G-quadruplex folding in Xist RNA antagonizes PRC2 activity for step-wise regulation of X-chromosome inactivation

How Polycomb repressive complex 2 (PRC2) is regulated by RNA remains an unsolved problem. While PRC2 binds G-tracts with potential to form RNA G-quadruplexes (rG4), whether rG4’s fold extensively in vivo and whether PRC2 binds folded or unfolded rG4 are unknown. Using the X-inactivation model, here we identify multiple folded rG4’s in Xist RNA and demonstrate that PRC2 preferentially binds folded rG4’s. High-affinity rG4 binding inhibits PRC2’s histone methyltransferase activity and stabilizing rG4 in vivo antagonizes H3K27me3 enrichment on the inactive X-chromosome. Surprisingly, mutagenizing the rG4 does not affect PRC2 recruitment but promotes its release and catalytic activation on chromatin. H3K27me3 marks are misplaced, however, and gene silencing is compromised. Xist-PRC2 complexes become entrapped in the S1 chromosome compartment, precluding the required translocation into the S2 compartment. Thus, Xist rG4 folding dynamics control PRC2 activity, H3K27me3 enrichment, and the step-wise regulation of chromosome-wide gene silencing.