Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi

Abstract

Genome-wide analysis of gene function is essential for the post-genome era, and development of efficient and economical technology suitable for it has been in demand. Here we report a large-scale inactivation of the expressed genes in the nematode Caenorhabditis elegans. For this purpose, we have established a high-throughput “RNAi-by-soaking” methodology by modifying the conventional RNAi method [ 1 Tabara H. Grishok A. Mello C.C. RNAi in C. eleganssoaking in the genome sequence. Science. 1998; 282 : 430-431 Crossref PubMed Scopus (511) Google Scholar , 2 Fire A. Xu S. Montgomery M.K. Kostas S.A. Driver S.E. Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998; 391 : 806-811 Crossref PubMed Scopus (11425) Google Scholar ]. A set of tag-sequenced, nonredundant cDNAs corresponding to approximately 10,000 genes [ 3 Fields S. Kohara Y. Lockhart D.J. Functional genomics. Proc Natl Acad Sci USA. 1999; 96 : 8825-8826 Crossref PubMed Scopus (64) Google Scholar ] (representing half of the predicted genes [ 4 The C. elegans Sequencing Consortium Genome sequence of the nematode C. elegansa platform for investigating biology. Science. 1998; 282 : 2012-2018 Crossref PubMed Scopus (3548) Google Scholar ]) was used for the systematic RNAi analysis. We have processed approximately 2500 genes to date. In development, 27% of them showed detectable phenotypes, such as embryonic lethality, post-embryonic lethality, sterility, and morphological abnormality. Of these, we analyzed the phenotypes of F1 sterility in detail, and we have identified 24 genes that might play important roles in germline development. Combined with the ongoing analysis of expression patterns of these cDNAs [ 3 Fields S. Kohara Y. Lockhart D.J. Functional genomics. Proc Natl Acad Sci USA. 1999; 96 : 8825-8826 Crossref PubMed Scopus (64) Google Scholar , 5 Tabara H. Motohashi T. Kohara Y. A multi-well version of in situ hybridization on whole mount embryos of Caenorhabditis elegans. Nucleic Acids Res. 1996; 24 : 2119-2124 Crossref PubMed Scopus (92) Google Scholar ], the functional information obtained in this work will provide a starting point for the further analysis of each gene. Another finding from this screening is that the incidence of essential genes is significantly lower in the X chromosome than in the autosomes.