Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions

By F. Simmer, C. Moorman, A. M. van der Linden, E. Kuijk, Peter V. E. van den Berghe, R. Kamath, Andrew G. Fraser, J. Ahringer, Ronald H. A. Plasterk. PLoS Biology, 2003

681 citations recorded by the source corpus.

RNA-mediated interference (RNAi) is a method to inhibit gene function by introduction of double-stranded RNA (dsRNA). Recently, an RNAi library was constructed that consists of bacterial clones expressing dsRNA, corresponding to nearly 90% of the 19,427 predicted genes of C. elegans. Feeding of this RNAi library to the standard wild-type laboratory strain Bristol N2 detected phenotypes for approximately 10% of the corresponding genes. To increase the number of genes for which a loss-of-function phenotype can be detected, we undertook a genome-wide RNAi screen using the rrf-3 mutant strain, which we found to be hypersensitive to RNAi. Feeding of the RNAi library to rrf-3 mutants resulted in additional loss-of-function phenotypes for 393 genes, increasing the number of genes with a phenotype by 23%. These additional phenotypes are distributed over different phenotypic classes. We also studied interexperimental variability in RNAi results and found persistent levels of false negatives. In addition, we used the RNAi phenotypes obtained with the genome-wide screens to systematically clone seven existing genetic mutants with visible phenotypes. The genome-wide RNAi screen using rrf-3 significantly increased the functional data on the C. elegans genome. The resulting dataset will be valuable in conjunction with other functional genomics approaches, as well as in other model organisms.

Subfields: Aging, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/be412b82377de1ffc778dd85dbfef4710d37cdb5

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Citations in the corpus

Dangerous liaisons: The symbiosis of entomopathogenic nematodes and bacteria (2006, background): “This is especially true when the procedure is performed in a mutant background such as the hypersensitive rrf-3: synthetic eVects (phenotypes associated with loss of more than one gene’s function) must be considered (Simmer et al., 2003).”
Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. (2004, background): “2), as opposed to the L4 stage in previous screens (Kamath et al. 2003; Simmer et al. 2003).”
Caenorhabditis elegans: An Emerging Model in Biomedical and Environmental Toxicology (2008, background): “Strategies to improve RNAi efficiency, especially in neurons, were further developed (Esposito et al., 2007; Lee et al., 2006; Simmer et al. 2002, 2003; Tabara et al., 2002; Tops et al., 2005).”