Recently, I've got very strange phenomena.
When I transfected a plasmid expressing protein 'A' with a plasmid expressing reporter mRNAs, which harbor specific 3' UTR, into HeLa cells, over-expressed protein 'A' repressed expression of the reporter mRNAs. However, over-expressed protein 'A' increased level of the endogenous mRNAs.
I don't know what it happened in cells, and I don't understand why over-expressed protein 'A' have made different effects on both the reporter mRNAs and the endogenous counterpart.
Is there anyone who has ever experience such case?
I see at least 2 possible reasons of such event: (1) your protein A triggers additional promoter (2) cycle dependence of the reporter mRNA related protein in your cells.
This is an interesting question. Let's assume there is also an endogenous form of "protein A" and that it regulates the endogenous mRNAs. Thus, when you transfected in and overexpressed the reporter mRNAs, maybe you altered the stochiometry of the system such that you have bound up most of the endogenous protein A (as well as the transfected protein A) with the reporter mRNAs. The reporter mRNAs may have increased affinity to protein A and become downregulated/degraded. However, the endogenous mRNAs are no longer under negative regulation by the endogenous protein A, due to lower affinity to protein A, and you see increased levels of the endogenous mRNA.
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