Chromatin+immunoprecipitation

=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