Target-selected gene inactivation in zebrafish

Methods in Cell Biology

Volumn 2004, Issue 77, 2004, Pages 69-90

  Wienholds, Erno ^a   Plasterk, Ronald H A ^a  

^a HUBRECHT INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; GENE LIBRARY; GENE SILENCING; GENE TARGETING; GENETICS; METHODOLOGY; MUTAGENESIS; NUCLEOTIDE SEQUENCE; ZEBRA FISH;

ANIMALS; DNA MUTATIONAL ANALYSIS; GENE LIBRARY; GENE SILENCING; GENE TARGETING; MUTAGENESIS; ZEBRAFISH;

EID: 16644396292     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0091-679x(04)77004-1     Document Type: Article

References (77)

1. Alonso, J. M., et al. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301, 653-657.
2. Altschul, S. F., et al. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Amsterdam, A. (2003). Insertional mutagenesis in zebrafish. Dev. Dyn. 228, 523-554.
4. Amsterdam, A., et al. (1999). A large-scale insertional mutagenesis screen in zebrafish. Genes Dev. 13, 2713-2724.
5. Ballinger, D. G., and Benzer, S. (1989). Targeted gene mutations in Drosophila. Proc. Natl. Acad. Sci. USA 86, 9402-9406.
6. Beier, D. R. (2000). Sequence-based analysis of mutagenized mice. Mamm. Genome 11, 594-597.
7. Bentley, A., MacLennan, B., Calvo, J., and Dearolf, C. R. (2000). Targeted recovery of mutations in Drosophila. Genetics 156, 1169-1173.
8. Brand, M., Granato, M., and Nusslein-Volhard, C. (2002). Keeping and raising zebrafish. In "Zebrafish" (C. Nusslein-Volhard and D. Ralf, eds.), Vol. 261, pp. 7-37. Oxford University Press, Oxford.
9. Capecchi, M. R. (1989). Altering the genome by homologous recombination. Science 244, 1288-1292.
10. Chasman, D., and Adams, R. M. (2001). Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation. J. Mol. Biol. 307, 683-706.
11. Chen, Y., et al. (2000). Genotype-based screen for ENU-induced mutations in mouse embryonic stem cells. Nat. Genet. 24, 314-317.
12. Coghill, E. L., et al. (2002). A gene-driven approach to the identification of ENU mutants in the mouse. Nat. Genet. 30, 255-256.
13. Colbert, T., et al. (2001). High-throughput screening for induced point mutations. Plant Physiol. 126, 480-484.
14. Cui, Z., et al. (2003). RecA-mediated, targeted mutagenesis in zebrafish. Mar. Biotechnol. (NY) 5, 174-184.
15. Dai, Y., et al. (2002). Targeted disruption of the alpha 1,3-galactosyltransferase gene in cloned pigs. Nat. Biotechnol. 20, 251-255.
16. Das, L., and Martienssen, R. (1995). Site-selected transposon mutagenesis at the hcf106 locus in maize. Plant Cell 7, 287-294.
17. Davidson, A. E., et al. (2003). Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon. Dev. Biol. 263, 191-202.
18. De Stasio, E., et al. (1997). Characterization of revenants of unc-93(e1500) in Caenorhabditis elegans induced by N-ethyl-N-nitrosourea. Genetics 147, 597-608.
19. de Wind, N., et al. (1995). Inactivation of the mouse Msh2 gene results in mismatch repair deficiency, methylation tolerance, hyperrecombination, and predisposition to cancer. Cell 82, 321-330.
20. Douglas, G. R., et al. (1995). Temporal and molecular characteristics of mutations induced by ethylnitrosourea in germ cells isolated from seminiferous tubules and in spermatozoa of lacZ transgenic mice. Proc. Natl. Acad. Sci. USA 92, 7485-7489.
21. Driever, W., et al. (1996). A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123, 37-46.
22. Elbashir, S. M., et al. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498.
23. Ewing, B., and Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194.
24. Golling, G., et al. (2002). Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat. Genet. 31, 135-140.
25. Gordon, D., Abajian, C., and Green, P. (1998). Consed: A graphical tool for sequence finishing. Genome Res. 8, 195-202.
26. Gordon, D., Desmarais, C., and Green, P. (2001). Automated finishing with autofinish. Genome Res. 11, 614-625.
27. Haffter, P., et al. (1996). The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123, 1-36.
28. Hanada, K., et al. (1997). RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA 94, 3860-3865.
29. Hurlstone, A. T., et al. (2003). The WNT/beta-catenin pathway regulates cardiac value formation. Nature 425, 633-637.
30. NT/beta-catenin pathway regulates cardiac value formation. Nature 425, 633-637.
31. Jansen, G., Hazendonk, E., Thijssen, K. L., and Plasterk, R. H. (1997). Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat. Genet. 17, 119-121.
32. Kaiser, K., and Goodwin, S. F. (1990). "Site-selected" transposon mutagenesis of Drosophila. Proc. Natl. Acad. Sci. USA 87, 1686-1690.
33. Kimmel, C. B. (1989). Genetics and early development of zebrafish. Trends Genet. 5, 283-288.
34. Koes, R., et al. (1995). Targeted gene inactivation in petunia by PCR-based selection of transposon insertion mutants. Proc. Natl. Acad. Sci. USA 92, 8149-8153.
35. Korswagen, H. C., Durbin, R. M., Smits, M. T., and Plasterk, R. H. (1996). Transposon Tcl-derived, sequence-tagged sites in Caenorhabditis elegans as markers for gene mapping. Proc. Natl. Acad. Sci. USA 93, 14680-14685.
36. Lander, E. S., et al. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
37. Lee, K. Y., et al. (2002). Cloned zebrafish by nuclear transfer from long-term-cultured cells. Nat. Biotechnol. 20, 795-799.
38. Lekven, A. C., et al. (2000). Reverse genetics in zebrafish. Physiol. Genom. 2, 37-48.
39. Liu, L. X., et al. (1999). High-throughput isolation of Caenorhabditis elegans deletion mutants. Genome Res. 9, 859-867.
40. Ma, C., et al. (2001). Production of zebrafish germ-line chimeras from embryo cell cultures. Proc. Natl. Acad. Sci. USA 98, 2461-2466.
41. Martin, E., et al. (2002). Identification of 1088 new transposon insertions of Caenorhabditis elegans: A pilot study toward large-scale screens. Genetics 162, 521-524.
42. McCallum, C. M., Comai, L., Greene, E. A., and Henikoff, S. (2000). Targeted screening for induced mutations. Nat. Biotechnol. 18, 455-457.
43. McCreath, K. J., et al. (2000). Production of gene-targeted sheep by nuclear transfer from cultured somatic cells. Nature 405, 1066-1069.
44. Meissner, R. C., et al. (1999). Function search in a large transcription factor gene family in Arabidopsis: Assessing the potential of reverse genetics to identify insertional mutations in R2R3 MYB genes. Plant Cell 11, 1827-1840.
45. Miao, Z. H., and Lam, E. (1995). Targeted disruption of the TGA3 locus in Arabidopsis thaliana. Plant J. 7, 359-365.
46. Morris, J. P. T., et al. (2003). Zebrafish sperm cryopreservation with N,N-dimethylacetamide. Biotechniques 35, 956-958, 960, 962 passim.
47. Mullins, M. C., Hammerschmidt, M., Haffter, P., and Nusslein-Volhard, C. (1994). Large-scale mutagenesis in the zebrafish: In search of genes controlling development in a vertebrate. Curr. Biol. 4, 189-202.
48. Nakamura, Y., Gojobori, T., and Ikemura, T. (2000). Codon usage tabulated from international DNA sequence databases: Status for the year 2000. Nucleic Acids Res. 28, 292.
49. Nasevicius, A., and Ekker, S. C. (2000). Effective targeted gene 'knockdown' in zebrafish. Nat. Genet. 26, 216-220.
50. Ng, P. C., and Henikoff, S. (2001). Predicting deleterious amino acid substitutions. Genome Res. 11, 863-874.
51. Nickerson, D. A., Tobe, V. O., and Taylor, S. L. (1997). Polyphred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745-2751.
52. Oleykowski, C. A., Bronson Mullins, C. R., Godwin, A. K., and Yeung, A. T. (1998). Mutation detection using a novel plant endonuclease. Nucleic Acids Res. 26, 4597-4602.
53. Parinov, S., et al. (1999). Analysis of flanking sequences from dissociation insertion lines: A database for reverse genetics in Arabidopsis. Plant Cell 11, 2263-2270.
54. Perry, J. A., et al. (2003). A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol. 131, 866-871.
55. Raz, E., et al. (1998). Transposition of the nematode Caenorhabditis elegans Tc3 element in the zebrafish Danio rerio. Curr. Biol. 8, 82-88.
56. Rong, Y. S., and Golic, K. G. (2000). Gene targeting by homologous recombination in Drosophila. Science 288, 2013-2018.
57. Rong, Y. S., and Golic, K. G. (2001). A targeted gene knockout in Drosophila. Genetics 157, 1307-1312.
58. Sessions, A., et al. (2002). A high-throughput Arabidopsis reverse genetics system. Plant Cell 14, 2985-2994.
59. Smits, B. M., Mudde, J., Plasterk, R. H., and Cuppen, E. (2004). Target-selected mutagenesis of the rat. Genomics 83, 332-334.
60. Solnica-Krezel, L., Schier, A. F., and Driever, W. (1994). Efficient recovery of ENU-induced mutations from the zebrafish germline. Genetics 136, 1401-1420.
61. Spradling, A. C., et al. (1999). The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics 153, 135-177.
62. Streisinger, G., et al. (1981). Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291, 293-296.
63. Sun, L., et al. (1995). ES-like cell cultures derived from early zebrafish embryos. Mol. Mar. Biol. Biotechnol 4, 193-199.
64. Sunyaev, S., et al. (2001). Prediction of deleterious human alleles. Hum. Mol. Genet. 10, 591-597.
65. Thompson, S., et al. (1989). Germ line transmission and expression of a corrected HPRT gene produced by gene targeting in embryonic stem cells. Cell 56, 313-321.
66. Till, B. J., et al. (2003). Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res. 13, 524-530.
67. Tissier, A. F., et al. (1999). Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: A tool for functional genomics. Plant Cell 11, 1841-1852.
68. van Eeden, F. J., Granato, M., Odenthal, J., and Haffter, P. (1999). Developmental mutant screens in the zebrafish. Methods Cell Biol. 60, 21-41.
69. Venter, J. C., et al. (2001). The sequence of the human genome. Science 291, 1304-1351.
70. Wienholds, E., et al. (2003a). The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat. Genet. 35, 217-218.
71. Wienholds, E., Schulte-Merker, S., Walderich, B., and Plasterk, R. H. (2002). Target-selected inactivation of the zebrafish rag1 gene. Science 297, 99-102.
72. Wienholds, E., et al. (2003b). Efficient target-selected mutagenesis in zebrafish. Genome Res. 13, 2700-2707.
73. Yanagihara, K., and Mizuuchi, K. (2002). Mismatch-targeted transposition of Mu: A new strategy to map genetic polymorphism. Proc. Natl. Acad. Sci. USA 99, 11317-11321.
74. Yang, B., et al. (2000). Purification, cloning, and characterization of the CEL I nuclease. Biochemistry 39, 3533-3541.
75. Zambrowicz, B. P., et al. (1998). Disruption and sequence identification of 2,000 genes in mouse embryonic stem cells. Nature 392, 608-611.
76. Zan, Y., et al. (2003). Production of knockout rats using ENU mutagenesis and a yeast-based screening assay. Nat. Biotechnol. 21, 645-651.
77. Zwaal, R. R., et al. (1993). Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank. Proc. Natl. Acad. Sci. USA 90, 7431-7435.