A Central Role for Canonical PRC1 in Shaping the 3D Nuclear Landscape

Abstract

Polycomb group (PcG) proteins silence gene expression by chemically and physically modifying chromatin. A subset of PcG target loci are compacted and cluster in the nucleus to form observable bodies; a conformation which is thought to contribute to gene silencing. However, how these interactions influence gross nuclear organisation and their relationship with transcription remains poorly understood. Here we examine the role of Polycomb Repressive Complex 1 (PRC1) in shaping 3D genome organization in mouse embryonic stem cells (mESCs). Using a combination of imaging and Hi-C analyses we show that PRC1-mediated long-range interactions are independent of CTCF and can bridge sites at a megabase scale. Impairment of PRC1 enzymatic activity does not directly disrupt these interactions. We demonstrate that PcG targets coalesce in vivo, and that developmentally induced expression of one of the target loci disrupts this spatial arrangement. Finally, we show that transcriptional activation and the loss of PRC1-mediated interactions are seperable events. These findings provide important insights into the function of PRC1, whilst highlighting the complexity of this regulatory system. HighlightsO_LILoss of RING1B substantially disrupts nuclear architecture. C_LIO_LIPRC1 mediated looping can occur at a Mb scale and is independent of CTCF. C_LIO_LIPolycomb mediated looping is driven by canonical PRC1 complexes. C_LIO_LIMultimeric PRC1-mediated interactions occur in vitro and in vivo. C_LIO_LIDisruption of PRC1-mediated looping is independent of gene activation. C_LI