Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that tri-methylates lysine 27 of histone H3 (H3K27me3) — a hallmark of repressed genes. It is required for cell fate and cell identity in multicellular organisms and is dysregulated in cancer and developmental disorders. Various accessory subunits are differentially associated with core PRC2 during development that modulate its activity and recruitment. RNA binds to PRC2 and inhibits its enzymatic activity, however the mechanism is poorly understood at the molecular level.
Through UV-crosslinking with mass spectrometry, complemented by biochemical and biophysical assays, we show that RNA binds to an allosteric regulatory site of PRC2. Specifically, RNA binds to the same site that binds regulatory peptides, which normally stimulate the histone methyltransferase activity of PRC2. Accordingly, regulatory peptides relieve RNA-mediated inhibition of PRC2. Chemical crosslinking mass spectrometry (XL-MS) with enzymatic assays indicates that the regulatory site of PRC2 remains exposed while PRC2 is in complexes with most of its accessory subunits, allowing RNA to bind and inhibit most types of PRC2 complexes. Competition with DNA or nucleosomes is not required for RNA-mediated inhibition of PRC2, and thus RNA can inhibit the methyltransferase activity of PRC2 toward non-histone substrates. Collectively, we show that the architecture of PRC2 allows it to bind to either its stimulatory (regulatory peptides) or inhibitory (RNA) signals through the same site while in a complex with most of its accessory subunits. Therefore, our data indicates for a unified model for RNA-mediated methyltransferase-inhibition of PRC2, and provides a mechanistic framework for RNA-mediated regulation of PRC2 throughout development. Of note, disease-associated and -driver mutations in the RNA-binding site of PRC2 provide a potential link between its RNA-binding activity to pathologies and could thus open a path for future therapeutics.