Yeast Deam-seq

Identification of protein-bound sites is key to understanding genome function and regulation, but protein-DNA interactions are difficult to study in living, unperturbed cells. UV footprinting has been used to study such interactions in vivo by detecting changes in DNA photoproduct formation in the presence of bound proteins, but so far only at a limited scale. Here we describe whole-genome deamination sequencing (Deam-seq), wherein pyrimidine dimers induced by high-dose UV irradiation manifest as easily detectable C>T mutations, enabling generation of a quantitative photofootprint of the yeast Saccharomyces Cerevisiae at ultra-deep (>7,000×) coverage. By comparing cellular and naked DNA, we find that this approach can resolve protein occupancy at high resolution, with differential signals commonly overlapping with DNase I footprints, ChIP peaks and predicted regulatory sites. Our results showcase Deam-seq as a complement to current protein-DNA mapping methods and provide proof of concept for the study of protein-DNA interaction using light and sequencing at genome scale.