Molecular Logic of DNMT3A1 Recruitment: Resolving Multivalency at the Chromatin Interface

Abstract

Histone modifications correlate with DNA methylation, but the underlying mechanisms remain unclear. The DNA methyltransferase DNMT3A1 engages nucleosomes through multivalent interactions with linker DNA, histone H3 tails, the acidic patch, and ubiquitinated H2A. Using binding assays, kinetic analyses, and nanopore sequencing of engineered nucleosomes, we show that DNMT3A1 binding reflects avidity, limiting the impact of individual contacts. Accordingly, disrupting single interactions minimally affects overall affinity, whereas isolated domains and truncations remain modification-sensitive. Although histone modifications have little effect on kcat/Km for linker methylation, disrupting ADD-H3K4me0 interactions redistributes methylation away from the nucleosome core particle. Nucleosome competition assays reveal that H3K4me0 and H3K36me2 promote selective linker methylation, whereas H3K27me3 and PRC2/EZH2 have no effect. Notably, despite strong UDR-dependent binding to H2AK119ub1-modified nucleosomes, this mark fails to enhance methylation over an unmodified competitor. We propose a model of commitment to catalysis to reconcile weak kinetic differences with strong substrate selectivity. These findings highlight avidity and commitment in governing DNMT3A1 nucleosome recognition and DNA methylation specificity.