Large-scale screening for targeted knockouts in the caenorhabditis elegans genome

Robert Barstead, Gary Moulder, Beth Cobb, Stephen Frazee, Diane Henthorn, Jeff Holmes, Daniela Jerebie, Martin Landsdale, Jamie Osborn, Cherilyn Pritchett, James Robertson, John Rummage, Ed Stokes, Malani Vishwanathan, Shohei Mitani, Keiko Gengyo-Ando, Osamu Funatsu, Sayaka Hori, Rieko Imae, Eriko Kage-NakadaiHiroyuki Kobuna, Etsuko Machiyama, Tomoko Motohashi, Muneyoshi Otori, Yuji Suehiro, Sawako Yoshina, Donald G. Moerman, Mark Edgley, Ryan Adair, BJ Allan, Vinci Au, Iasha Chaudhry, Rene Cheung, Owen Dadivas, Simon Eng, Lisa Fernando, Angela Fisher, Stephane Flibotte, Erin Gilchrist, Allison Hay, Peter Huang, Rebecca Worsley Hunt, Christine Kwitkowski, Joanne Lau, Norris Lee, Lucy Liu, Adam Lorch, Candy Luck, Jason Maydan, Sheldon McKay, Angela Miller, Greg Mullen, Candice Navaroli, Sarah Neil, Rebecca Hunt-Newbury, Mikhaela Partridge, Jaryn Perkins, Anna Rankin, Greta Raymant, Nadereh Rezania, Alexandra Rogula, Bin Shen, Greg Stegeman, Angela Tardif, Jon Taylor, Mariana Veiga, Tina Wang, Rick Zapf

Research output: Contribution to journalArticle

100 Citations (Scopus)

Abstract

The nematode Caenorhabditis elegans is a powerful model system to study contemporary biological problems. This system would be even more useful if we had mutations in all the genes of this multicellular metazoan. The combined efforts of the C. elegans Deletion Mutant Consortium and individuals within the worm community are moving us ever closer to this goal. At present, of the 20,377 protein-coding genes in this organism, 6764 genes with associated molecular lesions are either deletions or null mutations (WormBase WS220). Our three laboratories have contributed the majority of mutated genes, 6841 mutations in 6013 genes. The principal method we used to detect deletion mutations in the nematode utilizes polymerase chain reaction (PCR). More recently, we have used array comparative genome hybridization (aCGH) to detect deletions across the entire coding part of the genome and massively parallel short-read sequencing to identify nonsense, splicing, and missense defects in open reading frames. As deletion strains can be frozen and then thawed when needed, these strains will be an enduring community resource. Our combined molecular screening strategies have improved the overall throughput of our gene-knockout facilities and have broadened the types of mutations that we and others can identify. These multiple strategies should enable us to eventually identify a mutation in every gene in this multicellular organism. This knowledge will usher in a new age of metazoan genetics in which the contribution to any biological process can be assessed for all genes.

Original languageEnglish
Pages (from-to)1415-1425
Number of pages11
JournalG3: Genes, Genomes, Genetics
Volume2
Issue number11
DOIs
Publication statusPublished - 2012 Nov
Externally publishedYes

Keywords

  • Deletion
  • Families
  • Genomics
  • Knockouts
  • Multi-gene
  • Mutations

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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  • Cite this

    Barstead, R., Moulder, G., Cobb, B., Frazee, S., Henthorn, D., Holmes, J., Jerebie, D., Landsdale, M., Osborn, J., Pritchett, C., Robertson, J., Rummage, J., Stokes, E., Vishwanathan, M., Mitani, S., Gengyo-Ando, K., Funatsu, O., Hori, S., Imae, R., ... Zapf, R. (2012). Large-scale screening for targeted knockouts in the caenorhabditis elegans genome. G3: Genes, Genomes, Genetics, 2(11), 1415-1425. https://doi.org/10.1534/g3.112.003830