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Systematic Functional Analysis of the Caenorhabditis Elegans Genome Using Rnai articles Systematic functional analysis of the Caenorhabditis elegans genome using RNAi Ravi S. Kamath*†, Andrew G. Fraser*†§, Yan Dong*, Gino Poulin*, Richard Durbin‡, Monica Gotta*§, Alexander Kanapink, Nathalie Le Bot*, Sergio Moreno*{, Marc Sohrmann‡§, David P. Welchman*, Peder Zipperlen* & Julie Ahringer* * Wellcome Trust/Cancer Research UK Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK ‡ Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK k EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK { Centro de Investigacion del Cancer, CSIC / Univ. Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain † These authors contributed equally to this work ........................................................................................................................................................................................................................... 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. The ability to inactivate a target gene transiently by RNAi1 has of the yeast Sec13p protein implicated in protein trafficking from greatly accelerated the analysis of loss-of-function phenotypes in C. the endoplasmic reticulum to the Golgi8) results in sterility, elegans and other organisms. Although several large-scale RNAi- embryonic lethality or uncoordinated movement. To simplify based screens have been used to study gene function in C. elegans2–4, subsequent genomic analyses, we defined three mutually exclusive in total only about a third of the predicted genes have been analysed phenotypic classes: the nonviable (Nonv) class, consisting of so far. Genome-wide RNAi analyses would not only provide a key embryonic or larval lethality or sterility (with or without associated resource for studying gene function in C. elegans but should also post-embryonic defects); the growth defects (Gro) class, consisting address important issues in functional genomics, such as the global of slow or arrested post-embryonic growth; and the viable post- organization of gene functions in a metazoan genome. In addition, embryonic phenotype (Vpep) class, consisting of defects in post- because more than half of the genes in C. elegans have a human embryonic development (for example, in movement or body shape) homologue, this kind of functional analysis in the worm should without any associated lethality or slowed growth. The RNAi provide insights into human gene function. phenotypes obtained on each chromosome are summarized in Fig. 1a, and a full list of phenotypes by gene is given in Supplemen- Analysis of gene functions by RNAi tary Tables 2–4; these data are available publicly on Wormbase (http://www.wormbase.org). Loss-of-function RNAi phenotypes can be generated efficiently by To determine the effectiveness of the screen, we assessed our feeding worms with bacteria expressing double-stranded RNA (dsRNA) that is homologous to a target gene5–7; we previously ability to identify correctly the known loss-of-function phenotypes used this method to screen roughly 87% of predicted genes on for previously studied loci. Overall, we obtained RNAi phenotypes chromosome I of C. elegans (ref. 2). To screen most of the predicted for 63.5% of 323 detectable loci; almost all of those detected (92%) genes in C. elegans by RNAi, we constructed a library of bacterial produced an RNAi phenotype similar to the known mutant strains, each capable of expressing dsRNA designed to correspond phenotype (see Supplementary Tables 5 and 6). More loci with a to a single gene. The library consists of 16,757 bacterial strains, Nonv phenotype were detected (77.9%) than loci with a Vpep which in total correspond to about 86% of the 19,427 current phenotype (42.2%). This difference is likely to arise because certain classes of gene with Vpep phenotypes (for example, neuronally predicted genes in C. elegans with similar coverage across each 7,9 chromosome (see Supplementary Tables 1 and 2). Using this library, expressed genes) are relatively resistant to RNAi and because Vpep we screened wild-type C. elegans hermaphrodites to identify genes phenotypes are more difficult to detect in this screen (Methods). for which RNAi reproducibly results in sterility, embryonic or larval Notably, the estimated rate of false-positive RNAi phenotypes is lethality, slow post-embryonic growth, or a post-embryonic defect very low (,1%; see Supplementary Fig. 1). In addition, our results (Methods). Such phenotypes were obtained with 1,722 bacterial correlate well with, and are as sensitive as, previous RNAi screens strains (10.3% of those analysed; Fig. 1a). (refs 3, 4, and Supplementary Fig. 1), indicating that RNAi data are Many strains gave rise to several reproducible RNAi phenotypes, highly reproducible irrespective of the method used. indicating that the targeted gene has many developmental roles. For The most common RNAi phenotype is embryonic lethality, example, RNAi against Y77E11A.13a (which encodes a homologue which was observed for 929 strains (5.5%). On the basis of our efficiency of detecting known embryonic lethal loci, this probably § Present addresses: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK (A.G.F.); includes over 70% of embryonic lethal genes and thus will be an Institute of Biochemistry ETH Hoenggerberg, 8093-Zurich, Switzerland (M.G., M.S.).. excellent starting point for more detailed analyses of the molecular NATURE | VOL 421 | 16 JANUARY 2003 | www.nature.com/nature © 2003 Nature Publishing Group 231 articles mechanisms of embryogenesis in C. elegans. Of the post-embryonic In addition, highly conserved genes that are present as a single copy phenotypes detected, the largest class was uncoordinated movement in the C. elegans genome are more than twice as likely to have an (Unc), which is typically indicative of a defect in the neuromuscular RNAi phenotype as those that are present in more than one copy system. We also defined an RNAi phenotype for 33 close homo- (31% versus 12%); this suggests that many recently duplicated logues (BlastP E values less than 1026) of human disease genes paralogues are at least partially functionally redundant or have (Table 1). Notably, many of these genes had Vpep phenotypes (50% specialized functions that are not detectable in this screen. versus 16% among all genes with a phenotype), consistent with their The highest cross-species conservation is seen among genes with embryonic viability in humans, and thus may be useful for estab- a Nonv RNAi phenotype, of which 52% have an orthologue in lishing C. elegans models of some human diseases. another eukaryote; this shows that similar essential basal cellular A small percentage of the bacterial strains were predicted to target machinery is common to all eukaryotes. Indeed, 51% of C. elegans more than one predicted gene. Before carrying out global analyses, orthologues of yeast essential genes11 have a Nonv RNAi phenotype. we removed these ambiguous data to generate a set of 1,528 clones Consistent with these findings, genes involved in the basic metabo- for which RNAi phenotypes could be attributed to a single predicted lism and maintenance of the cell are significantly enriched for gene (Methods). having a Nonv RNAi phenotype (Fig. 2a); by contrast, genes involved in more complex processes that are expanded in metazoa, Conservation and gene function such as signal transduction and transcriptional regulation, are We and others have previously found relationships between the enriched for Vpep phenotypes (Fig. 2b). RNAi phenotype of a gene and its degree of conservation and putative molecular function, using relatively small datasets2–4,10. Domain evolution and gene function Using the larger dataset obtained here, we have confirmed and Tostudy further the relationship between the sequence and function extended those conclusions. We find that C. elegans genes with an of a gene, we examined the domain composition of genes in each orthologue in another eukaryote are much more likely to have a phenotypic class. Of the 200 most abundant InterPro domains12 in detectable RNAi phenotype than all other genes (21% versus 6%). the C. elegans genome, 28 show significant (P , 0.05) associations Figure 1 Summary of RNAi phenotypes. a, Number of bacterial strains associated with classes) categories are mutually exclusive; however, many genes are associated with each RNAi phenotype. The Nonv (nonviable, including all phenotypic classes that result in several specific RNAi phenotypes. Phenotypic classes are described in Methods. The lethality or sterility), Gro
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