SPECIFIC REACTIVITY OF ABASIC SITES WITH POLYAMINES ENABLES THEIR GENOMIC MAPPING

Apurinic/apyrimidinic (AP) sites are among the most abundant DNA lesions and key intermediates in the base excision DNA repair pathway. Knowing their genomic distribution is important for understanding the mechanisms of genotoxic agents. Although several methods exist for genomic mapping of AP sites, some suffer from limited specificity and/or complex multi-step workflows. Here, we describe APX-seq, a method based on the recently discovered reaction of AP sites with 1,2-diamines, enabling highly specific chemical labeling and enrichment of AP site-containing DNA fragments for subsequent sequencing. Following in vitro optimization and validation, we applied APX-seq to the genome of cultured HepG2 cells. Our findings reveal that AP sites are broadly distributed in the genome and enriched in euchromatin, consistent with prior studies, while treatments with a DNA-alkylating chemical (MMS) or X-ray radiation barely alter their global landscape. Remarkably, the alignment of APX-seq to the telomere-to-telomere (T2T) reference genome reveals a systematic enrichment of AP sites in pericentromeric HSAT2 and HSAT3 satellite repeats, with genotoxic agents further increasing AP site accumulation in HSAT2. In contrast, much lower AP site levels are observed in HOR α-satellite arrays and HSAT1 repeats. These findings identify pericentromeric satellite DNA as a novel reservoir of AP DNA damage.