Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase
Larry A. Gallagher, Elena Velázquez, S. Brook Peterson, James C. Charity, Matthew C. Radey, Michael J. Gebhardt, FoSheng Hsu, Lauren M. Shull, Kevin J. Cutler, Keven Macareno, Marcos H. de Moraes, Kelsi Penewit, Jennifer Kim, Pia A. Andrade, Thomas LaFramboise, Stephen J. Salipante, Michelle L. Reniere, Vı́ctor de Lorenzo, Paul A. Wiggins, Simon L. Dove, Joseph D. Mougous
Abstract
DNA-protein interactions are central to fundamental cellular processes, yet widely implemented technologies for measuring these interactions on a genome scale in bacteria are laborious and capture only a snapshot of binding events. We devised a facile method for mapping DNA-protein interaction sites in vivo using the double-stranded DNA-specific cytosine deaminase toxin DddA. In 3D-seq (DddA-sequencing), strains containing DddA fused to a DNA-binding protein of interest accumulate characteristic mutations in DNA sequence adjacent to sites occupied by the DNA-bound fusion protein. High-depth sequencing enables detection of sites of increased mutation frequency in these strains, yielding genome-wide maps of DNA-protein interaction sites. We validated 3D-seq for four transcription regulators in two bacterial species, Pseudomonas aeruginosa and Escherichia coli. We show that 3D-seq offers ease of implementation, the ability to record binding event signatures over time and the capacity for single-cell resolution.