H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [RNA-seq]

Polycomb Repressive Complex 2 (PRC2) deposits H3K27me3 to recruit canonical PRC1 (cPRC1) that establishes repressive heterochromatin. Higher order cPRC1-mediated chromatin interactions characterize early development and resolve during cell differentiation. Here, we use two opposing models of H3K27me3 dysregulation to elucidate how these long-range loops affect gene expression and cellular phenotypes. Aggressive gliomas driven by histone H3 Lys-27-Met (H3K27M) mutations or EZH-Interacting Protein (EZHIP) expression confine H3K27me3 deposition to PRC2 nucleation sites, while loss of the H3K36 methyltransferase NSD1 in pluripotent stem cells leads to its unrestrained spread from these sites. In H3K27M mutant tumours, focal H3K27me3 deposition concentrates chromatin occupancy of cPRC1 complexes, which results in long-range chromatin interactions anchored in polycomb bodies, mirroring patterns found in stem cells. Conversely, spread of H3K27me3 due to NSD1 loss dilutes cPRC1 deposition and disrupts polycomb body architecture. In H3K27M cells, H3K27me3 confinement sustains repression of genes tethered to the polycomb bodies, promoting self-renewing progenitor states required for tumour development. Maintenance of progenitor states depends on cPRC1 interaction with H3K27me3, as chemical allosteric modulation of chromodomains alleviates repression of transcription and promotes differentiation. These results suggest that H3K27me3 spread from CGIs modulates cPRC1 gene expression programs to orchestrate developmental transitions through the maintenance or dissolution of repressive 3D loop architecture at polycomb bodies. Imbalances in the spread of H3K27me3 altering chromatin architecture in disease including H3K27M-expressing neoplasms or following NSD1 loss contribute to explain pathogenic states.