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Systematic functional analysis of the Caenorhabditis elegans genome using RNAi

Abstract

A principal challenge currently facing biologists is how to connect the complete DNA sequence of an organism to its development and behaviour. Large-scale targeted-deletions have been successful in defining gene functions in the single-celled yeast Saccharomyces cerevisiae, but comparable analyses have yet to be performed in an animal. Here we describe the use of RNA interference to inhibit the function of 86% of the 19,427 predicted genes of C. elegans. We identified mutant phenotypes for 1,722 genes, about two-thirds of which were not previously associated with a phenotype. We find that genes of similar functions are clustered in distinct, multi-megabase regions of individual chromosomes; genes in these regions tend to share transcriptional profiles. Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans.

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Figure 1: Summary of RNAi phenotypes.
Figure 2: Relative enrichment of Nonv, Vpep and X chromosome genes for different functional classes.
Figure 3: Conservation of domains in genes with different RNAi phenotypes.
Figure 4: Distribution of RNAi phenotypes across the C. elegans chromosomes.

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Acknowledgements

We thank T. Blumenthal, B. Kelly, S. Kim and V. Reinke for discussions and sharing data before publication; B. Shumacher for assistance early in the project; and G. Chalklin, J. Peacock, J. Abbott and K. Rossiter for preparing the media. R.S.K. was supported by a Howard Hughes Medical Institute Predoctoral Fellowship; A.G.F. by a US Army Breast Cancer Research Fellowship; Y.D., R.D., M.G., D.P.W. and P.Z. by the Wellcome Trust; G.P. by the Canadian Institute of Health Research and the Wellcome Trust; A.K. by the European Molecular Biology Laboratory; N.L.B. by the European Molecular Biology Organization; S.M. by the Centro de Investigacion del Cancer; M.S. by a Swiss National Science Foundation fellowship and J.A. by a Wellcome Trust Senior Research Fellowship.

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Correspondence to Julie Ahringer.

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Kamath, R., Fraser, A., Dong, Y. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–237 (2003). https://doi.org/10.1038/nature01278

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