Fig. 4: Genome-wide analysis of DDX41 binding to chromatin and R-loops.

a Metagene profile showing the distribution of the GFP-DDX41 CUT&RUN signal in U2OS cells along expressed genes. b Genomic features overlapping GFP-DDX41 CUT&RUN peaks in U2OS cells. Features are color-coded as indicated in the legend. c MapR performed in n = 3 biologically  independent experiments in U2OS cells after 48 h knockdown with control siRNA, DDX41 siRNA, or treatment with 4 µM Actinomycin D for 6 h. Heatmaps of normalized read coverage ranging from ±2 kb around the transcription start site of expressed genes sorted by gene expression based on the RNA-sequencing analysis of U2OS cells. d Scatter plot of MapR regions in U2OS cells. Consensus regions were constructed using the intersection of peaks for the replicates in each condition (siCtrl and siDDX41). The union of these regions was used for further analysis and quantification of the coverage/FC. The mean log₂ fold change between siCtrl and siDDX41 is plotted against the log₂ average counts per million representing the coverage. Genomic regions that are differentially regulated (FC > 2) are highlighted in red (up) or in blue (down). e Genomic feature distribution of the regulated MapR regions in U2OS cells after DDX41 knockdown. Features are color-coded as indicated in the legend. f The proportion of genomic regions with R-loop gains or losses in U2OS cells overlapping CGIs or not-overlapping regions are depicted. g Reactome pathway over-representation analysis for genes with R-loop gains in U2OS cells. The adjusted p-values (Fisher’s exact test with Bonferroni-Holm correction) are indicated. h Representative snapshot of a genomic region depicting R-loops and GFP-DDX41 binding profiled by MapR and greenCUT&RUN, respectively, in U2OS cells.