New ways to admire zebrafish: Progress in functional genomics research methodology

BioTechniques

Volumn 38, Issue 6, 2005, Pages 897-906

  Teh, Cathleen ^b   Parinov, Serguei ^b   Korzh, Vladimir ^a  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; BIOTECHNOLOGY; GENES; GENETIC ENGINEERING; PROJECT MANAGEMENT;

GENOME SEQUENCING; GENOMIC TOOLS; ZEBRAFISH;

MICROORGANISMS;

ELECTROPORATION; FISH GENETICS; FUNCTIONAL GENOMICS; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC PROCEDURES; GENETIC SCREENING; GENETICS; KNOCKOUT GENE; METHODOLOGY; MUTAGENESIS; NONHUMAN; REVIEW; TRANSGENICS; ZEBRA FISH; ANIMAL; GENOMICS; MALE; MOLECULAR CLONING; RESEARCH; SPERMATOZOON; TRANSGENE; TRANSPOSON; ULTRASTRUCTURE;

DANIO RERIO;

HEAT SHOCK PROTEIN 70;

ANIMALS; CLONING, MOLECULAR; DNA TRANSPOSABLE ELEMENTS; ELECTROPORATION; GENOMICS; HSP70 HEAT-SHOCK PROTEINS; MALE; MUTAGENESIS; RESEARCH; SPERMATOZOA; TRANSGENES; ZEBRAFISH;

EID: 27744515738     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/05386rv01     Document Type: Review

References (80)

1. Mullins, M.C. 2002. Building-blocks of embryogenesis. Nat. Genet. 31:125-126.
2. Rasooly, R.S., D. Henken, N. Freeman, L. Tompkins, D. Badman, J. Briggs, and A.T. Hewitt. 2003. Genetic and genomic tools for zebrafish research: the NIH zebrafish initiative. Dev. Dyn. 228:490-496.
3. Postlethwait, J.H., Y.L. Yan, M.A. Gates, S. Horne, A. Amores, A. Brownlie, A. Donovan, E.S. Egan, et al. 1998. Vertebrate genome evolution and the zebrafish gene map. Nat. Genet. 18:345-349.
4. Gates, M.A., L. Kim, E.S. Egan, T. Cardozo, H.I. Sirotkin, S.T. Dougan, D. Lashkari, R. Abagyan, et al. 1999. A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res. 9:334-347.
5. Sampath, K., A.L. Rubinstein, A.M. Cheng, J.O. Liang, K. Fekany, L. Solnica-Krezel, V. Korzh, M.E. Halpern, et al. 1998. Induction of the zebrafish ventral brain and floorplate requires cyclops/nodal signalling. Nature 395:185-189.
6. Feldman, B., M.A. Gates, E.S. Egan, S.T. Dougan, G. Rennebeck, H.I. Sirotkin, A.F. Schier, and W.S. Talbot. 1998. Zebrafish organizer development and germ-layer formation require nodal-related signals. Nature 395:181-185.
7. North, T.E. and L.I. Zon. 2003. Modeling human hematopoietic and cardiovascular diseases in zebrafish. Dev. Dyn. 228:568-583.
8. Dooley, K. and L.I. Zon. 2000. Zebrafish: a model system for the study of human disease. Curr. Opin. Genet. Dev. 10:252-256.
9. Amatruda, J.F., J.L. Shepard, H.M. Stern, and L.I. Zon. 2002. Zebrafish as a cancer model system. Cancer Cell 1:229-231.
10. Furutani-Seiki, M., T. Sasado, C. Morinaga, H. Suwa, K. Niwa, H. Yoda, T. Deguchi, Y. Hirose, et al. 2004. A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes. Mech. Dev. 121:647-658.
11. Haffter, P., M. Granato, M. Brand, M.C. Mullins, M. Hammerschmidt, D.A. Kane, J. Odenthal, F.J. van Eeden, et al. 1996. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123:1-36.
12. Driever, W., L. Solnica-Krezel, A.F. Schier, S.C. Neuhauss, J. Malicki, D.L. Stemple, D.Y. Stainier, F. Zwartkruis, et al. 1996. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123:37-46.
13. Patton, E.E. and L.I. Zon. 2001. The art and design of genetic screens: zebrafish. Nat. Rev. Genet. 2:956-966.
14. TalbOt, W.S. and N. Hopkins. 2000. Zebrafish mutations and functional analysis of the vertebrate genome. Genes Dev. 14:755-762.
15. Rawls, J.F., M.R. Frieda, A.R. McAdow, J.P. Gross, C.M. Clayton, C.K. Heyen, and S.L. Johnson. 2003. Coupled mutagenesis screens and genetic mapping in zebrafish. Genetics 163:997-1009.
16. Wienholds, E., S. Schulte-Merker, B. Walderich, and R.H. Plasterk. 2002. Target-selected inactivation of the zebrafish rag 1 gene. Science 297:99-102.
17. Wienholds, E., F. van Eeden, M. Kosters, J. Mudde, R.H. Plasterk, and E. Cuppen. 2003. Efficient target-selected mutagenesis in zebrafish. Genome Res. 13:2700-2707.
18. Amsterdam, A., S. Burgess, G. Golling, W. Chen, Z. Sun, K. Townsend, S. Farrington, M. Haldi, et al. 1999. A large-scale insertional mutagenesis screen in zebrafish. Genes Dev. 13:2713-2724.
19. Amsterdam, A. 2003. Insertional mutagenesis in zebrafish. Dev. Dyn. 228:523-534.
20. Chen, W., S. Burgess, G. Golling, A. Amsterdam, and N. Hopkins. 2002. High-throughput selection of retrovirus producer cell lines leads to markedly improved efficiency of germ line-transmissible insertions in zebra fish. J. Virol. 76:2192-2198.
21. Golling, G., A. Amsterdam, Z. Sun, M. Antonelli, E. Maldonado, W. Chen, S. Burgess, M. Haldi, et al. 2002. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat. Genet. 31:135-140.
22. Amsterdam, A., R.M. Nissen, Z. Sun, E.C. Swindell, S. Farrington, and N. Hopkins. 2004. Identification of 315 genes essential for early zebrafish development. Proc. Natl. Acad. Sci. USA 101:12792-12797.
23. Danos, O. and J.M. Heard. 1992. Recombinant retroviruses as tools for gene transfer to somatic cells. Bone Marrow Transplant. 9(Suppl 1):131-138.
24. Izsvak, Z. and Z. Ivics. 2004. Sleeping beauty transposition: biology and applications for molecular therapy. Mol. Ther. 9:147-156.
25. Kempken, F. and F. Windhofer. 2001. The hAT family: a versatile transposon group common to plants, fungi, animals, and man. Chromosoma 110:1-9.
26. Ivics, Z., C.D. Kaufman, H. Zayed, C. Miskey, O. Walisko, and Z. Izsvak. 2004. The Sleeping Beauty transposable element: evolution, regulation and genetic applications. Curr. Issues Mol. Biol. 6:43-55.
27. Raz, E., H.G. van Luenen, B. Schaerringer, R.H. Plasterk, and W. Driever. 1998. Transposition of the nematode Caenorhabditis elegans Tc3 element in the zebrafish Danio rerio. Curr. Biol. 8:82-88.
28. Kawakami, K., A. Shima, and N. Kawakami. 2000. Identification of a functional transposase of the Tol2 element, an Ac-like element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage. Proc. Natl. Acad. Sci. USA 97:11403-11408.
29. Cui, Z., A.M. Geurts, G. Liu, C.D. Kaufman, and P.B. Hackett. 2002. Structure-function analysis of the inverted terminal repeats of the sleeping beauty transposon. J. Mol. Biol. 318:1221-1235.
30. Geurts, A.M., Y. Yang, K.J. Clark, G. Liu, Z. Cui, A.J. Dupuy, J.B. Bell, D.A. Largaespada, et al. 2003. Gene transfer into genomes of human cells by the sleeping beauty transposon system. Mol. Ther. 8:108-117.
31. Davidson, A.E., D. Balciunas, D. Mohn, J. Shaffer, S. Hermanson, S. Sivasubbu, M.P. Cliff, P.B. Hackett, et al. 2003. Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon. Dev. Biol. 263:191-202.
32. Parinov, S., I. Kondrichin, V. Korzh, and A. Emelyanov. 2004. Tol2 transposon-mediated enhancer trap to identify developmentally regulated zebrafish genes in vivo. Dev. Dyn. 231:449-459.
33. Kawakami, K., H. Takeda, N. Kawakami, M. Kobayashi, N. Matsuda, and M. Mishina. 2004. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev. Cell 7:133-144.
34. Smith, D., Y. Yanai, Y.G. Liu, S. Ishiguro, K. Okada, D. Shibata, R.F. Whittier, and N.V. Fedoroff. 1996. Characterization and mapping of Ds-GUS-T-DNA lines for targeted insertional mutagenesis. Plant J. 10:721-732.
35. Nasevicius, A. and S.C. Ekker. 2000. Effective targeted gene "knockdown" in zebrafish. Nat. Genet. 26:216-220.
36. Heasman, J. 2002. Morpholino oligos: making sense of antisense? Dev. Biol. 243:209-214.
37. Draper, B.W., P.A. Morcos, and C.B. Kimmel. 2001. Inhibition of zebrafish fgf8 pre-mRNA splicing with morpholino oligos: a quantifiable method for gene knockdown. Genesis 30:154-156.
38. Urtishak, K.A., M. Choob, X. Tian, N. Sternheim, W.S. Talbot, E. Wickstrom, and S.A. Farber. 2003. Targeted gene knockdown in zebrafish using negatively charged peptide nucleic acid mimics. Dev. Dyn. 228:405-413.
39. Chen, E., P.B. Hackett, and S.C. Ekker. 2004. Gene "knockdown" approaches using unconventional antisense oligonucleotides, p. 454-475. In Z. Gong and V. Korzh. (Eds.). Molecular Aspects of Fish and Marine Biology. World Scientific, Singapore.
40. Oates, A.C., A.E. Bruce, and R.K. Ho. 2000. Too much interference: injection of double-stranded RNA has nonspecific effects in the zebrafish embryo. Dev. Biol. 224:20-28.
41. Wargelius, A., S. Ellingsen, and A. Fjose. 1999. Double-stranded RNA induces specific developmental defects in zebrafish embryos. Biochem. Biophys. Res. Commun. 263:156-161.
42. Boonanuntanasarn, S., G. Yoshizaki, and T. Takeuchi. 2003. Specific gene silencing using small interfering RNAs in fish embryos. Biochem. Biophys. Res. Commun. 310:1089-1095.
43. Dodd, A., S.P. Chambers, and D.R. Love. 2004. Short interfering RNA-mediated gene targeting in the zebrafish. FEBS Lett. 561:89-93.
44. Finley, K.R., A.E. Davidson, and S.C. Ekker. 2001. Three-color imaging using fluorescent proteins in living zebrafish embryos. BioTechniques 31:66-72.
45. Gong, Z., B. Ju, and H. Wan. 2001. Green fluorescent protein (GFP) transgenic fish and their applications. Genetica 111:213-225.
46. Udvadia, A.J. and E. Linney. 2003. Windows into development: historic, current, and future perspectives on transgenic zebrafish. Dev. Biol. 256:1-17.
47. Hamer, L., T.M. DeZwaan, M.V. Montenegro-Chamorro, S.A. Frank, and J.E. Hamer. 2001. Recent advances in large-scale transposon mutagenesis. Curr. Opin. Chem. Biol. 5:67-73.
48. Balciunas, D., A.E. Davidson, S. Sivasubbu, S.B. Hermanson, Z. Welle, and S.C. Ekker. 2004. Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics 5:62.
49. Clark, K.J., A.M. Geurts, J.B. Bell, and P.B. Hackett. 2004. Transposon vectors for gene-trap insertional mutagenesis in vertebrates. Genesis 39:225-233.
50. Fadool, J.M., D.L. Hartl, and J.E. Dowling. 1998. Transposition of the mariner element from Drosophila mauritiana in zebrafish. Proc. Natl. Acad. Sci. USA 95:5182-5186.
51. Szabo, M., F. Muller, J. Kiss, C. Balduf, U. Strahle, and F. Olasz. 2003. Transposition and targeting of the prokaryotic mobile element IS30 in zebrafish. FEBS Lett. 550:46-50.
52. Miskey, C., Z. Izsvak, R.H. Plasterk, and Z. Ivics. 2003. The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells. Nucleic Acids Res. 31:6873-6881.
53. Ivics, Z., P.B. Hackett, R.H. Plasterk, and Z. Izsvak. 1997. Molecular reconstruction of Sleeping Beauty, a Tcl-like transposon from fish, and its transposition in human cells. Cell 91:501-510.
54. Balciunas, D., A.E. Davidson, S. Sivasubbu, S.B. Hermanson, Z. Welle, and S.C. Ekker. 2004. Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics 5:62.
55. Stanford, W.L., J.B. Cohn, and S.P. Cordes. 2001. Gene-trap mutagenesis: past, present and beyond. Nat. Rev. Genet. 2:756-768.
56. Jesuthasan, S. and S. Subburaju. 2002. Gene transfer into zebrafish by sperm nuclear transplantation. Dev. Biol. 242:88-95.
57. Thermes, V., C. Grabher, F. Ristoratore, F. Bourrat, A. Choulika, J. Wittbrodt, and J.S. Joly. 2002. I-SceI meganuclease mediates highly efficient transgenesis in fish. Mech. Dev. 118:91-98.
58. Gong, Z., Y.L. Wu, S.P. Mudumana, and S. Lin. Transgenic fish for developmental biology studies, p. 476-516. In Z. Gong and V. Korzh. (Eds.), Molecular Aspects of Fish and Marine Biology. World Scientific, Singapore.
59. Koster, R.W. and S.E. Fraser. 2001. Tracing transgene expression in living zebrafish embryos. Dev. Biol. 233:329-346.
60. Adam, A., R. Bartfai, Z. Lele, P.H. Krone, and L. Orban. 2000. Heat-inducible expression of a reporter gene detected by transient assay in zebrafish. Exp. Cell Res. 256:282-290.
61. Molina, A., F. Biemar, F. Muller, A. Iyengar, P. Prunet, N. Maclean, J.A. Martial, and M. Muller. 2000. Cloning and expression analysis of an inducible HSP70 gene from tilapia fish. FEBS Lett. 474:5-10.
62. Halloran, M.C., M. Sato-Maeda, J.T. Warren, F. Su, Z. Lele, P.H. Krone, J.Y. Kuwada, and W. Shoji. 2000. Laser-induced gene expression in specific cells of transgenic zebrafish. Development 127:1953-1960.
63. Bajoghli, B., N. Aghaallaei, T. Heimbucher, and T. Czerny. 2004. An artificial promoter construct for heat-inducible misexpression during fish embryogenesis. Dev. Biol. 271:416-430.
64. Bigey, P., M.F. Bureau, and D. Scherman. 2002. In vivo plasmid DNA electrotransfer. Curr. Opin. Biotechnol. 13:443-447.
65. Buono, R.J. and P.J. Linser. 1992. Transient expression of RSVCAT in transgenic zebrafish made by electroporation. Mol. Mar. Biol. Biotechnol. 1:271-275.
66. Patil, J.G. and H.W. Khoo. 1996. Nuclear internalization of foreign DNA by zebrafish spermatozoa and its enhancement by electroporation. J. Exp. Zool. 274:121-129.
67. Tawk, M., D. Tuil, Y. Torrente, S. Vriz, and D. Paulin. 2002. High-efficiency gene transfer into adult fish: a new tool to study fin regeneration. Genesis 32:27-31.
68. Teh, C., S.W. Chong, and V. Korzh. 2003. DNA delivery into anterior neural tube of zebrafish embryos by electroporation. BioTechniques 35:950-954.
69. Nakamura, H. and J. Funahashi. 2001. Introduction of DNA into chick embryos by in ovo electroporation. Methods 24:43-48.
70. Saito, T. and N. Nakatsuji. 2001. Efficient gene transfer into the embryonic mouse brain using in vivo electroporation. Dev. Biol. 240:237-246.
71. Haas, K., W.C. Sin, A. Javaherian, Z. Li, and H.T. Cline. 2001. Single-cell electroporation for gene transfer in vivo. Neuron 29:583-591.
72. Haas, K., K. Jensen, W.C. Sin, L. Foa, and H.T. Cline. 2002. Targeted electroporation in Xenopus tadpoles in vivo-from single cells to the entire brain. Differentiation 70:148-154.
73. Atkins, R.L., D. Wang, and R.D. Burke. 2000. Localized electroporation: a method for targeting expression of genes in avian embryos. BioTechniques 28:94-100.
74. Warga, R.M. and C.B. Kimmel. 1990. Cell movements during epiboly and gastrulation in zebrafish. Development 108:569-580.
75. Lyons, D.A., A.T. Guy, and J.D. Clarke. 2003. Monitoring neural progenitor fate through multiple rounds of division in an intact vertebrate brain. Development 130:3427-3436.
76. Dorsky, R.I., R.T. Moon, and D.W. Raible. 1998. Control of neural crest cell fate by the Wnt signalling pathway. Nature 396:370-373.
77. Reifers, F., E.C. Walsh, S. Leger, D.Y. Stainier, and M. Brand. 2000. Induction and differentiation of the zebrafish heart requires fibroblast growth factor 8 (fgf8/acerebellar). Development 127:225-235.
78. Hyatt, G.A., E.A. Schmitt, N. Marsh-Armstrong, P. McCaffery, U.C. Drager, and J.E. Dowling. 1996. Retinoic acid establishes ventral retinal characteristics. Development 122:195-204.
79. Lam, C.S., I. Sleptsova-Friedrich, A.D. Munro, and V. Korzh. 2003. SHH and FGF8 play distinct roles during development of noradrenergic neurons in the locus coeruleus of the zebrafish. Mol. Cell Neurosci. 22:501-515.
80. Bradbury, J. 2004. Small fish, big science. PLoS Biol. 2:E148.