Denaturing purifications support direct interaction between PRC2 and RNA in cells

ABSTRACT Polycomb Repressive Complex 2 (PRC2) maintains repression of genes specific for other cell differentiation states. PRC2 binds RNA in vitro with a preference for G-rich sequences. UV-based crosslinking coupled with immunoprecipitation (CLIP) experiments have shown that PRC2 also binds RNA in cells. Recently, Guo et al reported that a stringent denaturing variant of CLIP called CLAP did not detect PRC2 RNA binding in cells. We present a reanalysis of CLAP data that supports direct interaction of PRC2 with RNA in cells. CLAP for Halo-tagged PRC2 subunits from mixed populations of human and mouse cells specifically enriched for RNA from the species in which the proteins were tagged. The lack of apparent PRC2 RNA binding in Guo and colleagues’ analysis stems from a scaling step that deflates enrichment scores for low-complexity CLAP samples. Our findings pave the way for studies seeking to determine the physiological roles of PRC2 RNA binding activity.