Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [HO endonuclease]

Numerous methods are available for the mapping of DNA lesions ranging from double-strand breaks (DSBs) to incorporated ribonucleotides. We now present a technology based on the Genomewide Ligation of 3'-OH Ends (GLOE-Seq) and an associated computational pipeline designed for single-stranded breaks (SSBs), but versatile enough to be applied to any lesion that is convertible into a free 3'-OH terminus. We demonstrate its applicability to the mapping of Okazaki fragments without prior size selection and detect biases and asymmetries in the distribution of spontaneous SSBs in budding yeast and human DNA. Overall design: II. Mapping of 3'-ends of an HO-induced double-strand break GLOE-Seq was used to map the 3'-ends of a DNA double-strand break introduced into the budding yeast genome by galactose-induction of the HO endonuclease. Samples from raffinose-grown cells served as controls. Two replicates were used per condition.