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Another important technology is chromatin immunoprecipitation which is used to measure proteins bound to the DNA.  We would like to know where the binding takes place because it might tell us something about how genes are activated or suppressed. (1).

The bonds between the proteins and the DNA are quite unstable so the first step is to stabilize them using a chemical, usually formaldehyde (2). This makes the bonds more permanent so that the proteins remain bound during labeling and other procedures. The proteins of interest are labeled using a target antibody (3). Now we have a complex combination of antibody, protein, the binding agent and the DNA.

The DNA is then fragmented (4).  The fragments including the antibody are captured while the other fragments are washed away.  Ideally  all the remaining fragments include the tag and the bound protein, although in practice some tagged fragments are lost and some untagged fragments remain (5).  As a result, our DNA sample is enriched for tagged fragments, but still has a background of other fragments.

Finally, the bond between the protein and the DNA is broken, releasing the DNA. The DNA can then be measured using standard technologies. (6).

Very similar methods can also be used for other chemical modifications to the DNA such as methylation - tag, fragment, wash away untagged fragments, and then sequence what is left.