RNA interference can target pre-mRNA: Consequences for gene expression in a Caenorhabditis elegans operon

In nematodes, flies, trypanosomes, and planarians, introduction of double-s tranded RNA results in sequence-specific inactivation of gene function, a p rocess termed RNA interference (RNAi). We demonstrate that RNAi against the Caenorhabditis elegans gene lir-1, which is part of the lir-1/lin-26 opero n, induced phenotypes very different from a newly isolated lir-1 null mutat ion. Specifically, lir-1(RNAi) induced embryonic lethality reminiscent of m oderately strong lin-26 alleles, whereas the lir-1 null mutant was viable. We show that the lir-1 (RNAi) phenotypes resulted from a severe loss of lin -26 gene expression. In addition, we found that RNAi directed against lir-1 or lin-26 introns induced similar phenotypes, so we conclude that lir-1(RN Ai) targets the lir-1/lin-26 pre-mRNA. This provides direct evidence that R NA interference can prevent gene expression by targeting nuclear transcript s. Our results highlight that caution may be necessary when interpreting RN A interference without the benefit of mutant alleles.