PRC2 interacts with nascent RNA at essentially all active genes. (A) The overlap between genes with significant PRC2, FUS, and HNRNPC RNA crosslinks. (B) Scatter plot showing gene length (kb) and nuclear RNA abundance (reads) for all genes (black), genes with significant PRC2 crosslinks identified by iCLIP (red), and genes previously reported to produce PRC2 binding ezRNAs (blue) (Kaneko et al. 2013). (C) Cumulative frequency distribution of PRC2 (red), FUS (blue), and HNRNPC (green) crosslinks (RPKM) and total and nuclear RNA-seq RPKM for lincRNA genes (top) and protein-coding genes (bottom). (D) Scatter plot of nuclear RNA abundance (RPKM) against PRC2 crosslink density (RPKM). Genes marked in red are significantly enriched for PRC2 crosslinks compared with nuclear RNA abundance (FDR < 0.05). (E) Scatter plots showing frequency of significant crosslinks (RPKM) for FUS (left) and HNRNPC (right) versus PRC2. Genes significantly enriched for PRC2 crosslinks compared with RNA (from D) are marked in red and are not enriched compared with FUS and HNRNPC. (F) Ratio of PRC2 significant crosslink density to FUS (left) or HNRNPC significant crosslink density (right) at genes ranked by their relative proportion of exonic sequence (percentage). The trends (Loess) are marked by red lines.
