The three-dimensional structure of chromatin condensed by PRC1 is porous and accessible [ChIP-seq]

The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. Unexpectedly, PRC1-condensed chromatin is porous and forms a size-selective diffusion barrier that is stabilised through multivalent dynamic interactions. Accordingly, PRC1 remains dynamic within the condensate while maintaining the chromatin static. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of open and closed chromatin states and instead suggest that PRC1 permits size-selective accessibility of macromolecules into chromatin condensates. Chromatin immunoprecipitation (ChIP) using antibodies for CBX8 and H3K27me3 in J1 mouse embryonic stem cells after 48 hours of retinoic acid treatment