Chromatin immunoprecipitation (ChIP) is a technique used to identify DNA-protein binding sites on chromosomal DNA.
To carry out a ChIP experiment, formaldehyde treatment is used to covalently cross-link proteins with the DNA. An exonuclease is then used to cleave DNA not bound by a protein. Using an antibody targeting the protein of interest, the desired protein-DNA complex is precipitated and purified.
Originally, ChIP-on-Chip was used after the purification of the desired protein, using a microarray to identify the binding sites. However, ChIP-seq has become more dominant, using sequencing to map the protein binding sites to a reference genome. This provides highly accurate localisation of binding sites, which can be beneficial in identifying where transcription factors and other DNA-binding proteins interact.