Fig. 4

RLG and RLL peaks show distinct epigenetic features. a Heatmap indicating the relative enrichment or depletion of RLG and RLL peaks over specific chromatin features shown at right. The ratio of observed over expected overlaps between RLG and RLL peaks and matched R-loop control peaks was measured over each chromatin feature (see Methods) and shown as a color-coded heatmap (shown at left). Stars indicate the extent of overlap between R-loop peaks and each chromatin feature (* 10–25%; ** 25–50%; *** > 50%; no star < 10%). All values are significant with p-value < 0.008 (Monte-Carlo). b Distance between RLG and RLL peaks and H3K9me3 peaks (top) or LADs (bottom) compared to matched controls. Statistical significance was measured by Wilcoxon test. c Distance between all R-loop peaks and H3K9me3 peaks (top) or LADs (bottom) after clustering R-loop peaks according to the strength of signal change upon Top1 depletion (color-coded as in Fig. 2c). d Promoter density plotted along a region centered on LAD boundaries (shaded) for promoters driving transcription away from the boundary (left) or towards it (right), as indicated by the arrow. Genes were broken down between RLG genes (top), control matched genes (middle) and all genes (bottom)