Click-chemistry-aided quantitation and sequencing of oxidized guanines and apurinic sites uncovers their transcription-linked strand bias in human cells

DNA alterations are drivers of aging, neurodegeneration, carcinogenesis, and chemotherapy drug action. To understand the functional genomic roles of DNA modifications, it is critical to accurately map their diverse chemical forms with single-nucleotide precision in complex genomes, which however remains challenging. Click-code-seq is the click-chemistry-aided single-nucleotide-resolution method introduced to map oxidation in yeast DNA. Here, we upgraded click-code-seq to enable its first application for sequencing DNA oxidation and depurination in the human genome. For this, we developed a companion fluorescence tagging assay, click-fluoro-quant, to rapidly quantify common modifications. Moreover, we devised novel adapters to minimize false modification detection and assess modification frequency in cell populations. We uncovered that endogenous DNA oxidation in a human cell line has a highly similar pattern to the cancer mutational signatures associated with the effects of reactive oxygen species. We established that the chemotherapy drug irofulven preferentially depurinates ApA dimers and promoter regions. Intriguingly, we revealed that oxidized guanines and apurinic sites, both irofulven-induced and endogenous, are depleted in the transcribed strand of genes, and the strand bias widens with increasing gene expressions. This work advances click-code-seq for deciphering the impacts of key DNA modifications in the human genome on cellular physiology and toxicological responses. Overall design: Single-nucleotide-resolution genome-wide mapping click-code-seq of endogenous guanine oxidation in HAP1 wild-type cells in 3 replicates, and of abasic (AP) sites in U2OS wild-type cells that were exposed to 15 µM irofulven (HMAF) in 3 replicates or DMSO (as a control) in 2 replicates.