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

G3: Genes, Genomes, Genetics

Volumn 2, Issue 11, 2012, Pages 1415-1425

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

^a OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^b TOKYO WOMEN'S MEDICAL UNIVERSITY   (Japan)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Deletion; Families; Genomics; Knockouts; Multi gene; Mutations

Indexed keywords

ANIMALIA; CAENORHABDITIS ELEGANS; METAZOA;

ANIMAL; ARTICLE; CAENORHABDITIS ELEGANS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENE DELETION; GENE INACTIVATION; GENETIC SCREENING; GENETICS; GENOME; METHODOLOGY; POLYMERASE CHAIN REACTION;

ANIMALS; CAENORHABDITIS ELEGANS; COMPARATIVE GENOMIC HYBRIDIZATION; GENE DELETION; GENE KNOCKOUT TECHNIQUES; GENETIC TESTING; GENOME, HELMINTH; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84883153969     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.112.003830     Document Type: Article

References (62)

1. Altun, Z. F., B. Chen, Z. W. Wang, and D. H. Hall, 2009 High resolution map of Caenorhabditis elegans gap junction proteins. Dev. Dyn. 238: 1936-1950.
2. Ambros, V., 1997 Heterochronic genes, C. elegans II, Ed. 2, edited by D. L. Riddle, T. Blumenthal, B. J. Meyer, and J. R. Priess. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
3. Ambros, V., 2004 The functions of animal microRNAs. Nature 431: 350- 355.
4. Antebi, A., 2006 Nuclear hormone receptors in C. elegans (January 3, 2006), WormBook, ed. The C. elegans Research Community WormBook, doi/ 10.1895/wormbook.1.64.1, http://www.wormbook.org.
5. Ashrafi, K., F. Y. Chang, J. L. Watts, A. G. Fraser, R. S. Kamath et al., 2003 Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421: 268-272.
6. Avery, L., 1993 The genetics of feeding in Caenorhabditis elegans. Genetics 133: 897-917.
7. Bargmann, C. I., 1998 Neurobiology of the Caenorhabditis elegans genome. Science 282: 2028-2033.
8. Barstead, R., 2001 Genome-wide RNAi. Curr. Opin. Chem. Biol. 5: 63-66.
9. Barstead, R. J., and D. G. Moerman, 2006 C. elegans deletion mutant screening. Methods Mol. Biol. 351: 51-58.
10. Bessereau, J.-L., 2006 Transposons in C. elegans (January 18, 2006), WormBook, ed. The C. elegans Research Community WormBook, doi/ 10.1895/wormbook.1.70.1, http://www.wormbook.org.
11. Boch, J., 2011 TALEs of genome targeting. Nat. Biotechnol. 29: 135-136.
12. Bogdanove, A. J., and D. F. Voytas, 2011 TAL effectors: customizable proteins for DNA targeting. Science 333: 1843-1846.
13. Brenner, S., 1974 The genetics of Caenorhabditis elegans. Genetics 77: 71-94.
14. C. elegans Sequencing Consortium, 1998 Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
15. Cermak, T., E. L. Doyle,M. Christian, L.Wang, Y. Zhang et al., 2011 Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39: e82.
16. Chervitz, S. A., L. Aravind, G. Sherlock, C. A. Ball, E. V. Koonin et al., 1998 Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282: 2022-2028.
17. Edgley, M. L., D. L. Baillie, D. l. Riddle, and A. M. Rose, 1995 Genetic Balancers. Methods Cell Biol. 48: 147-184.
18. Edgley, M. L., A. D'Souza, G. Moulder, S. McKay, B. Shen et al., 2002 Improved detection of small deletions in complex pools of DNA. Nucleic Acids Res. 30: e52.
19. Fire, A., S. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver et al., 1998 Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
20. Flibotte, S., M. L. Edgley, I. Chaudry, J. Taylor, S. E. Neil et al., 2010 Wholegenome profiling of mutagenesis in Caenorhabditis elegans. Genetics 185: 431-441.
21. Fraser, A. G., R. S. Kamath, P. Zipperlen, M. Martinez-Campos, M. Sohrmann et al., 2000 Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408: 325-330.
22. Frøkjaer-Jensen, C., M. W. Davis, C. E. Hopkins, B. J. Newman, J. M. Thummel et al., 2008 Single-copy insertion of transgenes in Caenorhabditis elegans. Nat. Genet. 40: 1375-1383.
23. Frøkjaer-Jensen, C., M. W. Davis, G. Hollopeter, J. Taylor, T. W. Harris et al., 2010 Targeted gene deletions in C. elegans using transposon excision. Nat. Methods 7: 451-453.
24. Gengyo-Ando, K., and S.Mitani, 2000 Characterization of mutations induced by ethyl methanesulfonate, UV, and trimethylpsoralen in the nematode Caenorhabditis elegans. Biochem. Biophys. Res. Commun. 269: 64-69.
25. Giaever, G., A. M. Chu, L. Ni, C. Connelly, L. Riles et al., 2002 Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
26. Gönczy, P., C. Echeverri, K. Oegema, A. Coulson, S. J. Jones et al., 2000 Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408: 331-336.
27. Goodman, M. B., 2006 Mechanosensation (January 6, 2006), WormBook, ed. The C. elegans Research Community WormBook, doi/10.1895/ wormbook.1.62.1, http://www.wormbook.org.
28. Hutter, H., M. P. Ng, and N. Chen, 2009 GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes. BMC Genomics 10: 529.
29. Jansen, G., E. Hazendonk, K. L. Thijssen, and R. H. Plasterk, 1997 Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat. Genet. 17: 119-121.
30. Kamath, R. S., A. G. Fraser, Y. Dong, G. Poulin, R. Durbin et al., 2003 Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231-237.
31. Kaufman, E. J., and E. A. Miska, 2010 The microRNAs of Caenorhabditis elegans. Semin. Cell Dev. Biol. 21: 728-737.
32. Knight, S. W., and B. L. Bass, 2001 A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293: 2269-2271.
33. Krause, M., M. Wild, B. Rosenzweig, and D. Hirsh, 1989 Wild-type and mutant actin genes in Caenorhabditis elegans. J. Mol. Biol. 208: 381-392.
34. Li, C., and K. Kim, 2008 Neuropeptides (September 25, 2008), WormBook, ed. The C. elegans Research Community WormBook, doi/10.1895/wormbook.1. 142.1, http://www.wormbook.org.
35. Li, T., S. Huang, W. Z. Jiang, D. Wright, M. H. Spalding et al., 2011 TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res. 39: 359-372.
36. Liu, L. X., J. M. Spoerke, E. L. Mulligan, J. Chen, B. Reardon et al., 1999 High-throughput isolation of Caenorhabditis elegans deletion mutants. Genome Res. 9: 859-867.
37. MacQueen, A. J., J. J. Baggett, N. Perumov, R. A. Bauer, T. Januszewski et al., 2005 ACT-5 is an essential Caenorhabditis elegans actin required for intestinal microvilli formation. Mol. Biol. Cell 16: 3247-3259.
38. Manning, G., 2005 Genomic overview of protein kinases (December 13, 2005), WormBook, ed. The C. elegans Research Community Wormbook, doi/10.1895/wormbook.1.60.1, http://www.wormbook.org.
39. Mano, I., and M. Driscoll, 1999 DEG/ENaC channels: a touchy superfamily that watches its salt. Bioessays 21: 568-578.
40. Maydan, J. S., S. Flibotte, M. L. Edgley, J. Lau, R. R. Selzer et al., 2007 Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Res. 17: 337-347.
41. Maydan, J. S., A. Lorch, M. L. Edgley, S. Flibotte, and D. G. Moerman, 2010 Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics 11: 62.
42. McKay, S. J., and S. J. M. Jones, 2002 Bioinformatics 18: 1538-1539.
43. Miska, E. A., E. Alvarez-Saavedra, A. L. Abbott, N. C. Lau, A. B. Hellman et al., 2007 Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet. 3: e215.
44. Moerman, D. G., and R. J. Barstead, 2008 Towards a mutation in every gene in Caenorhabditis elegans. Brief. Funct. Genomics Proteomics 7: 195-203.
45. O'Brien, K. P., M. Remm, and E. L. Sonnhammer, 2005 Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33: D476-D480.
46. Pettitt, J., 2005 The cadherin superfamily (December 29, 2005), WormBook, ed. The C. elegans Research Community WormBook, doi/10.1895/wormbook. 1.50.1, http://www.wormbook.org.
47. Phelan, P., and T. A. Starich, 2001 Innexins get into the gap. Bioessays 23: 388-396.
48. Reece-Hoyes, J. S., B. Deplancke, J. Shingles, C. A. Grove, I. A. Hope et al., 2005 A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biol. 6: R110.
49. Robert, V., and J. Bessereau, 2007 Targeted engineering of the Caenorhabditis elegans genome following Mos1-triggered chromosome breaks. EMBO J. 26: 170-183.
50. Robertson, H. M., and J. H. Thomas, 2006 The putative chemoreceptor families of C. elegans (January 6, 2006), WormBook, ed. The C. elegans Research Community WormBook, doi/10.1895/wormbook.1.66.1, http:// www.wormbook.org.
51. Salkoff, L., A. D. Wei, B. Baban, A. Butler, G. Fawcett et al., 2005 Potassium channels in C. elegans (December 30, 2005), WormBook, ed. The C. elegans Research Community WormBook, doi/10.1895/wormbook.1.42.1, http://www.wormbook.org.
52. Sarin, S., S. Prabhu, M. M. O'Meara, I. Pe'er, andO.Hobert, 2008 Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat. Methods 5: 865-867.
53. Sulston, J. E., and H. R. Horvitz, 1977 Post-embryonic cell lineages of the nematode Caenorhabditis elegans. Dev. Biol. 56: 11-56.
54. Sulston, J. E., E. Schierenberg, J. G. White, and J. N. Thomson, 1983 The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100: 64-119.
55. Urnov, F. D., E. J. Rebar, M. C. Holmes, H. S. Zhang, and P. D. Gregory, 2010 Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 11: 636-646.
56. Wei, A., A. Yuan, G. Fawcett, A. Butler, T. Davis et al., 2002 Efficient isolation of targeted Caenorhabditis elegans deletion strains using highly thermostable restriction endonucleases and PCR. Nucleic Acids Res. 30: e110.
57. Weirauch, M. T., and T. R. Hughes, 2011 A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Subcell. Biochem. 52: 25-73.
58. White, J. G., E. Southgate, J. N. Thomson, and S. Brenner, 1976 The structure of the ventral nerve cord of Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 275: 327-348.
59. Willis, J. H., E. Munro, R. Lyczak, and B. Bowerman, 2006 Conditional dominant mutations in the Caenorhabditis elegans gene act-2 identify cytoplasmic and muscle roles for a redundant actin isoform. Mol. Biol. Cell 17: 1051-1064.
60. Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson et al., 1999 Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.
61. Wood, A. J., T. W. Lo, B. Zeitler, C. S. Pickle, E. J. Ralston et al., 2011 Targeted genome editing across species using ZFNs and TALENs. Science 333: 307.
62. Zwaal, R. R., A. Broeks, J. van Meurs, J. T. Groenen, and R. H. Plasterk, 1993 Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Proc. Natl. Acad. Sci. USA 90: 7431-7435.