Spatial partitioning of NSD2 defines H3K36me2 as an active mark for repetitive sequence activation

Histone H3 lysine 36 dimethylation (H3K36me2) plays a key role in transcriptional elongation and chromatin organization, yet how its deposition is spatially controlled across the genome remains unclear. Here, we identify TOP1 as a critical recruiter of the H3K36me2 methyltransferase NSD2 to gene bodies. Disruption of the TOP1–NSD2 interaction reduces H3K36me2 at gene bodies, impairs RNA polymerase II release, and represses transcription. Remarkably, loss of this recruitment increases H3K36me2 at repetitive sequences, licensing their aberrant transcriptional activation. We show that NSD2 is primarily responsible for depositing H3K36me2 at these loci. We further identify MTA1 as a recruiter of NSD2 to repetitive elements via recognition of the GATC consensus sequence. Together, TOP1 and MTA1 spatially partition NSD2 across the genome, enabling H3K36me2 to serve dual roles in regulating canonical gene expression and acting as an active mark for the transcriptional activation of repetitive sequences. The authors reveal how TOP1 and MTA1 direct the epigenetic enzyme NSD2 to different genomic regions, placing H3K36me2 on gene bodies to support transcription and on repetitive sequences to activate their expression.