Dispersal of PRC1 condensates disrupts polycomb chromatin domains and loops

Abstract

Polycomb repressive complex 1 (PRC1) strongly influences 3D genome organization, mediating local chromatin compaction and clustering of target loci. Several PRC1 subunits have the capacity to form biomolecular condensates through liquid–liquid phase separation in vitro and when tagged and over-expressed in cells. Here, we use 1,6-hexanediol, which can disrupt liquid-like condensates, to examine the role of endogenous PRC1 biomolecular condensates on local and chromosome-wide clustering of PRC1-bound loci. Using imaging and chromatin immunoprecipitation, we show that PRC1-mediated chromatin compaction and clustering of targeted genomic loci—at different length scales—can be reversibly disrupted by the addition and subsequent removal of 1,6-hexanediol to mouse embryonic stem cells. Decompaction and dispersal of polycomb domains and clusters cannot be solely attributable to reduced PRC1 occupancy detected by chromatin immunoprecipitation following 1,6-hexanediol treatment as the addition of 2,5-hexanediol has similar effects on binding despite this alcohol not perturbing PRC1-mediated 3D clustering, at least at the sub-megabase and megabase scales. These results suggest that weak hydrophobic interactions between PRC1 molecules may have a role in polycomb-mediated genome organization.

Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes

“…Mechanistically, increasing the concentration of PRC2 through CBX2 phase separation facilitates both nucleation and H3K27me3 spreading since a local high concentration can enhance reaction rates. Consistent with this hypothesis, our earlier studies have shown that LLPS speeds up the on-rate of the binding of CBX2 to chromatin 37 , and a recent study has indicated that phase-separated condensates play a role in the clustering of Polycomb target genes 96 . Taken together, these results suggest that sparse CBX2 nucleates PRC1 and PRC2 to assemble Polycomb condensates to create a high local concentration of PRC2 and to cluster Polycomb target genes, which facilitates H3K27me3 deposition and demarcates the spatial boundaries of H3K27me3 domains.…”

The role of physicochemical processes in the formation of the 3D genome and compartmentalization of the cell nucleus

“…As for facultative heterochromatin, several results indicate that chromatin segments inactivated by Polycomb complexes are phase condensates [33,119]. In agreement with this, treatment of cells with 2,6-hexanediol, an agent that destroys liquid-phase condensates, leads to the disintegration of Polycomb bodies [120].…”