The vast amount of sequence data now available has increased the demand for large-scale functional assays. Here, we propose to investigate the use of RNA-mediated interference (RNAi) in performing genome-wide surveys for the effects of gene loss in C. elegans. RNAi effects are currently too weak to produce reliable null allele phenocopies. The goals of this proposal are 1) to identify RNAi hypersensitive mutants and 2) to test the feasibility of using these mutants in generalized screening. Our first screen will be for mutations that increase the level of RNAi-mediated silencing of GFP expression from nerve and muscle-specific promoters. The second screen will rely on using RNAi to rescue worms from dauer development. We will also examine the sensitivity of the isolated mutant strains to dsRNAs for target genes expressed in a range of tissues. Phase II feasibility will depend on finding at least one mutation that increases dsRNA-dependent silencing of more than one gene with a five-fold or greater increase in penetrance. Phase II work will include cloning and further characterization of the RNAi hypersensitive mutants and construction of an RNAi array. PROPOSED COMMERCIAL APPLICATION: Implementation of RNAi arrays for function-based genome-wide screens will require the development of dsRNA arrays, materials for producing RNAi hypersensitivity in any strain background, protocols and materials for the screens, and informatics for handling the data from these tests. Eon will develop, manufacture and distribute ready-to-use dsRNA arrays and the associated infrastructure. Eon and its commercial partners will also employ these arrays in-house for functional genomics programs.
