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      High-throughput reverse genetics: RNAi screens in Caenorhabditis elegans

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      Author(s): 1 ,
      Publication date (Electronic):
      Journal: Genome Biology
      Publisher: BioMed Central

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          Abstract

          Two recent chromosome-wide screens for phenotypes caused by RNA-mediated interference (RNAi) in Caenorhabditis elegans have increased our understanding of essential genes in nematodes. These papers represent a major advance in functional genomics.

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          Specific interference by ingested dsRNA.

          L Timmons, A Fire (1998)
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            Functional genomic analysis of C. elegans chromosome I by systematic RNA interference.

            A. Fraser, R. S. Kamath, P Zipperlen … (2000)
            Complete genomic sequence is known for two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and it will soon be known for humans. However, biological function has been assigned to only a small proportion of the predicted genes in any animal. Here we have used RNA-mediated interference (RNAi) to target nearly 90% of predicted genes on C. elegans chromosome I by feeding worms with bacteria that express double-stranded RNA. We have assigned function to 13.9% of the genes analysed, increasing the number of sequenced genes with known phenotypes on chromosome I from 70 to 378. Although most genes with sterile or embryonic lethal RNAi phenotypes are involved in basal cell metabolism, many genes giving post-embryonic phenotypes have conserved sequences but unknown function. In addition, conserved genes are significantly more likely to have an RNAi phenotype than are genes with no conservation. We have constructed a reusable library of bacterial clones that will permit unlimited RNAi screens in the future; this should help develop a more complete view of the relationships between the genome, gene function and the environment.
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              Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.

              P Gönczy, C Echeverri, K. Oegema … (2000)
              Genome sequencing projects generate a wealth of information; however, the ultimate goal of such projects is to accelerate the identification of the biological function of genes. This creates a need for comprehensive studies to fill the gap between sequence and function. Here we report the results of a functional genomic screen to identify genes required for cell division in Caenorhabditis elegans. We inhibited the expression of approximately 96% of the approximately 2,300 predicted open reading frames on chromosome III using RNA-mediated interference (RNAi). By using an in vivo time-lapse differential interference contrast microscopy assay, we identified 133 genes (approximately 6%) necessary for distinct cellular processes in early embryos. Our results indicate that these genes represent most of the genes on chromosome III that are required for proper cell division in C. elegans embryos. The complete data set, including sample time-lapse recordings, has been deposited in an open access database. We found that approximately 47% of the genes associated with a differential interference contrast phenotype have clear orthologues in other eukaryotes, indicating that this screen provides putative gene functions for other species as well.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2001
                Publication date (Electronic): 31 January 2001
                Volume: 2
                Issue: 2
                Pages: reviews1005.1-reviews1005.3
                Affiliations
                [1 ]Howard Hughes Medical Institute, Departments of Anatomy and of Biochemistry and Biophysics, The University of California, San Francisco, CA 94143, USA. E-mail: cori@itsa.ucsf.edu
                Article
                Publisher ID: gb-2001-2-2-reviews1005
                PMC ID: 138903
                PubMed ID: 11182891
                SO-VID: 67ea0a60-9289-48c0-b66c-b117a488b66d
                Copyright © Copyright © 2001 BioMed Central Ltd
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                Subject: Minireview

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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