Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2

Plys, Aaron J.; Davis, Connor; Kim, Jongmin; Rizki, Gizem; Keenen, Madeline M.; Marr, Sharon K.; Kingston, Robert E.

doi:10.1101/gad.326488.119

Cited by 275 publications

(323 citation statements)

References 50 publications

(91 reference statements)

Supporting

Mentioning

299

Contrasting

Order By: Relevance

“…Disruption of the SAM domain ablates these interactions leading to the loss of both local interaction domains and PRC1 mediated looping ) and resulting in gene de-repression and skeletal abnormalities in mice (Isono et al 2013). Furthermore, loss of these architectural PRC1 subunits leads to the dissolution of nanometre scale 'polycomb bodies' containing high local concentrations of polycomb proteins (Isono et al 2013;Wani et al 2016;Plys et al 2019;Tatavosian et al 2019). These data support the idea that CBX and PHC proteins bestow cPRC1 with the capacity to fold chromatin into discrete nuclear domains and suggest a mechanistic role for chromatin interactions and nuclear clustering in PRC1-mediated transcriptional repression.…”

Section: Introductionsupporting

confidence: 63%

“…Published observations have suggested that cPRC1 complexes control polycomb-dependent 3D genome architecture, while ncPRC1s do not play a major role (Francis et al 2004;Grau et al 2011;Isono et al 2013;Wani et al 2016;Kundu et al 2017;Plys et al 2019;Tatavosian et al 2019). To tested this hypothesis genome-wide, we repeated our previous analysis, this time subdividing RING1B peaks based on the ratio of ChIP-seq signal between canonical and non-canonical PRC1 subunits (CBX2 vs. RYBP respectively (Deaton et al 2016;Rose et al 2016)).…”

Section: High Levels Of Canonical Prc1 Drive Distal Interactions Indementioning

confidence: 99%

“…Combinatorial deletion of PCGF1, 3, 5 and 6 in mouse embryonic stem cells (mESCs) leads to substantial gene misregulation and highlights the importance of vPRC1s in transcriptional control . In contrast, canonical PRC1 (cPRC1; core heterodimer of RING1A or B with PCGF2 or 4) has lower catalytic activity and is instead associated with subunits that alter chromatin structure and topology (Francis et al 2004;Grau et al 2011;Isono et al 2013;Blackledge et al 2014;Taherbhoy et al 2015;Wani et al 2016;Kundu et al 2017;Lau et al 2017;Plys et al 2019;Tatavosian et al 2019). In line with this function, a subset of PRC1 targets fold into short discrete self-interacting domains (20-140 kb), exemplified by the conformation of the transcriptionally-silent Hox clusters in mESCs (Eskeland et al 2010;Williamson et al 2014;Vieux-Rochas et al 2015;Kundu et al 2017).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Boyle

Flyamer

Williamson

et al. 2019

Preprint

View full text Add to dashboard Cite

Highlights:1. Loss of RING1B substantially disrupts nuclear architecture.2. PRC1 mediated looping can occur at a Mb scale and is independent of CTCF.3. Polycomb mediated looping is driven by canonical PRC1 complexes.4. Multimeric PRC1-mediated interactions occur in vitro and in vivo. Disruption of PRC1-mediated looping is independent of gene activation. AbstractPolycomb 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.

show abstract

Section: Introductionsupporting

confidence: 63%

Section: High Levels Of Canonical Prc1 Drive Distal Interactions Indementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Boyle

Flyamer

Williamson

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…The compacted states of polycomb and HP1α bound chromatin appear to form via a similar phase-separation mechanism mediated by multivalent interactions between specific CBX homologs. In vitro and in vivo, both CBX2 (polycomb subunit) and CBX5 (HP1α) are capable of forming condensates of polycomb bodies and constitutive heterochromatin, respectively (Larson et al, 2017;Plys et al, 2019;Tatavosian et al, 2019). Our data indicate that these different structures or condensates and associated chromatin have very different properties.…”

Section: Discussionmentioning

confidence: 82%

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

Belaghzal

Borrman

Stephens³

et al. 2019

Preprint

View full text Add to dashboard Cite

Highlights• Liquid chromatin Hi-C detects chromatin interaction dissociation rates genome-wide • Chromatin conformations in distinct nuclear compartments differ in stability • Stable heterochromatic associations are major drivers of chromatin phase separation • CTCF-CTCF loops are stabilized by encirclement of loop bases by cohesin ringsFigures 1-7 Methods Supplemental Figures S1-S6 Supplemental Tables S1-S3 Supplemental Movies S1-S2. 2 SUMMARYChromosomes are folded so that active and inactive chromatin domains are spatially segregated. Compartmentalization is thought to occur through polymer phase/microphase separation mediated by interactions between loci of similar type. The nature and dynamics of these interactions are not known. We developed liquid chromatin Hi-C to map the stability of associations between loci. Before fixation and Hi-C, chromosomes are fragmented removing the strong polymeric constraint to enable detection of intrinsic locus-locus interaction stabilities.Compartmentalization is stable when fragments are over 10-25 kb. Fragmenting chromatin into pieces smaller than 6 kb leads to gradual loss of genome organization. Dissolution kinetics of chromatin interactions vary for different chromatin domains. Lamin-associated domains are most stable, while interactions among speckle and polycomb-associated loci are more dynamic.Cohesin-mediated loops dissolve after fragmentation, possibly because cohesin rings slide off nearby DNA ends. Liquid chromatin Hi-C provides a genome-wide view of chromosome interaction dynamics.3

show abstract

“…The similarity between HP1-and Pc-domains/complexes extends to their ability to phase separate and to generate B-type heterochromatic compartmental domains in Hi-C maps. For one, the mammalian Pc homologue CBX2, like HP1 proteins, can promote phase separation that is dependent upon amino-acids in CBX2 necessary for nucleosome fibre compaction (197,198). Second, the histone modifications H3K9me2/3 and H3K27me3 are diagnostic for HP1-and Pc-dependent domains/complexes respectively (Table 1) (199) and are used, inter alia, to define B-type compartmental domains (170).…”

Section: "Epigenetic Compartmental Domains" (Ecds) and The Regulationmentioning

confidence: 99%

On the relation of phase separation and Hi-C maps to epigenetics

Singh

Newman²

2019

Preprint

View full text Add to dashboard Cite

The relationship between compartmentalisation of the genome and epigenetics is long and hoary. In 1928 Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller's (1930) discovery of position-effect variegation (PEV) went on to show that heterochromatin is a cytologically-visible state of heritable (epigenetic) gene repression. Current insights into compartmentalisation have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalisation seen in Hi-C maps is due to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5Mb) heterochromatin-like domains and smaller (less than 100Kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes enables cross-linking within and between chromatin fibres that contributes to polymer-polymer phase separation (PPPS) that packages epigenetically-heritable chromatin states during interphase. Contacts mediated by HP1 "bridging" are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic sub-compartment that emerges from contacts between large KRAB-ZNF heterochromatin-like domains. Further, mutational analyses have revealed a finer, innate, compartmentalisation in Hi-C experiments that likely reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres -where the HP1-H3K9me2/3 interaction represents the most evolutionarilyconserved paradigm -could drive and generate the fundamental compartmentalisation of the interphase nucleus.This has implications for the mechanism(s) that maintains cellular identity, be it a terminally-differentiated fibroblast or a pluripotent embryonic stem cell.

show abstract

Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2

Cited by 275 publications

References 50 publications

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

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

Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

On the relation of phase separation and Hi-C maps to epigenetics

Contact Info

Product

Resources

About