I have a transcription factor protein X and X has a co-activator protein Y. XY bind to the DNA and downstream expression of proteins occur. Now I block the activity of X through inhibitor but dont see any change in the binding of Y. When i check for downstream proteins, I observe low/reduced expression of downstream proteins. How is that possible if the XY binds normally? What could be the reasons? I am assuming there's change in the binding pattern of Y? Or the XY complex bind to the DNA in different pattern?
Hi,
To access this question, you might do the ChIP-seq on X & Y on untreated sample, then do the same on the sample after inhibition. If your inhibitor is blocking the binding of X, your X-peak on the enhancer of your protein of interest will disappear, while the peak Y will still be there. If the inhibitor is blocking the activity, but not the binding, the X-peak will still be present. With Y-antibody ChIP you may also check if the Y-binding pattern changed after the X-inhibition.
Best,
Michail
and also think that your X-Y model is very likely much tooo simple:
1) only a two component system?
2) what about other factors replacing the X-Y complex?
3) what about other pathways compensating for your pathway involving X-Y ???
I know questions over questions, hard to answer, but perhaps worthwhile doing...
Tobias Aurelius Knoch You are right! Indeed. I was searching for the whole interaction pathway and read articles to find that one of the other protein was competing for the X.
Thank you everyone for adding your views.
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