Genome-wide protein–DNA interaction site mapping using a double strand DNA-specific cytosine deaminase

DNA–protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; therefore, there is great interest in facile methods for defining the sites of DPI within cells. Here, we present a general method for mapping DPI sites in vivo using the double stranded DNA-specific cytosine deaminase toxin DddA. Our approach, which we term DddA-sequencing (3D-seq), entails generating a translational fusion of DddA to a DNA binding protein of interest, inactivating uracil DNA glycosylase, modulating DddA activity via its natural inhibitor protein, and DNA sequencing for genome-wide DPI detection. We successfully applied this method to four transcription regulators that represent divergent protein families and bind variable numbers of chromosomal locations in two bacterial species. Our data show that 3D-seq offers several advantages over existing technologies, including ease of implementation and the ability to measure DPIs at single-cell resolution. Genome-wide locations of GacA in a parental strain lacking retS and genome-wide locations of GcsR and FleQ in the wild type PAO1 background.