SPECIFIC REACTIVITY OF ABASIC SITES WITH POLYAMINES ENABLES THEIR GENOMIC MAPPING

Knowing their genomic distribution is important for understanding the mechanisms of genotoxic agents. Although several methods exist for genomic mapping of AP sites, some of them suffer from limited specificity and/or complex multi-step workflows.

Here, we present APX-seq, a novel method based on the recently discovered reaction of AP sites with 1,2-diamines, for highly specific chemical labelling, isolation and enrichment of AP site-containing genomic fragments for subsequent DNA sequencing. Following in vitro optimization and validation, we applied APX-seq to the genome of cultured HepG2 cells. Our finding reveal that AP sites are broadly distributed in the genome and are enriched in euchromatin, consistent with the prior studies.