Motif-driven interactions between RNA and PRC2 regulate transcription elongation of target genes

the nature of the interaction between RNA and Polycomb repressive complex 2 (PRC2) has been an area of intensive investigation. Although PRC2 is now established as a bona fide RNA-binding protein, specific motifs have not been fully elucidated, nor has the association of PRC2-RNA complexes with active genes been reconciled. Here we employ denaturing CLIP to identify RNA motifs demonstrating high-affinity binding to PRC2 (Kd 11-80 nM). Mutating the motifs diminishes binding affinity in vitro and attenuates PRC2's repressive function in vivo. A large fraction of interactions occurs at promoter-proximal regions and associates with POL-II pausing. Furthermore, although PRC2-associated nascent transcripts are highly expressed, ablating PRC2 further increases their expression. Thus, PRC2-RNA interactions are rheostats that operate at the level of transcription elongation to fine-tune gene activity, explaining why they frequently occur within active genes. PRC2-RNA interactions also impact expression of neighboring genes, supporting the classical model that RNA targets PRC2 to gene in cis. Our study supports a model in which RNA specifically targets PRC2 for two repressive functions — (i) control of POL-II pausing, and (ii) marking chromatin with H3K27me3. Overall design: Here we employ denaturing CLIP to identify RNA motifs demonstrating high-affinity binding to PRC2 (Kd 11-80 nM). We also utilize PRO-seq assay to measure active elongation.