DPC-seq enables genome-wide monitoring of DNA-protein crosslink induction and repair

Abstract DNA-protein crosslinks (DPCs) are highly toxic DNA lesions arising from a variety of endogenous and exogenous genotoxins including chemotherapeutic drugs. DPCs can be enzymatic or non-enzymatic in nature, with non-enzymatic DPCs arising from endogenous aldehydes such as formaldehyde constituting a potentially significant source of endogenous DNA damage. Mechanistic studies of non-enzymatic DPC repair have been hampered by the fact that any chromatin-associated protein could feasibly become crosslinked to DNA, making it challenging to assess the impact of genomic context on DNA induction and repair by conventional methods such as ChIP-seq. Here, we describe DPC-seq, a protocol by which researchers can purify and sequence genomic DNA that bore DPCs, where sequencing read coverage can be used to infer DPC occupancy at specific genomic loci.