My cell line has endogenous expression of Mol.A and B. But, when I overexpress A, I want to know whether it is altering endogenous expression of B or not. What experiment should I conduct to resolve this?
Hello, you could maybe try to compare/quantify the amount expressed using a Western Blot. Will not give you very accurate numbers but might be worth a quick go.
Beside Western blots and q-PCR, you can try confocal microscopy imaging for proteins' localization, co-localization, appearance and intensity signals. It can be done both on a single-or multiple-cell levels. They also give nice pictures for publications :)
Firstly, you should investigate wherether there are interaction beteween A and B through BIFC or yeast two-hybrid system. Secondly, you identify if A bind the promoter of B. or, A do not directly bind the promoter, but through other genes. last, you can test the expression of the A and B through qPCR.
You could also use an siRNA for A and analyze if B diminishes.
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