Context-specific Polycomb mechanisms in development

Abstract

Polycomb group (PcG) proteins are crucial chromatin regulators that maintain repression of lineage-inappropriate genes and are therefore required for stable cell fate. Recent advances show that PcG proteins form distinct multi-protein complexes in various cellular environments, such as in early development, adult tissue maintenance and cancer. This surprising compositional diversity provides the basis for mechanistic diversity. Understanding this complexity deepens and refines the principles of PcG complex recruitment, target-gene repression and inheritance of memory. We review how the core molecular mechanism of Polycomb complexes operates in diverse developmental settings and propose that context-dependent changes in composition and mechanism are essential for proper epigenetic regulation in development.

Figure 1 |. Composition and molecular functions of Polycomb complexes.

PRC2, ncPRC1 and cPRC1 have core components that form stable complexes with little variation between cell types (upper boxes) except when one paralog is switched with the other or accessory components are included (lower boxes). a | The core PRC2 complex can catalyze H3K27 methylation through the SET domain in EZH proteins. Sub-stoichiometric accessory proteins bind the N-terminal region of SUZ12. They can help PRC2 targeting. For example, PRC2.1 has PCL proteins that bind unmethylated CpG-rich DNA, and PRC2.2 has JARID2 that can bind H2AK119Ub1. Other accessory proteins such as PALI, EPOP and EZHIP modulate PRC2 catalytic activity. b, c | Both cPRC1 and ncPRC1 have RING and PCGF proteins that dimerize through their respective RING domains^,. RING1A/B has a RAWUL domain that binds either CBX proteins (for cPRC1), or RYBP/YAF2 (for ncPRC1). b | ncPRC1 can be defined by its specific PCGF paralog (for example, ncPRC1.1 contains PCGF1). In addition, each ncPRC1 has diverse accessory components that confer unique functions to the complexes. c | Cell type-specific cPRC1 complexes can be formed by combinatorial assembly of CBX, PHC and PCGF paralogs as shown in two examples of mESC and NPC-specific cPRC1s. In addition, SCM proteins can be incorporated in cPRC1 in a cell type-specific manner.

Figure 2 |. Formation of repressed domains by positive feedback of Polycomb complexes.

The process of Polycomb repressed domain formation by hierarchical recruitment of PcG complexes is represented. a | ncPRC1.1 can be targeted to hypomethylated CpG-rich promoters through its KDM2B subunit. KDM2B can be targeted to promoters regardless of its transcription status. Note that PRC2.1 can also be targeted to CpG-rich promoters through its PCL subunit, but that is not depicted here for simplicity and to emphasize the interplay between Polycomb complexes. b | PRC2.2 can be recruited to promoters by recognition of H2AK119Ub1 with its JARID2 subunit. Lack of transcription also contributes to PRC2 recruitment. c | H2AK119Ub1 and H3K27me3 modifications can spread beyond the initial recruitment site by 1) RYBP (ncPRC1) interaction with H2AK119Ub1, and 2) EED (PRC2) interaction with H3K27me3. d | The chromodomain in CBX proteins binds H3K27me3 and targets cPRC1 to the H3K27me3 enriched regions. CBX and PH subunits of cPRC1 compact nucleosome targets, bridge distant Polycomb bound regions, and phase separate to form Polycomb bodies. Modification of chromatin structure by cPRC1 can further help maintain high levels of H2AK119Ub1 and H3K27me3 as compacted and dense nucleosomes are better substrates for ncPRC1 and PRC2 enzymatic activities.

Figure 3 |. Examples of cell type-specific Polycomb complexes.

a | A cartoon describing mammalian development shows specific expression or phenotypes of PcG complex components in distinct cell types in embryogenesis or adult tissues. Inset shows paralog switching and accessory component incorporation in the transition from mESCs to differentiated cell types. b | Heat map showing mRNA expression of different PcG genes in the mouse embryo and adult tissues, as well as in cultured cell types, such as MEFs and mESCs. Note that core components of the complexes, such as Ring1b, Eed, show relatively uniform expression, while accessory components or components with many paralogs exhibit more variable or tissue-specific expression. Proliferation index represents how proliferative the cells are in the tissues and is derived from median FPKM of 16 cell cycle genes, including Mcms, Cyclins, Cdks. Data are from Gene Expression Omnibus GSE29278. XCI, X-chromosome inactivation; HSC, hematopoietic stem cell; ErP, erythroid progenitor; E, embryonic day; MEF, mouse embryonic fibroblast; FPKM, fragments per kilobase million.

Figure 4 |. Redistribution of Polycomb complexes.

Schematic representation of PcG complexes and related DNA and histone modifications in a genome browser format to show the level and breadth of enrichment. a | Loss of DNA methylation: while one class of promoters (PcG-low, DNA-methyl high) gain H3K27me3 as they lose DNA methylation, another class of promoters (PcG-high, DNA-methyl low) show decrease in H3K27me3, suggesting potential redistribution of PRC2 from PcG-high to PcG-low promoters by global loss of DNA methylation. In oocytes and preimplantation embryos with developmentally regulated genome-wide DNA hypomethylation, H3K27me3 undergoes global remodelling to localize at intergenic regions. b | Loss of H2AK119Ub1 deubiquitylase BAP1: Global increase in H2AK119Ub1 level results in redistribution and decrease of PRC1(RING1B) and PRC2(SUZ12) from promoters normally have high levels of PcG complexes, accompanied by gene derepression. c | Loss of activity of the opposing chromatin modifying complex, mSWI/SNF: degradation of BRG1, the catalytic component of mSWI/SNF results in the increase of PRC1(RING1B) and PRC2(SUZ12) occupancy at usually PcG-low promoters, accompanied by the decrease of PRC1 and PRC2 from normally PcG-high promoters and gene derepression. TSS, transcription start site; DNAme, DNA methylation; Dnmt, DNA methyltransferase.

Figure 5 |. Hypothetical models on different roles of Polycomb complexes in the maintenance of gene repression.

a | A schematic of a repressed Polycomb domain with H2AK119Ub1 and H3K27me3 modifications. b | Chromatin response (upper): When ncPRC1 activity is disrupted, initially H2AK119Ub1 is lost. Because H2AK119Ub1 recruits PRC2.2, over time H3K27me3 deposition and in turn cPRC1 recruitment is decreased. Cellular response (lower): It is possible that ubiquitylation is involved in direct gene repression. Therefore, loss of H2AK119Ub1 may result in fast and uniform derepression of PcG target genes. c | Chromatin response: When cPRC1 activity is lost, chromatin compaction and long-range interactions between PcG bound regions are disrupted. Because compacted and dense nucleosomes are better substrates for ncPRC1 and PRC2, loss of cPRC1 may eventually lead to decrease in H2AK119Ub1 and H3K27me3 levels over long term. Cellular response: Unlike ncPRC1, existing data are consistent with cPRC1 being involved in the memory of repression, resulting in slower and stochastic conversion to the “on” state of PcG target genes by loss of cPRC1 function. d | Chromatin response: When PRC2 activity is disrupted, H3K27me3 level is decreased at first, followed by the decrease in the cPRC1. Resulting disruption of Polycomb domain structure will negatively impact in reaching full H2AK119Ub1 level. Cellular response: Similar to cPRC1, PRC2 and H3K27me3 may also be involved in the memory of repression, resulting in slower and stochastic conversion of PcG targets to the “on” state by loss of PRC2 function.