The many faces of Polycomb regulation by RNA

Abstract

Many intricate pathways contribute to the timely control of gene expression during development. Polycomb repressive complexes (PRC1 and PRC2) and long non-coding RNAs (lncRNAs) are players associated with gene repression in various developmental processes such as X chromosome inactivation (XCI) and genomic imprinting. Historically, lncRNAs were proposed to directly recruit PRC2. However, recent evidence suggests that promiscuous interactions between PRC2 and RNA fine-tune the function of the complex through a multiplicity of mechanisms. A PRC2-recruitment model was definitively overturned in the paradigm of XCI by Xist RNA, being replaced by a novel mechanism which puts PRC1 in the spotlight. This review focuses on these recent advances in understanding the interplay between RNA and Polycomb complexes for gene expression control.

Figure 1

Polycomb repressive complexes subunits, recruitment mechanisms and catalytic activity in mammals. (a) PRC1 complexes are subdivided into canonical and non-canonical PRC1. Canonical PRC1 is characterised by the presence of one CBX protein (CBX2/4/6/7/8) that recognises H3K27me3 deposited by PRC2 and mediates recruitment of the complex and a PHC protein (PHC1/2/3), which dimerises and promotes chromatin folding. In this subtype of PRC1 complex, PCGF2 and PCGF4 bind in a mutually exclusive way to RING1A/B. Canonical PRC1 has residual catalytic activity (as represented by the dashed arrow). Non-canonical PRC1 complexes are the most catalytic active and deposit H2AK119ub1 at target genes (represented by full arrows). They are characterised by the presence of RYBP/YAF2 which are able to recognise the H2AK119ub1 mark and promote a positive feedback loop for reinforcement of non-canonical PRC1 recruitment. Non-canonical PRC1 complexes contain one of six PCGF proteins (PCGF1-6), some of which determine recruitment to specific targets due to interaction with other components like transcription factors (represented in grey). (b) PRC2 complexes are subdivided into PRC2.1 and PRC2.2 subtypes. Both subtypes share the same core components: EZH1/EZH2, the subunit that catalyses H3K27me3 deposition (as represented by the full arrows), EED which recognises H3K27me3 contributing to the propagation of PRC2 and reinforcement of its own mark (represented on the left), SUZ12, a vital structural component, and the subunit RBBP4/7. PRC2.1 includes the substoichiometric components PCL1/2/3, which are able to bind directly to CG-rich DNA and promote recruitment of this PRC2 subtype to target regions, and the mutually exclusive subunits EPOP and PALI1/2, which modulate its catalytic activity. PRC2.2 includes the substoichiometric components AEBP2 and JARID2, which also impact the catalytic activity of the complex. JARID2 is able to recognise the H2AK119ub1 mark deposited by PRC1 and this serves as a mechanism of recruitment for the PRC2.2 subtype.

Figure 2

PRC2-RNA interaction depends on RNA structure and composition modulating PRC2 function. (a) PRC2 binds to RNA molecules promiscuously but its affinity varies with the sequence and folding of the RNA: G-quadruplex structures have the highest affinity for PRC2 binding, with unstructured G-rich RNA showing an intermediate binding affinity (contrary to A-rich RNA which binds minimally to PRC2) and RNA stem loops low affinity binding. (b) PRC2 binds preferentially to G-quadruplex containing RNAs and these are able to compete with PRC2 binding to chromatin, resulting in its displacement and reduced H3K27me3 deposition. RNA binding to PRC2 can also directly inhibit its catalytic activity. (c) PRC2.1 containing EPOP maintains a low level of gene expression at its target genes. Enrichment of EPOP-PRC2.1 and/or transcription keeps PRC2.2 further away from chromatin at these targets and prevents accumulation of H3K27me3 and complete gene silencing. (d) Accumulation of nuclear pA⁺ RNAs in the absence of efficient RNA degradation by a nuclear RNA exosome-mediated pathway leads to destabilisation of the PRC2 complex.

Figure 3

Model illustrating Polycomb recruitment by Xist lncRNA. Expression of the lncRNA Xist promotes enrichment of all subtypes of Polycomb complexes on the inactive X chromosome. This is mediated by the direct interaction between the B/C-repeat region of the RNA and a nuclear matrix protein, hnRNPK, which specifically engages PCGF3/5-PRC1 complexes. Downstream of initial PCGF3/5-PRC1 catalytic activity, self-reinforcing loops of recruitment acting through the recognition mechanisms represented in Figure 1 involve all non-canonical PRC1 complexes (via RYBP binding H2AK119ub1), PRC2 (via JARID2 binding H2AK119ub1) and canonical PRC1 (via CBX binding H3K27me3 deposited by PRC2).