PRC1 catalytic activity is central to Polycomb system function. [RNA]

The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how it selects its target genes is poorly understood and whether its histone modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. To achieve this, we develop a new inducible mutation system in embryonic stem cells that completely removes PRC1 catalytic activity. Using this system, we demonstrate that catalysis by PRC1 is important for Polycomb chromatin domain formation and long-range chromatin interactions. Furthermore, we show that variant PRC1 complexes with DNA-binding activities occupy target sites independently of Polycomb chromatin domain formation, providing a putative mechanism for Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling new evidence that PRC1 catalysis is central to Polycomb system function and gene regulation. Overall design: Mouse embryonic stem cells in which all PRC1 complexes (PRC1CKO) or specifically PRC1 catalytic activity (PRC1CPM) can be conditionally removed, were profiled for gene expression using spike-in calibrated RNA-seq.