DNA (cytosine-5)-methyltransferase 3A

DNA (cytosine-5)-methyltransferase 3A is an enzyme that catalyzes the transfer of methyl groups to specific CpG structures in DNA, a process called DNA methylation. The enzyme is encoded in humans by the DNMT3A gene.[5][6]

DNMT3A
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 4U7T, 4QBR, 4U7P, 4QBS, 3A1B, 3LLR, 4QBQ, 3SVM, 3A1A, 2QRV
Identifiers
Aliases	DNMT3A, DNMT3A2, M.HsaIIIA, TBRS, DNA (cytosine-5-)-methyltransferase 3 alpha, DNA methyltransferase 3 alpha, HESJAS
External IDs	OMIM: 602769 MGI: 1261827 HomoloGene: 7294 GeneCards: DNMT3A
Gene location (Human) Chr. Chromosome 2 (human)[1] Band 2p23.3 Start 25,227,855 bp[1] End 25,342,590 bp[1]
Gene location (Mouse) Chr. Chromosome 12 (mouse)[2] Band 12|12 A1.1 Start 3,806,007 bp[2] End 3,914,443 bp[2]
RNA expression pattern More reference expression data
Gene ontology Molecular function • methyltransferase activity • transferase activity • DNA binding • DNA-methyltransferase activity • chromatin binding • metal ion binding • GO:0001948 protein binding • identical protein binding • DNA (cytosine-5-)-methyltransferase activity • GO:0001200, GO:0001133, GO:0001201 DNA-binding transcription factor activity, RNA polymerase II-specific • GO:0000980 RNA polymerase II cis-regulatory region sequence-specific DNA binding • GO:0001106 transcription corepressor activity • transcription factor binding Cellular component • cytoplasm • euchromatin • nuclear matrix • nucleoplasm • nuclear heterochromatin • heterochromatin • XY body • chromosome, centromeric region • cell nucleus Biological process • response to ionizing radiation • regulation of gene expression by genetic imprinting • C-5 methylation of cytosine • response to estradiol • positive regulation of cell death • cellular response to ethanol • aging • negative regulation of transcription from RNA polymerase II promoter • DNA methylation involved in gamete generation • response to vitamin A • DNA methylation • methylation • negative regulation of gene expression, epigenetic • response to nutrient levels • response to lead ion • methylation-dependent chromatin silencing • spermatogenesis • neuron differentiation • GO:0007067 mitotic cell cycle • cellular response to amino acid stimulus • regulation of gene expression • DNA methylation involved in embryo development • response to ethanol • response to toxic substance • cellular response to hypoxia • response to drug • hepatocyte apoptotic process • response to cocaine • DNA methylation on cytosine • chromatin organization Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	1788	13435
Ensembl	ENSG00000119772	ENSMUSG00000020661
UniProt	Q9Y6K1	O88508
RefSeq (mRNA)	NM_022552 NM_153759 NM_175629 NM_175630 NM_001320892 NM_001320893 NM_001375819	NM_001271753 NM_007872 NM_153743
RefSeq (protein)	NP_001307821 NP_001307822 NP_072046 NP_715640 NP_783328 NP_783329 NP_001362748	NP_001258682 NP_031898 NP_714965
Location (UCSC)	Chr 2: 25.23 – 25.34 Mb	Chr 12: 3.81 – 3.91 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

This enzyme is responsible for de novo DNA methylation. Such function is to be distinguished from maintenance DNA methylation which ensures the fidelity of replication of inherited epigenetic patterns. DNMT3A forms part of the family of DNA methyltransferase enzymes, which consists of the protagonists DNMT1, DNMT3A and DNMT3B.[5][6]

While de novo DNA methylation modifies the information passed on by the parent to the progeny, it enables key epigenetic modifications essential for processes such as cellular differentiation and embryonic development, transcriptional regulation, heterochromatin formation, X-inactivation, imprinting and genome stability.[7]

Gene

DNMT3A is a 130 kDa protein encoded by 23 exons found on chromosome 2p23 in humans.[8] There exists a 98% homology between human and murine homologues.[6]

Due to splicing, there exist two main murine RNA isoforms, Dnmt3a1 and Dnmt3a2. These isoforms exist in different cell types.[9]

Protein structure

DNMT3A consists of three major protein domains: the Pro-Trp-Trp-Pro (PWWP) domain, the ATRX-DNMT3-DNMT3L (ADD) domain and the catalytic methyltransferase domain. The ADD domain serves as an inhibitor of the methyltransferase domain until DNMT3A binds to the unmodified lysine 4 of histone 3 (H3K4me0) for its de novo methylating activity.[9] This protein thus seems to have an inbuilt control mechanism targeting histones only for methylation. Finally, the methyltransferase domain is highly conserved, even among prokaryotes![10]

Function

DNMT1 is responsible for maintenance DNA methylation while DNMT3A and DNMT3B carry out both maintenance – correcting the errors of DNMT1 – and de novo DNA methylation. After DNMT1 knockout in human cancer cells, these cells were found to retain their inherited methylation pattern,[11] which suggests maintenance activity by the expressed DNMT3s. DNMT3s show equal affinity for unmethylated and hemimethylated DNA substrates[11] while DNMT1 has a 10-40 fold preference for hemimethylated DNA.[12][13] The DNMT3s can bind to both forms and hence potentially do both maintenance and de novo modifications.

De novo methylation is the main recognized activity of DNMT3A, which is essential for processes such as those mentioned in the introductory paragraphs. Genetic imprinting prevents parthenogenesis in mammals,[14] and hence forces sexual reproduction and its multiple consequences on genetics and phylogenesis. DNMT3A is essential for genetic imprinting.[15]

Animal studies

In mice, this gene has shown reduced expression in ageing animals causes cognitive long-term memory decline.[16]

In Dnmt3a-/- mice, many genes associated with HSC self-renewal increase in expression and some fail to be appropriately repressed during differentiation.[17] This suggests abrogation of differentiation in hematopoietic stem cells (HSCs) and an increase in self-renewal cell-division instead. Indeed, it was found that differentiation was partially rescued if Dnmt3a-/- HSCs experienced an additional Ctnb1 knockdown – Ctnb1 codes for β-catenin, which participates in self-renewal cell division.[9]

Clinical relevance

This gene is frequently mutated in cancer, being one of 127 frequently mutated genes identified in the Cancer Genome Atlas project[18] DNMT3A mutations were most commonly seen in acute myeloid leukaemia (AML) where they occurred in just over 25% of cases sequenced. These mutations most often occur at position R882 in the protein and this mutation may cause loss of function.[19] DNMT3A mutations are associated with poor overall survival, suggesting that they have an important common effect on the potential of AML cells to cause lethal disease.[20] It has also been found that DNMT3A-mutated cell lines exhibit transcriptome instability, in that they have much more erroneous RNA splicing as compared to their isogenic wildtype counterparts.[21] Mutations in this gene are also associated with Tatton-Brown-Rahman syndrome, an over growth disorder.

Interactions

DNMT3A has been shown to interact with:

• DNMT1,[22]
• DNMT3B,[22][23][24]
• HDAC1,[25]
• Myc,[26]
• PIAS1,[23]
• PIAS2,[23]
• SUV39H1,[27]
• UBE2I[23] and
• ZNF238.[25]

Model organisms

Model organisms have been used in the study of DNMT3A function. A conditional knockout mouse line called Dnmt3a^{tm1a(KOMP)Wtsi} was generated at the Wellcome Trust Sanger Institute.[28] Male and female animals underwent a standardized phenotypic screen[29] to determine the effects of deletion.[30][31][32][33] Additional screens performed: - In-depth immunological phenotyping[34]

Dnmt3a knockout mouse phenotype

Characteristic	Phenotype
All data available at.[29][34]
Insulin	Normal
Homozygous viability at P14	Normal
Homozygous Fertility	Normal
Body weight	Normal
Neurological assessment	Normal
Grip strength	Normal
Dysmorphology	Normal
Indirect calorimetry	Normal
Glucose tolerance test	Normal
Auditory brainstem response	Normal
DEXA	Normal
Radiography	Normal
Eye morphology	Normal
Clinical chemistry	Normal
Haematology 16 Weeks	Normal
Peripheral blood leukocytes 16 Weeks	Normal
Salmonella infection	Normal

References

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2. GRCm38: Ensembl release 89: ENSMUSG00000020661 - Ensembl, May 2017
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4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. 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. S2CID 256263.
6. Xie S, Wang Z, Okano M, Nogami M, Li Y, He WW, Okumura K, Li E (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.
7. Jia, Yuanhui; Li, Pishun; Fang, Lan; Zhu, Haijun; Xu, Liangliang; Cheng, Hao; Zhang, Junying; Li, Fei; Feng, Yan (2016-04-12). "Negative regulation of DNMT3A de novo DNA methylation by frequently overexpressed UHRF family proteins as a mechanism for widespread DNA hypomethylation in cancer". Cell Discovery. 2: 16007. doi:10.1038/celldisc.2016.7. PMC 4849474. PMID 27462454.
8. Robertson KD, Uzvolgyi E, Liang G, Talmadge C, Sumegi J, Gonzales FA, Jones PA (June 1999). "The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors". Nucleic Acids Research. 27 (11): 2291–8. doi:10.1093/nar/27.11.2291. PMC 148793. PMID 10325416.
9. Yang L, Rau R, Goodell MA (2015). "DNMT3A in haematological malignancies". Nature Reviews. Cancer. 15 (3): 152–65. doi:10.1038/nrc3895. PMC 5814392. PMID 25693834.
10. Xu F, Mao C, Ding Y, Rui C, Wu L, Shi A, Zhang H, Zhang L, Xu Z (2010-01-01). "Molecular and enzymatic profiles of mammalian DNA methyltransferases: structures and targets for drugs". Current Medicinal Chemistry. 17 (33): 4052–71. doi:10.2174/092986710793205372. PMC 3003592. PMID 20939822.
11. Rhee I, Jair KW, Yen RW, Lengauer C, Herman JG, Kinzler KW, Vogelstein B, Baylin SB, Schuebel KE (April 2000). "CpG methylation is maintained in human cancer cells lacking DNMT1". Nature. 404 (6781): 1003–7. doi:10.1038/35010000. PMID 10801130. S2CID 4425037.
12. Pradhan S, Bacolla A, Wells RD, Roberts RJ (November 1999). "Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation". The Journal of Biological Chemistry. 274 (46): 33002–10. doi:10.1074/jbc.274.46.33002. PMID 10551868.
13. Pradhan S, Talbot D, Sha M, Benner J, Hornstra L, Li E, Jaenisch R, Roberts RJ (November 1997). "Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase". Nucleic Acids Research. 25 (22): 4666–73. doi:10.1093/nar/25.22.4666. PMC 147102. PMID 9358180.
14. Reik W, Walter J (January 2001). "Genomic imprinting: parental influence on the genome". Nature Reviews Genetics. 2 (1): 21–32. doi:10.1038/35047554. PMID 11253064. S2CID 12050251.
15. Kaneda M, Okano M, Hata K, Sado T, Tsujimoto N, Li E, Sasaki H (June 2004). "Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting". Nature. 429 (6994): 900–3. doi:10.1038/nature02633. PMID 15215868. S2CID 4344982.
16. Oliveira AM, Hemstedt TJ, Bading H (August 2012). "Rescue of aging-associated decline in Dnmt3a2 expression restores cognitive abilities". Nature Neuroscience. 15 (8): 1111–3. doi:10.1038/nn.3151. PMID 22751036. S2CID 10590208.
17. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA (January 2012). "Dnmt3a is essential for hematopoietic stem cell differentiation". Nature Genetics. 44 (1): 23–31. doi:10.1038/ng.1009. PMC 3637952. PMID 22138693.
18. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. (October 2013). "Mutational landscape and significance across 12 major cancer types". Nature. 502 (7471): 333–9. doi:10.1038/nature12634. PMC 3927368. PMID 24132290.
19. Shih AH, Abdel-Wahab O, Patel JP, Levine RL (September 2012). "The role of mutations in epigenetic regulators in myeloid malignancies". Nature Reviews. Cancer. 12 (9): 599–612. doi:10.1038/nrc3343. PMID 22898539. S2CID 20214444.
20. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, et al. (December 2010). "DNMT3A mutations in acute myeloid leukemia". The New England Journal of Medicine. 363 (25): 2424–33. doi:10.1056/NEJMoa1005143. PMC 3201818. PMID 21067377.
21. Banaszak, LG; Giudice, V; Zhao, X; Wu, Z; Gao, S; Hosokawa, K; Keyvanfar, K; Townsley, DM; Gutierrez-Rodrigues, F; Ibanez, MdPF; Kajigaya, S; Young, NS (2018). "Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing". Blood Cells, Molecules and Diseases. 69: 10–22. doi:10.1016/j.bcmd.2017.12.002. PMC 6728079. PMID 29324392.
22. 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.
23. 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.
24. 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. doi:10.1016/s0960-9822(03)00432-9. PMID 12867029. S2CID 2320997.
25. Fuks F, Burgers WA, Godin N, Kasai M, Kouzarides T (May 2001). "Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription". The EMBO Journal. 20 (10): 2536–44. doi:10.1093/emboj/20.10.2536. PMC 125250. PMID 11350943.
26. Brenner C, Deplus R, Didelot C, Loriot A, Viré E, De Smet C, Gutierrez A, Danovi D, Bernard D, Boon T, Pelicci PG, Amati B, Kouzarides T, de Launoit Y, Di Croce L, Fuks F (January 2005). "Myc represses transcription through recruitment of DNA methyltransferase corepressor". The EMBO Journal. 24 (2): 336–46. doi:10.1038/sj.emboj.7600509. PMC 545804. PMID 15616584.
27. Fuks F, Hurd PJ, Deplus R, Kouzarides T (May 2003). "The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase". Nucleic Acids Research. 31 (9): 2305–12. doi:10.1093/nar/gkg332. PMC 154218. PMID 12711675.
28. Gerdin AK (2010). "The Sanger Mouse Genetics Programme: high throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x. S2CID 85911512.
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31. Dolgin E (June 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi:10.1038/474262a. PMID 21677718.
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Further reading

• Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O (September 1995). "Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence" (PDF). Nature. 377 (6547 Suppl): 3–174. PMID 7566098.
• Bonaldo MF, Lennon G, Soares MB (September 1996). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Research. 6 (9): 791–806. doi:10.1101/gr.6.9.791. PMID 8889548.
• Robertson KD, Uzvolgyi E, Liang G, Talmadge C, Sumegi J, Gonzales FA, Jones PA (June 1999). "The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors". Nucleic Acids Research. 27 (11): 2291–8. doi:10.1093/nar/27.11.2291. PMC 148793. PMID 10325416.
• Fuks F, Burgers WA, Godin N, Kasai M, Kouzarides T (May 2001). "Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription". The EMBO Journal. 20 (10): 2536–44. doi:10.1093/emboj/20.10.2536. PMC 125250. PMID 11350943.
• Vaute O, Nicolas E, Vandel L, Trouche D (January 2002). "Functional and physical interaction between the histone methyl transferase Suv39H1 and histone deacetylases". Nucleic Acids Research. 30 (2): 475–81. doi:10.1093/nar/30.2.475. PMC 99834. PMID 11788710.
• Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M, Fuks F, Lo Coco F, Kouzarides T, Nervi C, Minucci S, Pelicci PG (February 2002). "Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor". Science. 295 (5557): 1079–82. doi:10.1126/science.1065173. PMID 11834837. S2CID 29532358.
• Hata K, Okano M, Lei H, Li E (April 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.
• Chen T, Ueda Y, Xie S, Li E (October 2002). "A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation". The Journal of Biological Chemistry. 277 (41): 38746–54. doi:10.1074/jbc.M205312200. PMID 12138111.
• 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.
• Yanagisawa Y, Ito E, Yuasa Y, Maruyama K (September 2002). "The human DNA methyltransferases DNMT3A and DNMT3B have two types of promoters with different CpG contents". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1577 (3): 457–65. doi:10.1016/S0167-4781(02)00482-7. PMID 12359337.
• Fatemi M, Hermann A, Gowher H, Jeltsch A (October 2002). "Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA". European Journal of Biochemistry / FEBS. 269 (20): 4981–4. doi:10.1046/j.1432-1033.2002.03198.x. PMID 12383256.
• Weisenberger DJ, Velicescu M, Preciado-Lopez MA, Gonzales FA, Tsai YC, Liang G, Jones PA (September 2002). "Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells". Gene. 298 (1): 91–9. doi:10.1016/S0378-1119(02)00976-9. PMID 12406579.
• Chedin F, Lieber MR, Hsieh CL (December 2002). "The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a". Proceedings of the National Academy of Sciences of the United States of America. 99 (26): 16916–21. doi:10.1073/pnas.262443999. PMC 139244. PMID 12481029.
• Robert MF, Morin S, Beaulieu N, Gauthier F, Chute IC, Barsalou A, MacLeod AR (January 2003). "DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells". Nature Genetics. 33 (1): 61–5. doi:10.1038/ng1068. PMID 12496760. S2CID 561490.
• Fuks F, Hurd PJ, Deplus R, Kouzarides T (May 2003). "The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase". Nucleic Acids Research. 31 (9): 2305–12. doi:10.1093/nar/gkg332. PMC 154218. PMID 12711675.
• Yakushiji T, Uzawa K, Shibahara T, Noma H, Tanzawa H (June 2003). "Over-expression of DNA methyltransferases and CDKN2A gene methylation status in squamous cell carcinoma of the oral cavity". International Journal of Oncology. 22 (6): 1201–7. doi:10.3892/ijo.22.6.1201. PMID 12738984.
• 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.