Genome-wide maps of double strand breaks after siRNA knockdown of DDX41 in HCT116 cells

We report the first genome-wide mapping of fragility hotspots after siRNA-mediated knockdown of the DEAD-box helicase DDX41 in HCT116 cells using sBLISS. DDX41 defficient cells display elevated levels of genomic instability. sBLISS analysis revealed that hotspots for genomic instability in the absence of DDX41 are located around the transcription start site of transcribed genes. Genome-wide mapping of DNA double-strand breaks by sBLISS upon siRNA-mediated knockdown of DDX41 was performed in human adenocarcinoma HCT116 cells. Non-targeting siRNA was used as a control. The experiment was carried out in biological replicates.