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, 2]. A set of tag-sequenced, nonredundant cDNAs corresponding to approximately 10,000 genes [3] (representing half of the predicted genes [4]) 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, 5], 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.

RNA interference in parasitic nematodes of animals: a reality check?

“…Specific gene silencing by RNA interference (RNAi) was first described in Caenorhabditis elegans and has been developed in this organism for high-throughout functional genomics [1][2][3]. The ease with which RNAi can be used in C. elegans, together with the fact that the RNAi mechanism itself is conserved in a large number of organisms [4][5][6], has almost automatically led to the assumption that RNAi could be applied to related parasitic nematodes.…”

Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis

“…To identify cases in which C. elegans homologues of B. malayi clusters have been surveyed for phenotypes in C. elegans using RNAi, the clusters with significant matches to C. elegans proteins were cross-referenced to a list of 17913 C. elegans genes for which information on RNAi-induced phenotypes was available (http://www.wormbase.org/) [24,25]. All matches with similarities with E-values less than or equal to 1e − 20 were reported.…”

“…Table 1). One hundred and sixty-nine of these (80%) have been studied by RNAi in C. elegans [24,25] (Suppl. Table 2), of which, 57 (57/169; 34%) had a reproduction phenotype such as sterility.…”

“…Two hundred and thirty-seven of these genes (237/303; 79%) have been studied by RNAi in C. elegans (Suppl. Table 2) [24,25], and 112 (112/237; 47%) of them had phenotypes. Most phenotypes were related to embryogenesis or embryo development.…”

“…Several histones and histone-like proteins are differentially expressed between males and hermaphrodites in C. elegans [20]. RNAi of his-71, a histone-like gene with a female-enriched homologue in T. vitrinus, resulted in embryonic lethality in C. elegans [24,25].…”