Chromatin immunoprecipiation

Chromatin immunoprecipitation (also chIP) is a technique used to determine the particular DNA sequences bound by specific proteins.

First the DNA and proteins are cross-linked (fixed together) by heat or UV treatment, then chromatin is isolated and fragmented by either sonication or digestion. Then immunoprecipitation is performed against the protein of interest (whether a transcription factor, acetylated histone, etc) and cross-linking is reversed to purify the DNA, while the protein is discarded. The DNA is then amplified by PCR for analysis:

1. PCR: using primers against a gene of interest to see if it interacts with the protein
2. qPCR: to quantify the level of protein binding
3. Microarray analysis (also chIP-on-chip): to determine if the protein binds to a large number of sequences, as well as relative affinities (i.e. have competing fluorescence between cDNAs from chIP analysis and cDNAs from unbound DNA)
4. chIP-seq: to determine all the sequences bound by the protein