The ChIP-Exo Method to Identify Genomic Locations of DNA-Binding Proteins at Near Single Base-Pair Resolution

Chromatin immunoprecipitation (ChIP) is a technique to determine whether a protein interacts with a specific DNA sequence. ChIP-sequencing (ChIP-seq) is one of the most widely used methods to identify genome-wide DNA-binding sites of nuclear proteins. Here, we describe the ChIP-exo method, which is a refined version of ChIP-seq combined with lambda exonuclease digestion. ChIP-exo can identify genomic locations of DNA-binding proteins at a near single base-pair (bp) resolution. It removes most of the background DNA signals. ChIP-exo has emerged as a powerful technique to study the genome-wide organization of DNA-binding proteins.