Biology:DNA (cytosine-5)-methyltransferase 3A

Short description: Protein-coding gene in the species Homo sapiens

Generic protein structure example

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.

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.

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.

DNMT3a is the gene most commonly found mutated in clonal hematopoiesis, a common aging-related phenomenon in which hematopoietic stem cells (HSCs) or other early blood cell progenitors contribute to the formation of a genetically distinct subpopulation of blood cells.

Gene

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

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

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. 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.

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, which suggests maintenance activity by the expressed DNMT3s. DNMT3s show equal affinity for unmethylated and hemimethylated DNA substrates while DNMT1 has a 10-40 fold preference for hemimethylated DNA. 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, and hence forces sexual reproduction and its multiple consequences on genetics and phylogenesis. DNMT3A is essential for genetic imprinting.

Animal studies

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

In Dnmt3a-/- mice, many genes associated with HSC self-renewal increase in expression and some fail to be appropriately repressed during differentiation. 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.

Clinical relevance

This gene is frequently mutated in cancer, being one of 127 frequently mutated genes identified in the Cancer Genome Atlas project 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. 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. 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. 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,
• DNMT3B,
• HDAC1,
• Myc,
• PIAS1,
• PIAS2,
• SUV39H1,
• UBE2I and
• ZNF238.

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. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens performed: - In-depth immunological phenotyping

Dnmt3a knockout mouse phenotype

Characteristic	Phenotype
All data available at.
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

Further reading

• "Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence". Nature 377 (6547 Suppl): 3–174. September 1995. PMID 7566098. http://www.columbia.edu/itc/biology/pollack/w4065/client_edit/readings/nature377_3.pdf. 
• "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Research 6 (9): 791–806. September 1996. doi:10.1101/gr.6.9.791. PMID 8889548. 
• "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. June 1999. doi:10.1093/nar/27.11.2291. PMID 10325416. 
• "Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription". The EMBO Journal 20 (10): 2536–44. May 2001. doi:10.1093/emboj/20.10.2536. PMID 11350943. 
• "Functional and physical interaction between the histone methyl transferase Suv39H1 and histone deacetylases". Nucleic Acids Research 30 (2): 475–81. January 2002. doi:10.1093/nar/30.2.475. PMID 11788710. 
• "Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor". Science 295 (5557): 1079–82. February 2002. doi:10.1126/science.1065173. PMID 11834837. Bibcode: 2002Sci...295.1079D. 
• "Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice". Development 129 (8): 1983–93. April 2002. doi:10.1242/dev.129.8.1983. PMID 11934864. 
• "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. October 2002. doi:10.1074/jbc.M205312200. PMID 12138111. 
• "Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases". The EMBO Journal 21 (15): 4183–95. August 2002. doi:10.1093/emboj/cdf401. PMID 12145218. 
• "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. September 2002. doi:10.1016/S0167-4781(02)00482-7. PMID 12359337. 
• "Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA". European Journal of Biochemistry 269 (20): 4981–4. October 2002. doi:10.1046/j.1432-1033.2002.03198.x. PMID 12383256. 
• "Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells". Gene 298 (1): 91–9. September 2002. doi:10.1016/S0378-1119(02)00976-9. PMID 12406579. 
• "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. December 2002. doi:10.1073/pnas.262443999. PMID 12481029. Bibcode: 2002PNAS...9916916C. 
• "DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells". Nature Genetics 33 (1): 61–5. January 2003. doi:10.1038/ng1068. PMID 12496760. 
• "The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase". Nucleic Acids Research 31 (9): 2305–12. May 2003. doi:10.1093/nar/gkg332. PMID 12711675. 
• "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. June 2003. doi:10.3892/ijo.22.6.1201. PMID 12738984. 
• "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. 2004. doi:10.1093/nar/gkh195. PMID 14752048.