PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [RNA-seq]

The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The interrelatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population, and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control. Mouse embryonic stem cells in which PRC1 can be depleted via the auxin-inducible degron (AID) system were profiled for gene expression using spike-in calibrated nuclear RNA-seq. Cells were treated with auxin for 2, 4, 8 or 24 hours in three independent biological replicates, and gene expression changes were analysed relative to the control untreated cells. Another mouse ESC line in which PRC2 can be depleted via the dTAG-inducible degron system was profiled in a similar manner to compare gene expression before and after 2 hours treatment with dTAG-13 compound.