RNAi affects mRNA or primary transcripts?

I’d like to know if when interferring with cDNA is the primmary transcript diced or only the mRNA?
Similarly, when interferring with genomic DNA is the primary transcript diced? The underlying question is whether the non-coding RNA’s located in introns are affected in any of the cases?


Our lab has a paper to deal with issue (http://www.nature.com/nature/journal/v465/n7301/full/nature09095.html).

After feeding RNAi targeting a mRNA, both the mRNA and pre-mRNA can be affected. However, we think that the pre-mRNA is likely modulated or processed by a different mechanism other than dicing.

We once tested to target only intron regions of 10 different lethal genes by feeding RNAi. None of these RNAi could induce a clear phenotype. One possible reason for this is that primary siRNA targeting intron regions are unable to be amplified in the cytoplasm by RdRP since there is no template there. NRDE-3 transports secondary siRNAs to the nucleus to induce nuclear RNAi.