DEPACE-seq enables high-fidelity, single-nucleotide-resolution mapping of abasic sites and characterization of dynamic and long-lived AP landscapes in mammalian genomes

High-fidelity single-nucleotide-resolution mapping of abasic (AP) sites in mammalian genomes remains technically challenging due to low abundance and high background. Here we present DEPACE-seq (Dual-End PAB-Conjugated Endo IV-Cleaved Sequencing), a robust and easy-to-implement method for precise genome-wide profiling of AP sites. DEPACE-seq employs an N-pyrrolyl-alanine-2,2'-(ethylenedioxy)bis(ethylamine)-biotin (PAB) probe that selectively conjugates AP sites via a mild Pictet-Spengler reaction. The resulting PAB-AP adducts are efficiently and specifically cleaved by endonuclease IV, while remaining inert to other aldehyde-containing DNA bases. Independent library construction from both cleavage ends and the intersection of the resulting signals enable high-confidence identification of AP sites at single-nucleotide resolution. Application of DEPACE-seq across different cell types and damage conditions enabled high-confidence characterization of two AP-site populations: long-lived sites enriched in satellite and intergenic regions, and repair-intermediate sites induced by transient damage and enriched in transcriptionally active regions, both exhibiting cell-type-dependent features. Molecular dynamics simulations further elucidate how endonuclease IV accommodates bulky PAB adducts. Together, DEPACE-seq provides a robust platform for high-confidence, single-nucleotide-resolution mapping of AP sites in mammalian genomes, enabling systematic investigations of genome instability, DNA repair, aging, and cancer.