Polycomb repressive complex 2 (PRC2) interacts with chromatin to trimethylate histone H3 at Lys27 (H3K27me3) and repress gene expression, a process that is often dysregulated in cancer. Beltran et al. now reveal that PRC2–chromatin binding is regulated by chromatin-associated G-quadruplex (G4)-containing RNA, which binds PRC2, removes it from chromatin and reactivates gene expression.

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The authors previously showed that PRC2 binds pre-mRNAs in mouse embryonic stem cells. Here, bioinformatics approaches suggested that PRC2 interacts with G-tracts within pre-mRNA and preferentially with G-tracts that form G4 structures. Indeed, in vitro, removal of the G4-forming G-tract from PIM1 RNA reduced its interaction with PRC2, and PRC2–PIM1 RNA binding was strongest in buffer permitting the formation of G4 structures. Thus, PRC2 interacts with G4 structures.

Of note, G4 structures inhibited PRC2–nucleosome interactions in vitro, as the presence of generic G4-forming RNA or of PIM1 RNA prevented interaction of the PRC2 catalytic core (which includes the methyltransferase EZH2) with substrate nucleosomes and removed it from nucleosomes to which it was already bound. To confirm that G4 structures removed PRC2 from nucleosomes in vivo the authors used nuclease-deactivated Cas9 in NIH3T3 cells to tether, to the 5′ end of the PRC2 target gene Fgf11, an artificial G-tract RNA or a G-tract RNA encoded by Fgf11. These G-tracts reduced binding of PRC2 to, and H3K27me3 at, Fgf11 compared with controls. Furthermore, PRC2 was shown to move from chromatin to pre-mRNA upon HRASV12-mediated activation of its target genes, and also to move from chromatin to tethered G-tract RNA in the absence of HRASV12, indicating that PRC2 moves from chromatin to RNA upon gene activation.

Finally, Beltran et al. asked whether G-tract RNA could reactivate CDKN2A (which encodes the tumour suppressor p16), which is adversely silenced by PRC2 in malignant rhabdoid tumours (MRTs). Indeed, targeting G-tracts to CDKN2A in MRT cells depleted the gene of PRC2 and H3K27me3, reactivated it and increased p16 levels to those achieved by the non-specific EZH2 inhibitor EI1.

G-tracts can reactivate PRC2-repressed genes

Thus, this study shows that G-tracts can reactivate PRC2-repressed genes and highlights their potential to do this at specific genes in cancer.