Extended Data Fig. 2: WRN depletion induces recurrent and overlapping DSBs in MSI cells.
From: Repeat expansions confer WRN dependence in microsatellite-unstable cancers
a, Genome browser screenshot displaying END-seq profiles as normalized read density (RPM) for HCT116-shWRN and KM12-shWRN cells treated with DMSO (NT) or doxycycline (shWRN), or transfected with non-targeting siRNAs (siCTRL) or WRN siRNAs (siWRN) for 72 h. b, Scatterplots of END-seq peak intensity between biological replicates of KM12-shWRN and HCT116-shWRN cells treated with doxycycline for 72 h. Pearson correlation coefficients are indicated. c, Venn diagrams showing overlap between peaks detected in HCT116-shWRN and KM12-shWRN cells treated with either doxycycline (shWRN) or WRN siRNAs (siWRN) for 72 h. n = 1,000 random datasets were generated to test significance of overlap using one-sided Fisher’s Exact test for both the Venn diagrams (P < 2.2 × 10−16 for both comparisons). d, Quantification of END-seq peak intensity for KM12-shWRN and SW837-shWRN cells treated with doxycycline for 72 h. n = 5,424 peaks were examined for statistical significance using one-sided Wilcoxon rank sum test. Box plots are as in Fig. 2a, b. ***P <2.2 × 10−16. e, Venn diagram showing overlap between peaks identified from END-seq and RPA-bound ssDNA ChIP–seq for KM12-shWRN cells treated with doxycycline for 72 h. n = 1,000 random datasets were generated to test significance of overlap using one-sided Fisher’s exact test (P < 2.2 × 10−16). f, Composite plot of END-seq (black: positive-strand reads, grey: negative-strand reads) and RPA-bound ssDNA ChIP–seq (blue: positive-strand reads, red: negative-strand reads) signal around DSB sites in KM12-shWRN cells treated with doxycycline for 72 h. g, Heat map displaying intensity of END-seq signal in KM12-shWRN cells treated with doxycycline for 72 h, relative to the centre of the gap between positive- and negative-strand peaks. Sites are ordered by the size of the gap, from smallest to largest. h, Calculated size distribution from the reference genome of (TA)n repeats either located in gaps between positive and negative END-seq peaks (black, broken sites) or located elsewhere in the genome (grey, non-broken sites), determined from KM12-shWRN cells treated with doxycycline for 72 h.
