Capturing the onset of PRC2-mediated repressive domain formation

Oksuz, Ozgur; Narendra, Varun; Lee, Chul-Hwan; Descostes, Nicolas; LeRoy, Gary; Raviram, Ramya; Blumenberg, Lili M.; Karch, Kelly R.; Rocha, Pedro; García, Benjamin A.; Skok, Jane; Reinberg, Danny

doi:10.1101/272989

Cited by 85 publications

(179 citation statements)

References 66 publications

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“…Recent studies reported that PRC2-chromatin interactions are transient, allowing the enzyme to readily translocate on the substrate for efficient spreading of repressive marks (27,34). Our data presented here show that PRC2-nucleosome linkages can also withstand high tensions, exhibiting mechanical stability comparable to the nucleosome itself.…”

Section: Discussionsupporting

confidence: 54%

“…Although direct evidence is still awaited, it can be envisioned that both stable and transient interactions are at work in order to accomplish de novo installation and self-propagation of H3K27me3 modifications ( Figure 6). The strong interactions may be required for PRC2 recruitment to the nucleation sites via either DNA or nucleosome contacts and for the deposition of initial H3K27me3 foci (34,35), presumably with slow kinetics; whereas the weak contacts facilitate efficient spreading by bridging either adjacent or distal nucleosomes. Indeed, we have shown that the mixture of unmodified and modified nucleosomes weakens PRC2 binding to the chromatin, so does the addition of AEBP2.…”

Section: Discussionmentioning

confidence: 99%

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PRC2 bridges non-adjacent nucleosomes to establish heterochromatin

Leicher

et al. 2019

Preprint

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Polycomb repressive complex 2 (PRC2) maintains transcriptionally silent heterochromatin by installing and spreading repressive histone methylation marks along nucleosome arrays. Despite extensive research, the mechanism by which PRC2 engages with chromatin remains incompletely understood. Here we employ single-molecule force spectroscopy and molecular dynamics simulations to dissect the interactions of PRC2 with polynucleosome substrates. Our results reveal an unexpectedly diverse repertoire of PRC2 binding configurations on chromatin. Besides interacting with bare DNA, mononucleosomes, and neighboring nucleosome pairs, PRC2 is also found to bridge non-adjacent nucleosomes, an activity associated with chromatin compaction. Furthermore, the distribution and stability of these PRC2-chromatin interaction modes are differentially modulated by accessory PRC2 cofactors, oncogenic histone mutations, and the methylation state of chromatin. Overall, this work provides a paradigm for understanding the physical basis of epigenetic maintenance mediated by Polycomb group proteins. Eukaryotic chromatin is modified by a plethora of epigenetic machineries that add or erase specific histone posttranslational modifications, thereby exerting transcriptional control (1). Some of these complexes are recruited to and stimulated by their own enzymatic products, which leads to the modification of neighboring nucleosomes and eventually the formation of large-scale chromatin domains. One preeminent example for such a positive feedback mechanism is mediated by the Polycomb repressive complex 2 (PRC2), which catalyzes methylation of the lysine 27 residue on histone H3 (H3K27), resulting in the final enzymatic product, trimethylated H3K27 (H3K27me3), a hallmark of facultative heterochromatin (2). PRC2 maintains transcriptional silencing of a large number of genes involved in development and cancer (3). The PRC2 core complex comprises four subunits: EED, EZH2, RBBP4, and SUZ12. In the proposed "read-and-write" model, EED recognizes an existing H3K27me3 mark and allosterically activates the methyltransferase EZH2, which in turn modifies a neighboring nucleosome (4,5). This model is supported by a recent cryo-electron microscopy (EM) structure of PRC2 engaging a dinucleosome, in which the EED subunit interacts with an H3K27me3-containing nucleosome and the EZH2 subunit of the same PRC2 complex engages an adjacent unmodified nucleosome (6). However, due to the prohibitive conformational heterogeneity of polynucleosome arrays, the binding configuration of PRC2 on its natural chromatin substrate has thus far been refractory to structural interrogation. Moreover, the activity of the PRC2 core complex is influenced by diverse regulatory factors, including accessory subunits, histone modifications, DNA methylation, and RNA [reviewed in (7,8)]. How PRC2 integrates signals from these regulatory factors to achieve chromatin targeting and H3K27me3 spreading remains incompletely understood. To address these knowledge gaps, in this work we developed experi...

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Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 99%

PRC2 bridges non-adjacent nucleosomes to establish heterochromatin

Leicher

et al. 2019

Preprint

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“…This could be an indirect consequence of reduced deposition of H3K27me3 levels together with a reduced affinity of PRC2.1 for target genes. Low H3K27me3 levels could reduce EED affinity for its target sites, compromising spreading and establishment of PcG domains Oksuz et al, 2018) . Reduced H3K27me3 deposition further correlated with specific cPRC1 displacement from all repressed target loci (represented by PCGF2 ChIP-seq), in agreement with cPRC1 being dependent on the deposition of this modification through the specific activity of CBX proteins (Bernstein et al, 2006;Cao et al, 2002).…”

Section: Discussionmentioning

confidence: 99%

Histone H2AK119 Mono-Ubiquitination is Essential for Polycomb-Mediated Transcriptional Repression

Tamburri

Lavarone

Fernández-Pérez

et al. 2019

Preprint

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The major function of Polycomb group proteins (PcG) is to maintain transcriptional repression to preserve cellular identity. This is exerted by two distinct repressive complexes, PRC1 and PRC2, that modify histones by depositing H2AK119ub1 and H3K27me3, respectively. Both complexes are essential for development and are deregulated in several types of human tumors. PRC1 and PRC2 exist in different variants and show a complex regulatory cross-talk. However, the contribution that H2AK119ub1 plays in mediating PcG repressive functions remains largely controversial. Coupling an inducible system with the expression of a fully catalytic inactive RING1B mutant, we demonstrated that H2AK119ub1 deposition is essential to maintain PcG-target genes repressed in ESC. Loss of H2AK119ub1 induced a rapid displacement of PRC2 activity and a loss of H3K27me3 deposition. This affected both PRC2.1 and PRC2.2 variants and further correlated with a strong displacement and destabilization of canonical PRC1. Finally, we find that variant PRC1 forms can sense H2AK119ub1 deposition, which contributes to their stabilization specifically at sites where this modification is highly enriched. Overall our data place H2AK119ub1 deposition as central hub that mount PcG repressive machineries to preserve cell transcriptional identity.

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“…While we now have a good picture of the accessory subunits interacting with PRC2, their precise roles are only partially understood. This might be due to compensatory mechanisms, such that interfering both with PRC2.1 and PRC2.2 is required to inhibit PRC2 recruitment 19 as observed upon loss of SUZ12 20 .…”

Section: Theirmentioning

confidence: 99%

EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells

Ragazzini

Pérez-Palacios

Baymaz

et al. 2019

Preprint

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The Polycomb machinery is required for the proper orchestration of gene expression by virtue of its critical role in maintaining transcriptional silencing. It is composed of several chromatin modifying complexes, including Polycomb Repressive Complex 2 (PRC2), which deposits H3K27me2/3. Here, we report the identification of a new cofactor of PRC2, EZHIP (EZH1/2 Inhibitory Protein), expressed predominantly in the gonads. EZHIP limits the enzymatic activity of PRC2 and lessens the interaction between the core complex and its accessory subunits, but does not interfere with PRC2 recruitment to chromatin. Deletion of Ezhip leads to a global increase in H3K27me2/3 deposition both during spermatogenesis and at late stages of oocyte maturation. This alteration of the epigenetic content of mature oocytes does not affect the initial number of follicles but is associated with a reduction of follicles in aging mice. We provide evidences that mature oocytes Ezhip -/-are not fully functional and that fertility is strongly impaired in Ezhip -/-females. Altogether, our study uncovers EZHIP as a novel functional player in the comprehensive chromatin remodeling that occurs in the gonads.

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Capturing the onset of PRC2-mediated repressive domain formation

Cited by 85 publications

References 66 publications

PRC2 bridges non-adjacent nucleosomes to establish heterochromatin

PRC2 bridges non-adjacent nucleosomes to establish heterochromatin

Histone H2AK119 Mono-Ubiquitination is Essential for Polycomb-Mediated Transcriptional Repression

EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells

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