Hi,
I´m investigating the homo- and heterodimer formation of two proteins (A & B). For further results, I would like to perform experiments to understand where the homodimeric complexes (A-A, B-B) bind to DNA in comparison to the heterodimer (A-B). I think that this question can not be answered by performing traditional ChIP-Seq analysis with anti-A and anti-B-antibodies.
Does anybody know if there is an appropriate method for answering this question?
Thank you!
Dear Nils,
I think ChIP-seq with anti-A and anti-B antibodies should give you some good information on their binding sites. Theoretically, the overlapped sites would be from binding of the heterodimer A-B, while sites specific for A or B should come from binding of A-A or B-B homodimers. Another feature of DNA sites for binding protein homodimers is that they often have some level of sequence symmetry. Hope this would help.
One thing you can do is DNase footprinting matched with a motif analysis depend on if they have different binding motifs or not. You can also do a sequential ChIP experiment with Anti A and then Anti B. This should give you the regions were both are bound. Then you can do a ChIP with just Anti A and/or just Anti B to find overlapping and unique sites.
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