New publication in "J. Biol. Chem."
Specific DNA methylation at CpG and non-CpG sites is essential for chromatin regulation. The DNMT3A DNA methyltransferase interacts with target sites surrounded by variable DNA sequences with its TRD and RD loops. We investigated methylation of CpG and non-CpG sites in randomized sequence context using wildtype DNMT3A and serval DNMT3A variants containing mutations at DNA interacting residues. Our data show that DNMT3A methylates CpG target sites with more than 100-fold different rates depending on the flanking sequence. We identify several residues that are responsible for flanking sequence interaction and mediate a dynamic connection of the CpG readout and flanking sequence contacts. Among them, R836 is responsible for the strong preferences of DNMT3A for methylation of CA sites in a CAC context, while N838 buffers the R836 effect and prevents that the preference for a C at the +1 flank site becomes too strong. L883 is unfavorable for activity but required to bring the RD loop in a conformation needed for DNMT3A-specific flanking sequence interactions. Our data reveal that DNMT3A forms a flexible and interdependent network of interactions with the CpG target site and flanking residues that ensures recognition of the CpG and efficient methylation of the cytosine in contexts of variable flanking sequences.