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 Saccharomyces cerevisiae 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.