Footprint-seq: a simple method to quantitatively map in vitro protein-DNA interactions on a genome-wide scale at high spatial resolution

Abstract

Protein-DNA interactions underlie essential cellular processes. The position and/or strength of protein interactions with DNA have historically been studied for short DNA regions using in vitro assays. More recent microarray- and sequencing-based assays have been developed to map protein-DNA interactions on a genome-wide scale. However, these genome-scale methods offer limited spatial resolution and have not been effectively applied to determine dissociation constants for individual sites. Here, we introduce Footprint-seq, a simple, sequencing-based method that maps and quantifies protein-DNA interactions in vitro with high resolution on a genome-wide scale. Footprint-seq measures local protection from transposition in the presence of a DNA-binding protein. Using the well-studied Escherichia coli DNA-binding protein, CRP, as a test case, we show that Footprint-seq detects CRP binding sites with high resolution across plasmid or genomic DNA. Moreover, we show that Footprint-seq enables inference of dissociation constants for hundreds of genomic sites. Thus, Footprint-seq provides a rapid, accessible, and quantitative method for mapping protein-DNA interactions in bacteria and other systems.