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Functional genomic analysis of C. elegans chromosome I by systematic RNA interference

Author

Listed:
  • Andrew G. Fraser

    (Wellcome/CRC Institute, University of Cambridge)

  • Ravi S. Kamath

    (Wellcome/CRC Institute, University of Cambridge)

  • Peder Zipperlen

    (Wellcome/CRC Institute, University of Cambridge)

  • Maruxa Martinez-Campos

    (Wellcome/CRC Institute, University of Cambridge)

  • Marc Sohrmann

    (The Sanger Centre, Wellcome Trust Genome Campus)

  • Julie Ahringer

    (Wellcome/CRC Institute, University of Cambridge)

Abstract

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.

Suggested Citation

  • Andrew G. Fraser & Ravi S. Kamath & Peder Zipperlen & Maruxa Martinez-Campos & Marc Sohrmann & Julie Ahringer, 2000. "Functional genomic analysis of C. elegans chromosome I by systematic RNA interference," Nature, Nature, vol. 408(6810), pages 325-330, November.
    • Handle: RePEc:nat:nature:v:408:y:2000:i:6810:d:10.1038_35042517
    DOI: 10.1038/35042517
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    Cited by:

    1. Sihai Yang & Xian-Hua Han & Yen-Wei Chen, 2023. "GND-PCA Method for Identification of Gene Functions Involved in Asymmetric Division of C. elegans," Mathematics, MDPI, vol. 11(9), pages 1-15, April.
    2. How to Reconstruct a Large Genetic Network from n Gene Perturbations in Fewer than n2 Easy Steps, 2001. "How to Reconstruct a Large Genetic Network from," Working Papers 01-09-047, Santa Fe Institute.
    3. Arles Urrutia & Víctor A García-Angulo & Andrés Fuentes & Mauricio Caneo & Marcela Legüe & Sebastián Urquiza & Scarlett E Delgado & Juan Ugalde & Paula Burdisso & Andrea Calixto, 2020. "Bacterially produced metabolites protect C. elegans neurons from degeneration," PLOS Biology, Public Library of Science, vol. 18(3), pages 1-31, March.
    4. Yan-Ping Zhang & Wen-Hong Zhang & Pan Zhang & Qi Li & Yue Sun & Jia-Wen Wang & Shaobing O. Zhang & Tao Cai & Cheng Zhan & Meng-Qiu Dong, 2022. "Intestine-specific removal of DAF-2 nearly doubles lifespan in Caenorhabditis elegans with little fitness cost," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Aqilah Amran & Lara Pigatto & Johanna Farley & Rasoul Godini & Roger Pocock & Sandeep Gopal, 2024. "The matrisome landscape controlling in vivo germ cell fates," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    6. Samim Sharifi & Prerana Chaudhari & Asya Martirosyan & Alexander Otto Eberhardt & Finja Witt & André Gollowitzer & Lisa Lange & Yvonne Woitzat & Eberechukwu Maryann Okoli & Huahui Li & Norman Rahnis &, 2024. "Reducing the metabolic burden of rRNA synthesis promotes healthy longevity in Caenorhabditis elegans," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    7. Hope Dang & Raul Castro-Portuguez & Luis Espejo & Grant Backer & Samuel Freitas & Erica Spence & Jeremy Meyers & Karissa Shuck & Emily A. Gardea & Leah M. Chang & Jonah Balsa & Niall Thorns & Caroline, 2023. "On the benefits of the tryptophan metabolite 3-hydroxyanthranilic acid in Caenorhabditis elegans and mouse aging," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Changnan Wang & Bingying Wang & Taruna Pandey & Yong Long & Jianxiu Zhang & Fiona Oh & Jessica Sima & Ruyin Guo & Yun Liu & Chao Zhang & Shaeri Mukherjee & Michael Bassik & Weichun Lin & Huichao Deng , 2022. "A conserved megaprotein-based molecular bridge critical for lipid trafficking and cold resilience," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    9. Wei Cao & Qi Fan & Gemmarie Amparado & Dean Begic & Rasoul Godini & Sandeep Gopal & Roger Pocock, 2024. "A nucleic acid binding protein map of germline regulation in Caenorhabditis elegans," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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