Light-based footprinting of a eukaryotic genome

Identification of protein-bound DNA sites is key to understanding genome function and regulation, but studying protein-DNA interactions in living, unperturbed cells remains challenging. UV footprinting has been used to study such interactions in vivo by detecting changes in DNA photoproduct formation at protein-bound sites, but only on a limited scale. Here, we describe whole-genome deamination sequencing (Deam-seq), wherein photoproducts (pyrimidine dimers) induced by UV irradiation are revealed as mutations, enabling generation of quantitative photofootprints of the yeast <i>Saccharomyces cerevisiae</i> at ultradeep coverage. By comparing cellular and naked DNA, we find that this approach can resolve protein occupancy at high resolution without preference toward accessible regions. Cell/naked differential signals commonly aligned with predicted regulatory sites, ChIP peaks and DNase I protection footprints, and supported that yeast DNA binding proteins typically exhibit protective effects on UV damage. Our results provide proof of concept for using light and sequencing to study protein-DNA interactions in their native cellular context at genome scale.