Dual Chemical Labeling Enables Nucleotide-Resolution Mapping of DNA Abasic Sites and Common Alkylation Damage in Human Mitochondrial DNA

Understanding the genomic locations of DNA modifications is pivotal for deciphering their roles in gene regulation, mutagenesis, and pathology. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the specificity of labeling and enrichment of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mitochondrial DNA (mtDNA) from cultured human cells under different biological conditions. Also, we demonstrated the broader applicability of the method in sequencing additional DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples. We created a dual chemical labeling-assisted sequencing which is a sensitive and specific approach for sequencing AP sites and other DNA modifications. When coupled with parallel sample processing and lesion-specific repair enzymes, DCL-seq is promised to be a powerful approach for sequencing multiple DNA modifications in a biological sample.