Fig. 5: DDX41 loss leads to DSBs in promoters and inflammatory response.

a Representative snapshot of a genomic region depicting DNA fragility profiled by sBLISS in wild type and DDX41 knockdown HCT116 cells. b Metagene profile showing the double-strand break (DSB) signal distribution profiled by sBLISS along genes in wild type and DDX41 knockdown HCT116 cells. c Genomic features overlapping DNA fragility hotspots mapped by sBLISS in wild type and DDX41 knockdown HCT116 cells. Features are color-coded as indicated in the legend. d Venn diagram showing the number of unique and overlapped peaks mapped by sBLISS in wild type and DDX41 knockdown HCT116 cells. e Pie chart showing the percentage of double-strand breaks (DSB) gains (fold change (FC) > 2) mapped to promoters in DDX41 knockdown HCT116 cells that overlap or not with R-loops mapped in DDX41 knockdown (KD) HCT116 cells. f Representative snapshot of a genomic region showing accumulation of R-loops and DSBs profiled by MapR and sBLISS, respectively, in HCT116 cells. g Network of the Reactome pathway enrichment analysis of upregulated genes after DDX41 knockdown compared to control knockdown based on RNA-seq. All expressed genes were used as background. The size of the dots indicates the number of genes contributing to the displayed term. Gradual coloring represents the adjusted p-values based on Fisher’s exact test with Bonferroni correction for multiple comparisons. h Immunofluorescence analysis of p65 after 48 h of indicated knockdowns in U2OS cells. Dots represent measurements of individual cells, black line indicates the median of the population with interquartile range. Representative data of n = 2 biologically independent experiments. p-value < 0.0001 derived from n > 100 cells using unpaired, two-sided Students’s t-test. Source data are provided as a Source Data file.