Title: Negative regulation of RNA interference in Caenorhabditis elegans
Description: RNA interference (RNAi) was formally described in Caenorhabditis elegans ( C. elegans ) as the process by which long double-stranded RNA (dsRNA) post-transcriptionally induces potent silencing of an endogenous gene that is homologous to the trigger. We now understand RNAi-related silencing mechanisms to function in endogenous processes throughout phylogeny. The inability of RNAi to target specific genes and tissues has raised questions about the molecular and evolutionary basis for these limitations. This dissertation describes an investigation into genes whose wild-type function is to restrict the potency of exogenous RNAi in C. elegans. Genetically screening for mutants displaying an enhanced response to exogenous dsRNAs, we isolated mutations in genes encoding known interactors of the central player of small-RNA-mediated pathways--the endoribonuclease Dicer--which all exhibit pleiotropic phenotypes such as sterility. We focused on non-sterile mutants from the screen, with the expectation that they would outline a novel mechanism for the negative regulation of RNAi. The non-sterile mutants define at least five genes.

We isolated mutations in two adjacent, divergently-transcribed open reading frames that fail to complement. Using RT-PCR and expressed sequence tag analysis, we show that eri-6 and eri-7 produce separate pre-mRNAs that are remarkably trans -spliced to form a functional hybrid mRNA, eri-6/7, that is orthologous to the mRNA encoded by a single gene in several wild isolates of C. elegans and in the related nematode C. briggsae. This is the first example of such noncanonical trans -spicing in C. elegans and only the third in biology. Southern blotting and PCR confirm that a ∼930-basepair (bp) direct repeat, containing within it a 25-bp inverted repeat, that flanks the eri-6 gene does not mediate genomic rearrangement to create a fused eri-6/7 gene, but has likely mediated rearrangement throughout evolution, and is required for rescue of eri-6/7 (-) mutant phenotypes. Adenosine to inosine editing within the eri-7 mRNA 5' untranslated region points toward a double-stranded pre-mRNA intermediate, mediated by the ∼930-nucleotide direct repeat; suggestive of a feedback loop whereby transcripts of a gene regulating RNAi are, in turn, regulated by RNAi. eri-6/7 encodes a superfamily I helicase that negatively regulates exogenous RNAi, perhaps via its positive role in the endogenous RNAi pathway, as determined by Northern blotting.