DNA-binding activator / responder elements which are part of a 2 component transcriptional regulation system are a method of gene regulation.
I am assuming that the DNA-binding activator proteins fall under the domain of a prokaryotic transcription factor (please correct me if I am wrong). However, I am confused on where these particular protein (DNA-binding activators) bind to on the DNA. Do these protein bind right beside (or a little upstream) from RNA polymerase protein, or do they bind to enhancer regions which are far apart from the start site(however, I believe that bacteria do not have enhancer regions).
If I where to design primers to isolate the promoter region with the DNA-binding activator, how far upstream from the start codon should the primers isolate to insure that the DNA-binding site for this protein is present?
Thanks,
ADAM
I am not sure either that bacteria have enhancer regions. In this case, the binding site of your activator protein should be in the promoter region of your activated / responder gene, i.e. in the upstream 0-5 kb (might be muck less than 5 kb in bacteria). I don't know what you want to do with primers and isolating the binding region, clone it? If you have an antibody against your TF (activator), you can perform ChIP-seq, then you'll have all the binding sites of your activator genome-wide. If you assume that your activator only activates one or few genes, then you can design tiling oligos on the whole promoter sequence and do ChIP-qPCR to identify the region bound by your activator. ChIP is the only method to be sure that your activator is binding DNA and where. Good luck!
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