This unit describes the ChIP-exo methodology, which combines chromatin 
immunoprecipitation (ChIP) with lambda exonuclease digestion followed by 
high-throughput sequencing. ChIP-exo allows identification of a nearly complete 
set of the binding locations of DNA-binding proteins at near-single-nucleotide 
resolution with almost no background. The process is initiated by cross-linking 
DNA and associated proteins. Chromatin is then isolated from nuclei and 
subjected to sonication. Subsequently, an antibody against the desired protein 
is used to immunoprecipitate specific DNA-protein complexes. ChIP DNA is 
purified, sequencing adaptors are ligated, and the adaptor-ligated DNA is then 
digested by lambda exonuclease, generating 25- to 50-nucleotide fragments for 
high-throughput sequencing. The sequences of the fragments are mapped back to 
the reference genome to determine the binding locations. The 5' ends of DNA 
fragments on the forward and reverse strands indicate the left and right 
boundaries of the DNA-protein binding regions, respectively.