Genome-wide mapping of 5ʹ-aldehyde terminus induced by reactive oxygen species

DNA single strand breaks (SSBs) are abundant lesions due to cell metabolism and reactive oxygen species (ROS) and can lead to replication folk collapse, double strand break formation, genome rearrangements, cell death and disease. Among numerous chemical forms of SSBs, 5ʹ-aldehyde terminus are the most abundant generated by hydroxyl radicals and pose significant challenge for cellular repair machinery due to the lack of specific end processing process, potentially leading to more severe biological consequences than other readily repairable SSBs. Herein we developed a new strategy to locate 5ʹ-aldehyde terminus in genomic DNA at single-nucleotide resolution. The principle involves labelling the 5ʹ-aldehyde terminus with an aminooxy-functionalized oligonucleotide, giving rise to a biocompatible altered DNA linkage and allowing labelled sites to be amplified by polymerase chain reaction. We sequenced the 5ʹ-aldehyde terminus distribution in genomic DNA, nuclei, and cells following activation of the Fenton reaction. The results revealed a significant preference for adenine bases in DNA lesions and provided insights into the genome-wide distribution of such DNA damage, correlating with genomic features and chromatin accessibility. This method provide a new strategy for studies aiming to understand the biological and toxicological impacts of 5ʹ-aldehyde termini in DNA as the form species of single strand break induced by reactive oxygen species from a human genome.