Live-cell DNMT3A "catalysome" mapping using engineered methyl-transfer pathways

Catalytic interplay among three major DNA methyltransferases (DNMTs) establishes and maintains genomic modification patterns that define mammalian cell identity and transitions during development. Despite extensive molecular characterization, mechanisms and precise contributions of DNMT-specific methylation in native cellular contexts remain elusive. To address this, we employed structure-guided engineering of DNMT3A to enable catalytic transfer of extended azide tags from a synthetic cofactor analog, Ado-6-azide, onto DNA. By coupling orthogonal biocatalysis with pulse-internalization of Ado-6-azide or with metabolic conversion of the cofactor precursor, azido-methionine, we established two strategies for DNMT3A catalysis-dependent genome tagging in live mESCs under near-physiological conditions. Genome-wide mapping of DNMT3A catalysis (catalysome) in primed mouse embryonic stem cells facilitated discovery of opposing DNMT3A and TET dioxygenase activities at boundaries of CpG islands, promoter-proximal regions, and enhancers. DNMT3A also exhibited a strong enrichment at pericentric major satellites, reinforcing its key role in shaping the epigenetic centromere identity. Collectively with a complementary DNMT1-engineered cell line, we present a versatile platform for direct, selective, and time-resolved interrogation of individual DNA methylation writers in live cells under physiological conditions.