DNMT3A DNA-Binding Residues Provide Specificity for CpG DNA Methylation

The de novo DNA methyltransferases DNMT3A and DNMT3B establish DNA methylation primarily at CpG dinucleotides, and their enzymatic activity is regulated by the DNMT3-like protein DNMT3L. DNA methylation is often dysregulated in cancer, with DNMT3A mutations occurring frequently in patients with hematologic malignancies. However, the molecular mechanism by which DNMT3A promotes methylation and the basis for the preference toward CpGs remain poorly understood. To better understand the enzymatic function of DNMT3A, Zhang, Lu, and colleagues determined the crystal structure of DNMT3A in complex with DNMT3L and a CpG-containing DNA molecule to 2.65 Å. This structure revealed that two DNMT3A monomers simultaneously bind to the same DNA duplex containing two CpG dinucleotides 14 base pairs apart, each of which is targeted by one DNMT3A monomer. The DNA-binding surface is created by three DNMT3A domains: a loop from the target recognition domain (TRD; residues R831–F848), the catalytic loop (residues G707–K721), and the DNMT3A–DNMT3A homodimeric interface. Arg836 of the DNMT3 TRD interacted with CpGs, conferring a specificity for CpG DNA that was lost when the arginine was mutated to an alanine. DNMT3L did not directly contact the DNA, but stabilized DNMT3A DNA-binding sites to promote enzymatic activity. DNA binding to DNMT3A stabilized the TRD loop via hydrogen bonding affecting Q886 and R882, which is commonly mutated in leukemia. A number of other mutations associated with hematologic cancer also occurred in the DNA binding residues of DNMT3A including S714, V716, P718, R792, T835, R836, N838, and K841, and these mutations resulted in reduced CpG methylation in vitro. Further evaluation of three of the mutants, V716D, R792H, and K841E, showed that the DNMT3A mutants also acted as dominant negatives, suppressing the activity of wild-type DNMT3A, and promoted cellular transformation. Collectively, these findings elucidate the structural mechanisms by which DNMT3A promotes CpG methylation and by which cancer-associated DNMT3A mutations promote transformation.

Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, et al. Structural basis for DNMT3A-mediated de novo DNA methylation. Nature 2018;554:387–91.

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