While in literature there is no report, to my knowledge, to silence one transgene in Arabidopsis (under 35S promoter) using another transgene (artificial microRNA, under inducible system). I think 35S promoter is too strong to be silenced by pINDEX3 vector (Ouwerkerk et al. 2001) driven amiR. Can inducible promoter driven amiR silence an overexpressed transgene, like GFP? amIRs when driven by 35S promoter can silence many endogenous genes, but here the case is opposite, the targeted gene is strongly expressed while targeting amiR is inducibly produced.
To my understanding, over expression is a transcriptional process while gene silencing using miRNA is a post transcriptional process. Therefore, if the miRNA is able to activate the silencing mechanism (i.e. the dicers), then it should be possible to wipe out the over-expressed RNA target produced by strong promoter.
On the other hand, since over expression produce such a large number of transcript, it may be possible there is a "time delay" before they get wipe out. If we associate this with the phenotype changes, the transgenic plants way still be phenotypically a wild type at the early stage of miRNA expression and gradually changed intosilenced phenotype as the silencing progressed.
Since you have inducible promoter for your miRNA, then the silencing will only happen when the inducible promoter is activated (i.e. in a tissue specific or inducer specific manner, depending on the type of the inducible promoter).
Good luck...
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