Fig. 6.

Protein binding to RNA relates to local chromatin. Because chromatin marks measured by RRBS (DNA methylation) or ChIP-Seq (histone modifications and modifiers) correlate with gene abundance (Fig. S16 in Additional file 1), we plotted this relationship separately for genes bound and unbound by each protein. a DNMT1-bound RNAs have less DNA methylation in their promoter, shown as a scatter plot of every gene with a generalized additive model regression. b WDR5-bound RNAs have more H3K4me3 in their promoter. c For each chromatin mark and protein, we plotted the difference between the bound and unbound regression lines as a heat map (“Materials and methods”), revealing a clear difference in the relationship of certain proteins to activating chromatin marks. d CHST2 exemplifies a WDR5-bound RNA with ample H3K4me3