Molecular Characterization of Mammalian De Novo DNA Methyltransferase Chromatin Recruitment

Precise deposition of CpG methylation is critical for mammalian development and tissue homeostasis and is often dysregulated in human diseases. The genomic localization of de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) is facilitated in part by chromatin “reader” domains to establish DNA methylation patterns genome-wide. Recent work has highlighted a role for the PWWP reader domain in directing recruitment of DNMT3B to actively transcribed gene bodies. However, our understanding of de novo DNA methyltransferase chromatin recruitment remains incomplete. Here I demonstrate using a variety of biochemical and cellular techniques that DNMT3A genomic localization is regulated by competing chromatin recruitment pathways. Under steady-state conditions, DNMT3A is targeted to non-coding intergenic regions through PWWP reader domain recognition of H3K36me2, an abundant histone post-translational modification (PTM) in cells. Following depletion of cellular H3K36me2 levels, DNMT3A is re-targeted to actively transcribed gene bodies through PWWP domain interaction with H3K36me3, thereby resembling the genomic localization of DNMT3B. Lastly, loss of PWWP domain reader functionality reveals the presence of a previously uncharacterized chromatin reader domain within DNMT3A that serves as an alternative targeting mechanism to facilitate de novo methylation of Polycomb-regulated regions, including a subset of CpG islands. Perturbations to these recruitment mechanisms may underlie the pathology of developmental overgrowth and undergrowth syndromes associated with distinct germline mutations in DNMT3A and may also contribute to the altered DNA methylation landscapes observed in diverse cancers