Structural basis for the allosteric regulation and dynamic assembly of DNMT3B

Oligomerization of DNMT3B, a mammalian de novo DNA methyltransferase, critically regulates its chromatin targeting and DNA methylation activities. However, how the N-terminal PWWP and ADD domains interplay with the C-terminal methyltransferase (MTase) domain in regulating the dynamic assembly of DNMT3B remains unclear. Here, we report the cryo-EM structure of DNMT3B under various oligomerization states. The ADD domain of DNMT3B interacts with the MTase domain to form an autoinhibitory conformation, resembling the previously observed DNMT3A autoinhibition. Our combined structural and biochemical study further identifies a role for the PWWP domain and its associated ICF mutation in the allosteric regulation of DNMT3B tetramer, and a differential functional impact on DNMT3B by potential ADD-H3K4me0 and PWWP-H3K36me3 bindings. In addition, our comparative structural analysis reveals a coupling between DNMT3B oligomerization and folding of its substrate-binding sites. Together, this study provides mechanistic insights into the allosteric regulation and dynamic assembly of DNMT3B. Graphical Abstract

Automated summary

This study reveals the mechanism of allosteric regulation and dynamic assembly of DNMT3B by investigating its cryo-EM structure under different oligomerization states. The interaction between the ADD domain and the MTase domain of DNMT3B forms an autoinhibitory conformation, similar to the previously observed DNMT3A autoinhibition. The PWWP domain and its associated ICF mutation are found to play a role in the allosteric regulation of DNMT3B tetramer, and the bindings of ADD-H3K4me0 and PWWP-H3K36me3 have differential functional impacts on DNMT3B.