A more general approach to improving the resolution of chromatin mapping assays is the ChIP-exo assay developed by Pugh and colleagues, in which material isolated by chromatin immunoprecipitation is treated with λ exonuclease prior to crosslink reversal and cloning of purified DNA (Rhee and Pugh 2011). The rationale behind this assay is that shearing and other chromatin fragmentation methods leave heterogeneous DNA ends on either side of the protein of interest. Exonuclease treatment is thus used to digest excess DNA surrounding the protein-DNA crosslink, providing a consistent DNA end a few nucleotides away from the crosslink site which cannot enter the exonuclease. ChIP-exo thus provides a far more precise footprint of proteins on DNA than do methods relying on shearing for chromatin fragmentation. For example, for the yeast TF Reb1, the known Reb1 binding motif occurs precisely at the center of ChIP-exo peaks with a standard deviation of <1 nt, while it is found within ∼25 nt of the center of a traditional ChIP-seq peak. Demonstrating the power of ChIP-exo as a tool for structural biology, comparison of protein-DNA crystal
