Reviewer 1's Review

“Below I describe a number of issues that should be addressed:
1) The authors seem to detect two classes of small RNA directed against suffix: siRNAs and piRNAs. In the text describing the dicer experiment, the authors seem to take the result as evidence that the suffix siRNAs are dicer dependent. However , they do not not show this, as they show no control of wt ovary: here the siRNAs should be visible if there experiment is to mean anything with regard to the suffix siRNAs. They ignore at that stage of the manuscript that there is a population of bigger small RNAs: of course these could be rasiRNAs, as described by a number of labs before. Indeed, these are Dicer1 and Dicer 2 independent (Vagin et al, Science, 2006). The authors only briefly touch upon this in the discussion, while I think that this is actually one of the more interesting results described in this manuscript.
2) On page 11 the authors discuss the dicer dependence of the detected small RNAs in pupae. The dicer experiment was only done in ovary, so nothing can be said about the dicer dependence in pupae.
3) The "RNAi products" described in fig 7c may just as well be aspecific degradation products. There is no indication for specificity (eg are these products RNAi dependant?) So the authors should show that when for example dAgo2 is depleted, these products will disappear (or at least their abundance should go down).
4) the RNA localisation of F-element RNA in the oocyte should be discussed. This seems to colocalize with bicoid mRNA. Any idea why that should be?
5) The notion the mRNAs become susceptible to RNAi when a sequence is present for which there are siRNAs is an open door. So of course, when a mRNA carries suffix sequences it will be silenced by RNAi (endogenous or exogenous) against suffix.”

N.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.