DPC-Seq: Investigating the genome-wide distribution of DNA-Protein Crosslinks in time

Abstract DNA-protein crosslinks (DPCs) arise from enzymatic intermediates, metabolism or exogenous chemicals like chemotherapeutics. DPCs are highly cytotoxic as they interfere with DNA-based processes such as replication and transcription. To investigate the genome-wide distribution of DPCs, we have adapted previously published K-SDS precipitation protocols for analysis by quantitative PCR or next generation sequencing to determine the distribution of DPCs throughout the genome. After the induction of DPCs, the DPCs are isolated and subsequently the DPC-associated DNA is purified. This DNA can be analysed by real-time quantitative PCR or next generation sequencing. By performing this assay at different timepoint after damage induction, genomic regions that are preferentially repaired can be identified. This protocol can be used in wild-type and compared with cells deficient for repair proteins to study their involvement during DPC repair.