Fig. 6: R-loops and DDR identify TRC sites and are a source of genome instability.

a Overlap of genes showing both R-loops and DDR markers from DRIP-seq and CUT&RUN data, respectively. Statistical significance of intersections assessed via one-tailed hypergeometric test (Null-hp P[X ≤ x]). Raw gene numbers and overlap percentages are shown. b Cumulative plot of R-loop distribution relative to pS2RNApol II stalling start sites (SSS), grouped into quartiles (Q1–Q4, increasing stalling). A −0.5 to +0.8 Kb window centered on SSS is displayed. Red shading highlights R-loop coverage in tIMEC-A for each stalling quartile. c Heatmaps of pRPA32 and R-loops at regions where both signals co-occur (n = 7486), sorted by decreasing size. The same region order is used across panels. Dashed lines mark region ends. Schematic of proposed TRC model aligns with heatmap features observed in tIMEC-A. d Barplot of the percentage of genes exhibiting R-TRCs (pRPA32 + R-loops) in each cell line. Raw gene counts are indicated above the bars. e Tukey boxplot (25th to 75th percentile and median) of R-loop length (bp) at TRC regions (pRPA32 + R-loops; tIMEC = 376, tIMEC-A = 5527, tIMEC-A-H1 = 5211) vs. non-TRC regions (R-loops only; tIMEC = 33,626, tIMEC-A = 76,270, tIMEC-A-H1 = 83,901). R-loop peaks are shared by three biological replicates intersected with a representative replicate for pRPA32. Two-tailed unpaired t-test p values are shown. f Gene ontology enrichment for R-TRC genes. Terms and −log10(p value) from Fisher's exact test are shown. Colors indicate the reference database from which the terms were obtained. g Distribution of common fragile sites (CFSs) and their chromosomal locations (blue), alongside alteration frequencies in basal BC patients (black lines). h Density plot showing proximity of TRC regions (red) to nearest CFS breakpoint. R-loop-only (green), pRPA32-only (blue), and three sets of matched random regions (dashed lines) serve as controls.