Unpuzzling DNMT3A as a Key Epigenetic Player

DNA methyltransferase 3-alpha (DNMT3A) effects de novo cytosine methylation in embryonic and somatic cells through the transfer of a methyl group from S-Adenosyl-L-methionine (SAM) to the cytosine-C5 position of newly created CpG DNA residues. In somatic cells, 60 to 80% of these structures are methylated at any given time. Nonetheless, clusters of CpG residues (islands) are principally found in promoter regions and tend to be unmethylated. This pattern of cytosine residue methylation in promoters and gene bodies plays a crucial role in regulating gene expression, gene silencing, X-chromosome inactivation, genomic imprinting, cellular differentiation, and mammalian development. Dysmethylation of CpG islands and at locations increasingly distant from CpG islands (“shores,” “shelves,” and “open sea,” respectively) influences several disease states and genomic stability. Temporally, DNMT3A primarily methylates a set of genes and sequences at early embryonic, primordial germ cell, and late stage of embryonic development. After birth it expresses ubiquitously at low levels and figures prominently in hematopoiesis.¹

The Long and Short DNMT3A Isoforms

Full-length DNMT3A is 912 amino acids in length. Its predicted mass of 102 kDa is at odds with an electrophoretic mobility that seems to put it at 120 to 130 kDa. A shortened, 723 amino acid isoform (DNMT3A2) is also produced and spatially restricted to the testis/ovary, spleen, and thymus. DNMT3A stably associates with chromatin that features CpG islands and repetitive DNA elements. It is also present in transcriptionally silent pericentromeric heterochromatin. These associations imply that DNMT3A may function primarily as a transcriptional repressor. On the other hand, DNMT3A2 is found at transcriptionally active euchromatin and may act to modulate active gene expression.²

Structurally, DNMT3A2 lacks the N-terminal most 223 amino acid sequence have, which allows DNMT3A to bind DNA. Otherwise, the two isoforms are identical. Further, both isoforms contain a Pro-Trp-Trp-Pro (PWWP) domain, an ATRX-DNMT3-DNMT3L (ADD) domain, and the signature methyltransferase (MTase) domain. The PWWP domain interacts with histone H3K36m3 marks in heterochromatin and metaphase chromosomes. The ADD domain interfaces with transcription factors and epigenetic regulators, such as Myc, p53, HDAC1, and EZH2. It also interacts with unmethylated histone H3K4 marks. The MTase domain not only catalyzes methylation, but also coordinates the dimerization of DNMT3A and the assembly of this dimer with the regulatory protein, DNMT3L, to form the fully functional heterotetramer (DNMT3L-DNMT3A-DNMT3A-DNMT3L).²

Understanding DNMT3A in Cancers & Genetic Conditions

In some cancers, such as hepatocellular cancer and melanoma, upregulated expression of intact DNMT3A precipitates oncogenic and immunosuppressive dysmethylation patterns.²

The prevalence of loss of function (LOF) DNMT3A mutations was first noted in acute myeloid leukemia (AML). Since then, such mutations are known to influence other hematological cancers. The latest work seems to show that the hypomethylation caused by such damage acts globally to upregulate genes for hematopoietic cell expansion, while simultaneously downregulating genes that promote hematopoietic cell differentiation. This is a tempting explanation for the prevalence of DNMT3A LOF mutations in pre-leukemic conditions, like myelodyplastic syndrome.³

In Tatton-Brown-Rahman syndrome (TBRS), heterozygous DNMT3A LOF mutations are sufficient to cause significant hypomethylation near genes involved in morphogenesis, development, and differentiation, causing the disorder’s distinctive overgrowth and intellectual disability.⁴

Conversely, in Pheochromocytoma/Paraganglioma (PCC/PGL), a rare and deadly heritable condition, heterozygous DNMT3A alterations result in gain-of-function (GOF), producing site-specific hypermethylation at genes involved in dopaminergic neurogenesis, neural crest differentiation, and embryonic morphogenesis. Likewise, other specific DNMT3A heterozygous GOF mutations cause the hypermethylation of developmental and morphogenic genes, producing Heyn-Sproul-Jackson syndrome (microcephalic dwarfism), a disorder characterized by extreme global growth failure, reduced head size, and decreased height.⁴

DNMT3A and its partners establish a delicate epigenetic balance that we are only beginning to understand.

References

1. Chaudry, S.F. and Chevassut, T.J.T. (2017) Epigenetic Guardian: A Review of the DNA Methyltransferase DNMT3A in Acute Myeloid Leukaemia and Clonal Haematopoiesis. BioMed Research International, vol. 2017, Article ID 5473197. https://doi.org/10.1155/2017/5473197
2. Chen, B-F. and Chan, W-Y. (2014) The de novo DNA methyltransferase DNMT3A in development and cancer. Epigenetics, 9:5, 669-677. https://doi.org/10.4161/epi.28324
3. Venugopal, K. et al. (2021) Alterations to DNMT3A in Hematologic Malignancies. Cancer Res. 81 (2): 254–263. https://doi.org/10.1158/0008-5472.CAN-20-3033
4. Norvil, A.B., et al. (2019) Effect of Disease-Associated Germline Mutations on Structure Function Relationship of DNA Methyltransferases. Genes 10(5): 369. https://doi.org/10.3390/genes10050369