The histone methyltransferase Polycomb repressive complex 2 (PRC2) interacts with RNAs, but there is ongoing debate as to the functional consequences of this interaction. RNase A treatment during chromatin immunoprecipitation (rChIP) reduces chromatin occupancy of PRC2, with this data supporting a model whereby RNA ‘bridges’ PRC2 to chromatin [1]. A separation-of-function PRC2 mutant, defective in RNA binding but active in methyltransferase, was defective in H3K27me3 deposition in cells, which further supported a function for the RNA binding activity of PRC2 [1].
Here we show that RNase A treatment during chromatin immunoprecipitation leads to the apparent loss of all facultative heterochromatin, including PRC2 and its H3K27me3 mark genome-wide [2]. We track this artificial displacement of PRC2 to a gain of DNA from non-targeted chromatin following RNA degradation. This DNA is then sequenced at the expense of specific DNA, thereby reducing specific ChIP-seq signals. Furthermore, part of the RNA-binding surface in a previously studied PRC2 mutant [1] is required for chromatin modification, yet this activity is independent of RNA. Instead, a portion of the RNA-binding surface is required for chromatin modification through interactions with nucleosomal DNA. Conversely, another RNA-binding defective mutant [3] exhibited normal chromatin modification activity in cells. Collectively, we uncover a critical role for RNA in maintaining the solubility of chromatin while also showing that part of the RNA-binding surface of PRC2, rather than its RNA-binding activity, is required for the methylation of chromatin in vitro and in cells.
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