ChIP, an abbreviation for chromatin immunoprecipitation, determines whether or not a protein interacts with specific sites on a strand of DNA. The process has three basic steps. First, proteins are allowed to bind to the DNA inside living cells. This step, sometimes called cross linking, takes place in formaldehyde. Second, the strands of DNA are cut around the binding protein so that this segment of DNA can be analyzed separately. Third, the pieces of DNA that the protein is bound to need to be separated from the rest of the DNA. To achieve this, antibodies that bind to the protein being studied are introduced. This step is called precipitation.
After the segments of DNA that the protein binds to have been separated from the rest of the DNA, the sites need to be analyzed to determine where they were in the original DNA strand. This is done by comparing the strands to the map of the human genome that was finished in 2003, or to a similar genome map if non-human cells are being studied.
ChIP-Seq takes advantage of bioinformatic techniques to increase the speed and reduce the cost of research. Bioinformatic techniques are necessary because of two major complications that arise during the ChIP process. Sometimes problems such as contamination arise during the ChIP process, which can lead to errors when sequencing the DNA strands that are left over. Genome sequence analyzers are able to clean the data set of low-quality data points. Another complication is that proteins may bind to numerous sites along a strand of DNA, but might not bind to each site with equal probability. A genome analyzer will match the strands to each site along the reference genome and provide distributions of which sites the protein is most likely to bind to. These programs are also able to make comparisons between the different genes that the protein binds to.