Chromatin Immunoprecipitation (ChIP) is used to determine the interactions of proteins with their binding sites in vivo. It is a technique to investigate a particular protein-DNA interaction, several protein-DNA interactions, or interactions across the whole genome or a subset of genes.
The living cells used in the technique should be handled with chemical cross-linkers to bind proteins with each other and then with their DNA targets. Once cross-linked to the associated proteins, sonication is used to extract and fragment chromatin. Specific antibodies against the target protein are immunoprecipitated with the protein-DNA complexes to isolate them. The cross-links are then reversed and sequencing of the DNA fragments is determined.20
The sequence reads will contain tags that are used to know the positions next to where the protein was bound to DNA. As a result peaks of reads will accumulate next to DNA bound to protein. Detection of the accumulation of peaks can be used for mapping.
20. Song C, Zhang S, Huang H. "Choosing a suitable method for the identification of replication origins in microbial genomes." Front Microbiol. 2015 Sep 30;6:1049. doi: 10.3389/fmicb.2015.01049. PMID: 26483774; PMCID: PMC4588119.
