Suppose a protein , i.e. Transcription factor, may be a regulator of a gene, in that case which one will be first experiment to further take ahead? Y1H, EMSA, ChIP, or in-vivo transactivation ?
hi :)
I would try ChIP first if i had access to the antibody of that TF protein, if not, i would have tried EMSA first. in case of positive result, i would have backed it up with a complementary supporting experiment.
I would try ChIP and EMSA both. ChIP can confirm in vivo interaction and EMSA can confirm direct interaction (since binding observed in ChIP can be indirect).
Depending on the TF you might not see initial binding in ChIP, if activation or expression of the TF depends on specific conditions.
Depending on how easy your model organism is to transform/transfect, an in vivo transactivation/repression test with expression of your TF and a promoter reporter plasmid might be the easiest step for an initial indication. Also you would directly have an idea whether your factor is an activator or repressor on that promoter. Anyways, I would recommend to use at least 2 of the suggested methods, just to be on the safe side.
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