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

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. VI. Genomewide mapping of lesions in DNA following MMS damage in yeast GLOE-Seq was applied to samples of yeast genomic DNA isolated from cells challenged or not with 0.02% MMS, after treatment with hAAG and APE1 for conversion of alkylated bases to nicks. To map the endogenous repair intermediates, the same samples were not subjected to hAAG/APE1 treatment. Two replicates were used per condition.