CNCC: an analysis tool to determine genome-wide DNA break end structure at single-nucleotide resolution.

For the first time, on a genome-wide scale, our analysis revealed the increase in the 5' to 3' end resection following etoposide treatment, and the global progression of the resection. Furthermore, our method distinguished the change in the pattern of DSB end structure with increasing doses of the drug. The ability of this method to determine DNA break end structures without a priori knowledge of break sequences or genomic position should have broad applications in understanding genome instability.