Genome footprinting by high-throughput sequencing (GeF-seq) resolves DNA-binding sites of targeted proteins with an accuracy comparable to in vitro DNase I footprinting

Chromatin immunoprecipitation (ChIP) is a common method to map protein-binding sites in vivo. Combining this method with microarray (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows us to detect protein-binding sites scattered across the entire genome. An enduring challenge for these methods, however, is how to increase theirpositional resolution. Here, we describe a new method, “Genome Footprinting by high-throughput sequencing (GeF-seq)”, to attain high-resolution mapping of protein-binding sites by combining in vivo DNase I digestion and ChIP-seq. We used GeF-seq to determine the binding site of Bacillus subtilis transition state regulator, AbrB, across the genome. GeF-seq can resolve closely positioned binding sites that appear as single peak in the ChAP-chip and ChAP-seq methods. The binding sites of AbrB determined by GeF-seq are comparable to the resolution achieved by in vitroDNase I footprinting. The results enable us not only to confirm a minimal element in AbrB recognition sequences, previously determined as the AbrB binding motif (TGGNA) by in vitro analysis, but also to find new types of AbrB recognition sequences.