Patent ID: 8367334

Claim:
A method of identifying a plurality of locations which a protein of interest binds to in a genome, the method comprising the steps of: (a) subjecting a plurality of cells or extract thereof to a chromatin immunoprecipitation assay using one or more antibodies that specifically bind to a protein of interest and resulting in double-stranded nucleic acid fragments bound to the protein of interest; (b) subjecting the double-stranded nucleic acid fragments bound to the protein of interest to exonuclease treatment and resulting in single-stranded nucleic acid fragments containing the plurality of locations which the protein of interest binds to, wherein each of the single-stranded nucleic acid fragments has an exonuclease-treated end sequence and the exonuclease treatment is carried out using a double-stranded nucleic acid-specific exonuclease that degrades a nucleic acid in only a 5′-to-3′ or only a 3′-to-5′ direction and a single-stranded nucleic acid-specific exonuclease that degrades a nucleic acid in the same direction as the double-stranded nucleic acid-specific exonuclease; (c) converting the single-stranded nucleic acid fragments to double-stranded nucleic acid fragments having exonuclease-treated end sequences; (d) identifying the exonuclease-treated end sequences; and (e) mapping the plurality of locations which the protein of interest binds to in the genome by identifying the exonuclease-treated end sequences.