Structure of DNA methyltransferases DNMT3A/DNMT3B bound to a nucleosome [seq]

CpG methylation by the de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes yet cannot methylate the DNA wrapped around the nucleosome core2, and favor the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-EM structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3, and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur. We verified the catalytic activity of wildtype and mutant DNMT3A2/3B3 complex using bisulfite sequencing. We also used limited micrococcal nuclease (MNase) digestion followed by sequencing to map the binding of DNMT3A2/3B3 complex to in vitro assembled nucleosome.