The three-dimensional structure of chromatin condensed by PRC1 is porous and accessible [ATAC_CP15]
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. Overall design: ATAC-seq for mouse embryonic stem cells that have a TetO-GFP reporter gene cassette integrated into chromosome 15 and a TetR-CBX8 construct constitutively expressed. Cells were treated with dox to induce eviction of TetR-CBX8 from the TetO array