Fig. 4: Analysis of DNA damage along the cell cycle in siINO80 and siSMARCA5 cells.

a Quantification of RNAPII-S2P + PCNA PLA (TRCs) foci in control (siC), siSMARCA5 and siINO80 cells. Data presented as scatter plot (n > 50 cells examined over 3 independent experiments). Median values are indicated. (Mann-Whitney U test, two-tailed). b Percentage of cells with more than 5 FANCD2 foci in siC, siSMARCA5 and siINO80 cells that overexpress (+) or not (−) RNH1. Data expressed as relative to siC. Mean + SEM are plotted (n = 5 (RNH1−) and n = 6 (RNH1+) independent experiments). (Unpaired Student’s t test, one-tailed). c Representative screenshot of a genome region showing co-localization of R-loops (DRIPc; light blue), SMARCA5 (yellow), YY1 (INO80; green), SMARCA4 (red) and FANCD2 (purple) at sites with high R-loop abundance. Replication fork directionality (RFD) is also shown. d Zoomed-in examples of R-loops (DRIPc; light blue), SMARCA5 (yellow), YY1 (INO80; green), SMARCA4 (red) and FANCD2 (purple) colocalization. e Venn diagram showing correlation between SMARCA4 (red), SMARCA5 (yellow) and YY1 (INO80; green) peaks colocalizing with R-loops. f Metapeak analysis of FANCD2 at R-loops colocalizing with SMARCA4, SMARCA5 or YY1. Transcription direction is indicated. g Venn diagram showing R-loop (DRIPc; light blue), FANCD2 (purple) and SMARCA5 (yellow) genome-wide co-occurrence in control K562 cells. h Venn diagram showing R-loop (DRIPc; light blue), FANCD2 (purple) and YY1 (INO80; green) genome-wide co-occurrence in control K562 cells. Representative images, with nuclear perimeter highlighted (yellow dashed line), are shown. Scale bars and p values are indicated. RFD replication fork directionality, trx transcription. Arrows under trx indicate transcription direction. Source data are provided as a Source data file. See also Supplementary Fig. 4.