DNMT3B

DNA (cytosine-5-)-methyltransferase 3 beta
PDB rendering based on 1khc.
Available structures PDB Ortholog search: PDBe, RCSB List of PDB id codes 3FLG​, 3QKJ​
Identifiers
Symbols	DNMT3B ; ICF; ICF1; M.HsaIIIB
External IDs	OMIM: 602900 MGI: 1261819 HomoloGene: 56000 ChEMBL: 6095 GeneCards: DNMT3B Gene
EC number	2.1.1.37
Gene ontology Molecular function • chromatin binding • transcription corepressor activity • DNA (cytosine-5-)-methyltransferase activity • protein binding • DNA-methyltransferase activity • histone deacetylase binding • unmethylated CpG binding • metal ion binding • DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates Cellular component • nucleus • nucleoplasm • nuclear heterochromatin • cytoplasm • intracellular membrane-bounded organelle Biological process • negative regulation of transcription from RNA polymerase II promoter • response to hypoxia • DNA methylation • methylation-dependent chromatin silencing • regulation of gene expression by genetic imprinting • response to toxic substance • response to ionizing radiation • DNA methylation on cytosine within a CG sequence • gene expression • positive regulation of gene expression • response to activity • response to caffeine • protein complex localization • response to estradiol • DNA methylation on cytosine • response to vitamin A • regulation of gene expression, epigenetic • response to cocaine • response to drug • positive regulation of neuron differentiation • negative regulation of gene expression, epigenetic • S-adenosylhomocysteine metabolic process • S-adenosylmethioninamine metabolic process • positive regulation of histone H3-K4 methylation • negative regulation of histone H3-K9 methylation • inactivation of X chromosome by DNA methylation • cellular response to amino acid stimulus • cellular response to hyperoxia • cellular response to dexamethasone stimulus • C-5 methylation of cytosine Sources: Amigo / QuickGO
RNA expression pattern
More reference expression data
Orthologs
Species	Human	Mouse
Entrez	1789	13436
Ensembl	ENSG00000088305	ENSMUSG00000027478
UniProt	Q9UBC3	O88509
RefSeq (mRNA)	NM_001207055	NM_001003960
RefSeq (protein)	NP_001193984	NP_001003960
Location (UCSC)	Chr 20: 32.76 – 32.81 Mb	Chr 2: 153.65 – 153.69 Mb
PubMed search

DNA (cytosine-5-)-methyltransferase 3 beta, also known as DNMT3B, is a protein associated with immunodeficiency, centromere instability and facial anomalies syndrome.

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. Mutations in this gene cause the immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. Eight alternatively spliced transcript variants have been described. The full length sequences of variants 4 and 5 have not been determined.^[1]

Interactions

DNMT3B has been shown to interact with:

• CBX5,^[2]
• DNMT1,^[2][3]
• DNMT3A,^[2][3][4]
• KIF4A,^[5]
• NCAPG,^[5]
• SMC2,^[5]
• SUMO1^[6] and
• UBE2I.^[6]

References

1. "Entrez Gene: DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta".
2. Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T, Peters AH (Jul 2003). "Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin". Curr. Biol. 13 (14): 1192–200. doi:10.1016/s0960-9822(03)00432-9. PMID 12867029.
3. Kim GD, Ni J, Kelesoglu N, Roberts RJ, Pradhan S (Aug 2002). "Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases". EMBO J. 21 (15): 4183–95. doi:10.1093/emboj/cdf401. PMC 126147. PMID 12145218.
4. Ling Y, Sankpal UT, Robertson AK, McNally JG, Karpova T, Robertson KD. "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 Res. 32 (2): 598–610. doi:10.1093/nar/gkh195. PMC 373322. PMID 14752048.
5. Geiman TM, Sankpal UT, Robertson AK, Chen Y, Mazumdar M, Heale JT, Schmiesing JA, Kim W, Yokomori K, Zhao Y, Robertson KD. "Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery". Nucleic Acids Res. 32 (9): 2716–29. doi:10.1093/nar/gkh589. PMC 419596. PMID 15148359.
6. Kang ES, Park CW, Chung JH (Dec 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". Biochem. Biophys. Res. Commun. 289 (4): 862–8. doi:10.1006/bbrc.2001.6057. PMID 11735126.

Further reading

• Wijmenga C, Hansen RS, Gimelli G; et al. (2001). "Genetic variation in ICF syndrome: evidence for genetic heterogeneity.". Hum. Mutat. 16 (6): 509–17. doi:10.1002/1098-1004(200012)16:6<509::AID-HUMU8>3.0.CO;2-V. PMID 11102980.
• Okano M, Xie S, Li E (1998). "Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases.". Nat. Genet. 19 (3): 219–20. doi:10.1038/890. PMID 9662389.
• Robertson KD, Uzvolgyi E, Liang G; et al. (1999). "The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors.". Nucleic Acids Res. 27 (11): 2291–8. doi:10.1093/nar/27.11.2291. PMC 148793. PMID 10325416.
• Xie S, Wang Z, Okano M; et al. (1999). "Cloning, expression and chromosome locations of the human DNMT3 gene family.". Gene 236 (1): 87–95. doi:10.1016/S0378-1119(99)00252-8. PMID 10433969.
• Okano M, Bell DW, Haber DA, Li E (1999). "DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.". Cell 99 (3): 247–57. doi:10.1016/S0092-8674(00)81656-6. PMID 10555141.
• Hansen RS, Wijmenga C, Luo P; et al. (2000). "The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome.". Proc. Natl. Acad. Sci. U.S.A. 96 (25): 14412–7. doi:10.1073/pnas.96.25.14412. PMC 24450. PMID 10588719.
• Xu GL, Bestor TH, Bourc'his D; et al. (2000). "Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene.". Nature 402 (6758): 187–91. doi:10.1038/46052. PMID 10647011.
• Hartley JL, Temple GF, Brasch MA (2001). "DNA cloning using in vitro site-specific recombination.". Genome Res. 10 (11): 1788–95. doi:10.1101/gr.143000. PMC 310948. PMID 11076863.
• Fuks F, Burgers WA, Godin N; et al. (2001). "Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription.". EMBO J. 20 (10): 2536–44. doi:10.1093/emboj/20.10.2536. PMC 125250. PMID 11350943.
• Kang ES, Park CW, Chung JH (2002). "Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1.". Biochem. Biophys. Res. Commun. 289 (4): 862–8. doi:10.1006/bbrc.2001.6057. PMID 11735126.
• Deloukas P, Matthews LH, Ashurst J; et al. (2002). "The DNA sequence and comparative analysis of human chromosome 20.". Nature 414 (6866): 865–71. doi:10.1038/414865a. PMID 11780052.
• Rhee I, Bachman KE, Park BH; et al. (2002). "DNMT1 and DNMT3b cooperate to silence genes in human cancer cells.". Nature 416 (6880): 552–6. doi:10.1038/416552a. PMID 11932749.
• Hata K, Okano M, Lei H, Li E (2002). "Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice.". Development 129 (8): 1983–93. PMID 11934864.
• Beaulieu N, Morin S, Chute IC; et al. (2002). "An essential role for DNA methyltransferase DNMT3B in cancer cell survival.". J. Biol. Chem. 277 (31): 28176–81. doi:10.1074/jbc.M204734200. PMID 12015329.
• Saito Y, Kanai Y, Sakamoto M; et al. (2002). "Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, associated with DNA hypomethylation on pericentromeric satellite regions during human hepatocarcinogenesis.". Proc. Natl. Acad. Sci. U.S.A. 99 (15): 10060–5. doi:10.1073/pnas.152121799. PMC 126624. PMID 12110732.
• Kim GD, Ni J, Kelesoglu N; et al. (2002). "Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases.". EMBO J. 21 (15): 4183–95. doi:10.1093/emboj/cdf401. PMC 126147. PMID 12145218.
• Deplus R, Brenner C, Burgers WA; et al. (2002). "Dnmt3L is a transcriptional repressor that recruits histone deacetylase.". Nucleic Acids Res. 30 (17): 3831–8. doi:10.1093/nar/gkf509. PMC 137431. PMID 12202768.
• Shen H, Wang L, Spitz MR; et al. (2002). "A novel polymorphism in human cytosine DNA-methyltransferase-3B promoter is associated with an increased risk of lung cancer.". Cancer Res. 62 (17): 4992–5. PMID 12208751.
• Shirohzu H, Kubota T, Kumazawa A; et al. (2003). "Three novel DNMT3B mutations in Japanese patients with ICF syndrome.". Am. J. Med. Genet. 112 (1): 31–7. doi:10.1002/ajmg.10658. PMID 12239717.

External links

• DNMT3b at the US National Library of Medicine Medical Subject Headings (MeSH)
• EC 2.1.1.37