Long non-coding RNA-polycomb intimate rendezvous

Abstract

The interaction between polycomb-repressive complexes 1/2 (PRC1/2) and long non-coding RNA (lncRNA), such as the X inactive specific transcript Xist and the HOX transcript antisense RNA (HOTAIR), has been the subject of intense debate. While cross-linking, immuno-precipitation and super-resolution microscopy argue against direct interaction of Polycomb with some lncRNAs, there is increasing evidence supporting the ability of both PRC1 and PRC2 to functionally associate with RNA. Recent data indicate that these interactions are in most cases spurious, but nonetheless crucial for a number of cellular activities. In this review, we suggest that while PRC1/2 recruitment by HOTAIR might be direct, in the case of Xist, it might occur indirectly and, at least in part, through the process of liquid-liquid phase separation. We present recent models of lncRNA-mediated PRC1/2 recruitment to their targets and describe potential RNA-mediated roles in the three-dimensional organization of the nucleus.

Keywords: HOTAIR RNA; RNA secondary structure; RNA–protein interaction; Xist RNA; long non-coding RNAs (lncRNA); phase separation; polycomb-repressive complexes 1/2 (PRC1/2).

Figure 1.

Xist and HOTAIR interactions with Polycomb proteins. (a) Schematic representation of possible PRC1/2 interactions via the Xist A- [51] and B- [52] repeats (black lines). The question marks indicates the debated interaction of PRC2 with the A-repeat (b) Schematic representation of HOTAIR interaction at domain 1 (D1), helix 7 (H7) [53] with PRC2 (black lines).

Figure 2.

Xist and HOTAIR RNA predicted structure and interaction propensity and super-resolution microscopy. (a). Xist interaction propensity profile (Z-normalized binding propensities of RNA regions) calculated with catRAPID indicates that the binding of HNRNPK is in the region comprising the Xist Rep B and the Xist Rep C [35], in agreement with experimental evidence [54]. (b) Xist and PRC2 do not directly interact. Representative image of Xist and PRC2 catalytic subunit Ezh2 from Cerase et al. [57]. Reproduced with the permission of the editor, PNAS February 11, 2014 111 (6) 2235–2240. (c) HOTAIR interaction propensity calculated with catRAPID indicates the binding of EZH2 in the D1 domain [66], in agreement with experimental evidence [57,58]_.

Figure 3.

Xist and HOTAIR phase separation propensity and phase separation by Xist RNA through recruitment of phase-separating proteins. (a) Phase separation propensities profiles reveal that structurally disordered regions in EZH2 (https://pfam.xfam.org/protein/Q15910) and HNRNPK (https://pfam.xfam.org/protein/P61979) promote the formation of high-order assemblies. HNRNPK shows higher phase separation propensity than EZH2. (b) Comparison between Xist and HOTAIR interactomes indicates that Xist interactions are enriched in elements prone to phase separation (***p-value < 0.001; Kolmogorov–Smirnov test, table 1). Comparison with control RNA (antisense of the 3′ UTR of Alpha Synuclein) [80] indicates that HOTAIR has non-negligible propensity to associate with phase-separating proteins (***p-value < 0.001; Kolmogorov–Smirnov test). (c) The most-likely Xist-mediated PRC2 recruitment pathway involves PRC1 recruitment via repeat B interaction through HNRNPK direct interaction (light green). H2A ubiquitination by PRC1 may induce PRC2 recruitment on the Xi as previously shown (see main text). We suggest that Xist might also recruit PRC1/2 complexes by phase separation through mediation of structurally disordered proteins the Xist binding repeat E. Phase-separated PRC1/2 recruitment could occur through a direct interaction with repeat Xist E. We suggest that the PRC1/2 oligomerization can further recruit repressive proteins and/or disordered proteins, contributing to the eviction of Pol II and basic transcription factors, recruiting more structurally disordered proteins and in turn, inducing further granule formation, heterochromatinization and gene repression. Xist repeats are shown; A repeat (pink), B repeat (orange); E repeat (blue). Proteins are shown by name. Waved grey profiles on proteins, indicate intrinsically disordered regions; Xist RNA (black line).

Figure 4.

RNA sustains Polycomb complexes functions. RNA can facilitate PRC1/2 complex and sustain three-dimensional contacts and loops (also mediated by the cohesin complex; red/blue ring) to coordinate gene expression by brining co-regulated genes together (gene A, green; Gene B, purple; green/blue ribbons represent nascent RNA from gene A/B). Rixosome could also be participating to these interactions. (B) RNA inhibits PRC2 catalytic activity. RNA (green) can inhibit PRC2 catalytic activity. Its activity can be relieved by H3K27me3 tails (red lollipop) or methylated Jarid2 proteins.