcript variants have been described. The full length sequences of variants 4 and 5 have not been determined.^[5]

Clinical significance

Immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome is a result of defects in lymphocyte maturation resulting from aberrant DNA methylation caused by mutations in the DNMT3B gene.^[6]

Variants of the gene can also contribute to nicotine dependency.^[7]

Interactions

DNMT3B has been shown to interact with:

References

^ ^a ^b ^c GRCh38: Ensembl release 89: ENSG00000088305 – Ensembl, May 2017
^ ^a ^b ^c GRCm38: Ensembl release 89: ENSMUSG00000027478 – Ensembl, May 2017
^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^ ^a ^b "Entrez Gene: DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta".
^ ^a ^b Ehrlich M (October 2003). "The ICF syndrome, a DNA methyltransferase 3B deficiency and immunodeficiency disease". Clinical Immunology. 109 (1): 17–28. doi:10.1016/S1521-6616(03)00201-8. PMID 14585272.
^ Hancock DB, Guo Y, Reginsson GW, Gaddis NC, Lutz SM, Sherva R, et al. (October 2017). "Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence". Molecular Psychiatry. 23 (9): 1911–1919. doi:10.1038/mp.2017.193. PMC 5882602. PMID 28972577.
^ ^a ^b ^c Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T, Peters AH (July 2003). "Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin". Current Biology. 13 (14): 1192–200. Bibcode:2003CBio...13.1192L. doi:10.1016/s0960-9822(03)00432-9. PMID 12867029. S2CID 2320997.
^ ^a ^b Kim GD, Ni J, Kelesoglu N, Roberts RJ, Pradhan S (August 2002). "Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases". The EMBO Journal. 21 (15): 4183–95. doi:10.1093/emboj/cdf401. PMC 126147. PMID 12145218.
^ Ling Y, Sankpal UT, Robertson AK, McNally JG, Karpova T, Robertson KD (2004). "Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription". Nucleic Acids Research. 32 (2): 598–610. doi:10.1093/nar/gkh195. PMC 373322. PMID 14752048.
^ ^a ^b ^c Geiman TM, Sankpal UT, Robertson AK, Chen Y, Mazumdar M, Heale JT, Schmiesing JA, Kim W, Yokomori K, Zhao Y, Robertson KD (2004). "Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery". Nucleic Acids Research. 32 (9): 2716–29. doi:10.1093/nar/gkh589. PMC 419596. PMID 15148359.
^ ^a ^b Kang ES, Park CW, Chung JH (December 2001). "Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1". Biochemical and Biophysical Research Communications. 289 (4): 862–8. doi:10.1006/bbrc.2001.6057. PMID 11735126.

External links

DNMT3b at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
EC 2.1.1.37

[refGRCh38Ensembl-1] GRCh38: Ensembl release 89: ENSG00000088305 – Ensembl, May 2017

[refGRCm38Ensembl-2] GRCm38: Ensembl release 89: ENSMUSG00000027478 – Ensembl, May 2017

[3] "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[4] "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[entrez-5] "Entrez Gene: DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta".

[Ehrlich_2003-6] Ehrlich M (October 2003). "The ICF syndrome, a DNA methyltransferase 3B deficiency and immunodeficiency disease". Clinical Immunology. 109 (1): 17–28. doi:10.1016/S1521-6616(03)00201-8. PMID 14585272.

[HancockGuo2017-7] Hancock DB, Guo Y, Reginsson GW, Gaddis NC, Lutz SM, Sherva R, et al. (October 2017). "Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence". Molecular Psychiatry. 23 (9): 1911–1919. doi:10.1038/mp.2017.193. PMC 5882602. PMID 28972577.

[pmid12867029-8] Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T, Peters AH (July 2003). "Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin". Current Biology. 13 (14): 1192–200. Bibcode:2003CBio...13.1192L. doi:10.1016/s0960-9822(03)00432-9. PMID 12867029. S2CID 2320997.

[pmid12145218-9] Kim GD, Ni J, Kelesoglu N, Roberts RJ, Pradhan S (August 2002). "Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases". The EMBO Journal. 21 (15): 4183–95. doi:10.1093/emboj/cdf401. PMC 126147. PMID 12145218.

[pmid14752048-10] Ling Y, Sankpal UT, Robertson AK, McNally JG, Karpova T, Robertson KD (2004). "Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription". Nucleic Acids Research. 32 (2): 598–610. doi:10.1093/nar/gkh195. PMC 373322. PMID 14752048.

[pmid15148359-11] Geiman TM, Sankpal UT, Robertson AK, Chen Y, Mazumdar M, Heale JT, Schmiesing JA, Kim W, Yokomori K, Zhao Y, Robertson KD (2004). "Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery". Nucleic Acids Research. 32 (9): 2716–29. doi:10.1093/nar/gkh589. PMC 419596. PMID 15148359.

[pmid11735126-12] Kang ES, Park CW, Chung JH (December 2001). "Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1". Biochemical and Biophysical Research Communications. 289 (4): 862–8. doi:10.1006/bbrc.2001.6057. PMID 11735126.

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