NSD1 deposits Histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons [ChIP-seq vitro]

During postnatal development the DNA methyltransferase DNMT3A deposits high levels of nonCG cytosine methylation in neurons. This unique methylation is critical for transcriptional regulation in the mature mammalian brain, and loss of this mark is implicated in DNMT3Aassociated neurodevelopmental disorders (NDDs). The mechanisms determining genomic nonCG methylation profiles are not well defined however, and it is unknown if this pathway is disrupted in additional NDDs. Here we show that genome topology and gene-expression converge to shape Histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. Brain-specific deletion of NSD1, the H3K36 methyltransferase mutated in the NDD Sotos syndrome, disrupts megabase-scale H3K36me2 patterns, causing alterations in non-CG methylation and transcription that overlap models of DNMT3A disorders. Our findings indicate that H3K36me2 deposited by NSD1 is an important determinant of neuronal non-CG DNA methylation and implicates disruption of this methylation in Sotos syndrome. Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for histone histone modifications H3K36me2 and DNA methyltransferase DNMT3A in DIV12 primary cultured neurons