After cell lysis, the chromatin is sheared by sonication or enzymatic digestion, and specific DNA sequences associated with a particular protein are subjected to precipitation with specfic antibodies. Subsequently, the purified DNA products are analyzed by various molecular techniques to determine the genomic localization of DNA. In addition, proteins are separated by affinity purification, then analyzed by MS.
ChIP: Chromatin immunoprecipitation; LC-MS: Liquid chromotography-mass spectrometry; MS: Mass spectrometry.