Co-immunoprecipitation in Chip-Seq

Question

[Opt]

Chip-Seq works by immunoprecipitating the relevant protein via an antibody and thus extracting any DNA that protein may be bound to. However wouldn't this also extract DNA that is bound to proteins that form complexes with the protein in question?

(I understand that sonication which is often used to break DNA could also affect the protein complex but would the effect of that be enough?)

Answer 1

[Devon Ryan]

Yes, cross linking can cause you to pull down indirect (or fleeting) interaction partner. Often people try to minimize the cross linking (or simply not do it) to avoid this.

[Opt]

How would you preserve the binding between the DNA and the protein without cross-linking?

[Devon Ryan]

You either have to be very gentle or come up with clever methods. See "organic Chip-Seq" as an example.