The iesRNA pathway is a small RNA pathway involved in the excision of internal eliminated sequences (IESs) during Paramecium development. iesRNAs appear late in development, after IES excision (both scnRNA dependent and independent) has been initiated. Evidence suggests that iesRNAs are formed directly from excised IESs, but the mechanism for this putative transcription is not clear. Many iesRNA-affected IESs are only 27 bp long, and iesRNAs bind perfectly to the ends of the IESs. The transcription of a Dicer cleavage substrate from such a short DNA template seems unlikely.
We wish to investigate the iesRNA pathway in more detail, via a number of approaches. We are examining the robustness of iesRNA-guided IES excision via the introduction of artificial iesRNAs, and by inducing the removal of both endogenous and cryptic IESs via the introduction of IES-like dsDNAs. Of particular interest are iesRNA precursors, the identity of which has proven elusive. We investigate the possibility of IES concatamer formation, which would provide a mechanistic explanation for the formation of iesRNAs from excised IESs.