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; a conformation that is thought to contribute to gene silencing. However, how these interactions influence gross nuclear organization 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 separable events. These findings provide important insights into the function of PRC1, while highlighting the complexity of this regulatory system.

Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy

“…To investigate whether the stable binding events we observe in SPT are representative of PRC1 behaviour at known sites of chromatin interaction, we focussed on Polycomb bodies. Polycomb bodies are cytologically distinct foci that correspond to a subset of PRC1-bound regions of the genome, including the Hox gene clusters, that have very large Polycomb chromatin domains 24 , 56 , 76 – 78 . Live-cell imaging of RING1B revealed approximately one hundred Polycomb bodies per nucleus (Fig.…”

Epigenetic memory as a time integral over prior history of Polycomb phase separation

“…Moreover, as with Cbx2 condensates, over time H2AK119Ub marks appear where RNF2-condensates formed(Figure 4E). Consistent with RNF2 directly writing this ubiquitin mark, Corelets formed with an enzymatically dead mutant, RNF2_D56K, showed a slightly reduced colocalisation with the H2AK119Ub mark, although the effect was small, likely due to RNF2_D56K retaining an ability to recruit endogenous WT RNF2, and other PRC RING components (Figure 4E, Figure S3C,D)(37,38). Thus, Cbx2 and RNF2 collaborate to read and write the histone code.…”

“…Polycomb condensates have previously been proposed to function by bringing distant chromatin loci together (38,(51)(52)(53)(54). This picture distinguishes the catalytic activity (Cbx2, RNF2) of PRC1 from its potential role in chromatin remodelling, which could rely on strong oligomerizing of Bmi1 and PHC1 (35,51,53).…”

Heterochromatin and Polycomb as regulators of haematopoiesis

“…All forms of PRC1 are comprised of a catalytic core formed by a really interesting new gene (RING) E3 ubiquitin ligase RING1A or RING1B and one of six Polycomb group ring finger (PCGF) proteins, with canonical PRC1 containing PCGF2/4 and CBX subunits, and variant forms containing any of the six PCGF proteins and RYBP or YAF2 in place of CBX [ 39 ] ( Figure 2B ). Interestingly, canonical PRC1 has lower catalytic activity than variant PRC1 but has important roles in shaping three-dimensional genome organisation and chromosomal architecture [ 40 ]. There is also a complex reciprocal relationship between PRC1 and PRC2 complexes, with each deposited histone mark facilitating binding of the other complex, and they often unsurprisingly co-occupy genomic loci [ 41 ].…”