Does that mean transcription factor binding to a specific DNA sequence? How can I identify the proteins and where they bind?
Hi,
To answer this question, you need to do ChIP sequencing. First, you crosslink your DNA and TFs, which sit on it (UV/PFA). Then you shear the DNA with ultrasound. Then you immunoprecipitate the sample with anti-TF antibody, ending with enrichment for the DNA-protein pieces, where your TF was bound. After that you de-crosslink the pieces and proceed with a normal DNA NGS library preparation. Finally, after sequencing, you will see an enrichment of reads in the areas, where your TF was bound.
Best,
Michail
I agree that ChIP-seq will give you a whole genome view of where your transcription factor binds, which can include both its direct binding to the DNA elements and indirect binding through other proteins. But you mentioned that your factor is a sequence-specific binding factor. Thus, you need to characterize and define the exact DNA sequence(s) for its binding. Then you can use the binding site DNA (can be synthetic DNA sequences) to perform affinity purification of your transcription factor. This is a well-established method by Dr. Robert Tjian many years ago.
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