Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation

Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain repression of genes specific for other cell lineages. In vitro, RNA inhibits PRC2 activity, but the effect of RNA on PRC2 in cells is less clear, with studies concluding that RNA either antagonizes or promotes PRC2 chromatin association. The addition of RNase A to chromatin immunoprecipitation reactions has been reported to reduce detection of PRC2 target sites, suggesting the existence of RNA bridges connecting PRC2 to chromatin. Here, we show that the apparent loss of PRC2 chromatin association after RNase A treatment is due to non-specific chromatin precipitation. RNA degradation precipitates chromatin out of solution, thereby masking enrichment of specific DNA sequences in chromatin immunoprecipitation reactions. Maintaining chromatin solubility by the addition of poly-L-glutamic acid rescues detection of PRC2 chromatin occupancy upon RNA degradation. These findings undermine support for the model that RNA bridges PRC2 and chromatin in cells. [Display omitted] •rChIP has suggested the presence of RNA bridges that connect PRC2 to chromatin•RNase A treatment in rChIP experiments causes non-specific chromatin precipitation•Non-specific precipitation masks enrichment of sites of PRC2 and H3K27me3 occupancy•PGA prevents background precipitation and rescues detection of chromatin occupancy The reduced detection of PRC2 target sites upon the addition of RNase A to chromatin immunoprecipitation experiments suggests the existence of RNA bridges that connect PRC2 to chromatin. Hall Hickman and Jenner report that this effect is an artifact of non-specific chromatin precipitation that occurs upon RNA degradation.