Ad-Seq, a genome-wide DNA-adduct profiling assay

Abstract

SummaryCarcinogens form adducts with the DNA which, when not properly repaired, can lead to mutations and drive oncogenesis. The identity, sequence specificity and mutagenicity of most DNA-adducts is however poorly understood and current molecular assays are limited in their scope and scalability. We present a novel genome-wide DNA adduct sequencing (Ad-Seq) assay to map the location of DNA-adducts at single-nucleotide resolution. Ad-Seq enriches for DNA fragments containing nuclease digestion resistant DNA-adducts. The genomic location of the resulting reads is aggregated in a quantitative profile showing the DNA-adduct sequence context. Ad-Seq is quantitative and confirms known specificity of damages from Ultra-Violet light (di-pyrimidine) and cisplatin (AG and GG di-purines). Furthermore, in cells, Ad-Seq profile can be compared to chromatin segments to show that cisplatin associated adducts are depleted in open and active chromatin regions. The Ad-Seq assay can therefore generate a broad DNA signature of DNA damage and, by comparing to mutagen exposure or downstream mutational profile and signatures, be used to improve our understanding of cancer molecular etiology.