Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

Nat Commun. 2020 Jul 3;11(1):3355. doi: 10.1038/s41467-020-17109-4.


Mammalian DNA methylation patterns are established by two de novo DNA methyltransferases, DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Catalytic Domain
  • Cell Line
  • CpG Islands / genetics*
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism*
  • DNA (Cytosine-5-)-Methyltransferases / ultrastructure
  • DNA Methylation*
  • DNA Methyltransferase 3A
  • Embryonic Stem Cells
  • Enzyme Assays
  • Epigenesis, Genetic
  • Face / abnormalities
  • Humans
  • Mice
  • Mutation
  • Primary Immunodeficiency Diseases / genetics
  • Structure-Activity Relationship
  • Substrate Specificity / genetics
  • X-Ray Diffraction


  • DNMT3A protein, human
  • Dnmt3a protein, mouse
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA Methyltransferase 3A
  • DNA methyltransferase 3B

Supplementary concepts

  • Immunodeficiency syndrome, variable