Sriramachandran, A. M. et al. Mol. Cell https://doi.org/10.1016/j.molcel.2020.03.027 (2020).
Sequencing-based methods have been developed to detect DNA damage events and reveal their genome-wide distribution. Single-strand breaks (SSBs) are one of the most frequent types of DNA damage in the genome and have been profiled by methods involving poly(A) tailing or labeling during nick translation, which may reduce the resolution of the original position of break sites. To obtain a map with nucleotide resolution, Sriramachandran et al. developed genome-wide ligation of 3′-OH ends followed by sequencing (GLOE-Seq), which detects free 3′-OH termini resulted from SSBs, lesions or other repair intermediates. In GLOE-Seq, genomic DNA is heat-denatured and ligated to a biotinylated adapter with the assistance of a splinter oligonucleotide, followed by fragmentation and capture on streptavidin beads. GLOE-Seq has been applied in mapping DNA SSBs and lesions in yeast and human chromatin. The researchers also provide a software pipeline for annotating and visualizing strand breaks.