Functional genomics tools for the analysis of zebrafish pigment

Pigment Cell Research

Volumn 17, Issue 5, 2004, Pages 461-470

  Pickart, Michael A ^a,b,c   Sivasubbu, Sridhar ^b,c   Nielsen, Aubrey L ^b,c   Shriram, Sabitha ^d   King, Richard A ^d   Ekker, Stephen C ^b,c  

^a MinnCResT ^*  (United States)

^b Dept of Genet Cell Biol/Devmt   (United States)

^c Minnesota Medical School Minneapolis   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Antisense; Genomics; Morpholinos; Pigment; Transposons; Zebrafish

Indexed keywords

MORPHOLINE DERIVATIVE; MORPHOLINOPHOSPHORODIAMIDATE OLIGONUCLEOTIDE; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

GENE FUNCTION; GENE TARGETING; GENETIC SCREENING; GENOMICS; KNOCKOUT GENE; MUTAGENESIS; NONHUMAN; PIGMENT CELL; PROTEOMICS; REVIEW; TRANSGENICS; TRANSPOSON; ZEBRA FISH;

ANIMALS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE TARGETING; GENOMICS; MUTAGENESIS; OLIGONUCLEOTIDES, ANTISENSE; PIGMENTATION; PIGMENTS, BIOLOGICAL; ZEBRAFISH; ZEBRAFISH PROTEINS;

DANIO; DANIO RERIO; TRANSPOSONS; VERTEBRATA;

EID: 4644239351     PISSN: 08935785     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1600-0749.2004.00189.x     Document Type: Review

References (100)

1. Amatruda JF, Shepard JL, Stern HM, Zon LI. Zebrafish as a cancer model system. Cancer Cell 2002;1:229-231
2. Dodd A, Curtis PM, Williams LC, Love DR. Zebrafish: bridging the gap between development and disease. Hum Mol Genet 2000;9:2443-2449
3. Dooley K, Zon LI. Zebrafish: a model system for the study of human disease. Curr Opin Genet Dev 2000;10:252-256
4. Langheinrich U. Zebrafish: a new model on the pharmaceutical catwalk. Bioessays 2003;25:904-912
5. Nasevicius A, Ekker SC. Effective targeted gene 'knockdown' in zebrafish. Nat Genet 2000;26:216-220
6. Shin JT, Fishman MC. From Zebrafish to human: modular medical models. Annu Rev Genomics Hum Genet 2002;3:311-340
7. Sumanas S, Larson JD. Morpholino phosphorodiamidate oligonucleotides in zebrafish: a recipe for functional genomics? Brief Funct Genomics Proteomics 2002;1:239-256
8. Sumanas S, Lin S. Zebrafish as a model system for drug target screening and validation. Drug Discov Today Targets 2004;3:89-96
9. Pichler FB, Laurenson S, Williams LC, Dodd A, Copp BR, Love DR. Chemical discovery and global gene expression analysis in zebrafish. Nat Biotechnol 2003;21:879-883
10. Parng C, Seng WL, Semino C, McGrath P. Zebrafish: a preclinical model for drug screening. Assay Drug Dev Technol 2002;1:41-48
11. Oberemm A. The use of a refined zebrafish embryo bioessay for the assessment of aquatic toxicity. Lab Animal 2000;29:32-40
12. Streisinger G, Walker C, Dower N, Knauber D, Singer F. Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 1981;291:293-296
13. Grunwald DJ, Eisen JS. Headwaters of the zebrafish - emergence of a new model vertebrate. Nat Rev Genet 2002;3:717-724
14. Rasooly RS, Henken D, Freeman N, Tompkins L, Badman D, Briggs J, Hewitt AT. Genetic and genomic tools for zebrafish research: the NIH zebrafish initiative. Dev Dyn 2003;228:490-496
15. Wixon J. Featured organism: Danio rerio, the zebrafish. Yeast 2000;17:225-231
16. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 2000;10:1890-1902
17. Anderson KV, Ingham PW. The transformation of the model organism: a decade of developmental genetics. Nat Genet 2003;33(Suppl.):285-293
18. Lister JA. Development of pigment cells in the zebrafish embryo. Microsc Res Tech 2002;58:435-441
19. Rawls JF, Mellgren EM, Johnson SL. How the zebrafish gets its stripes. Dev Biol 2001;240:301-314
20. Quigley IK, Parichy DM. Pigment pattern formation in zebrafish: a model for developmental genetics and the evolution of form. Microsc Res Tech 2002;58:442-455
21. Ziegler I. The pteridine pathway in zebrafish: regulation and specification during the determination of neural crest cell-fate. Pigment Cell Res 2003;16:172-182
22. Kelsh RN, Schmid B, Eisen JS. Genetic analysis of melanophore development in zebrafish embryos. Dev Biol 2000;225:277-293
23. Groves AK, Bronner-Fraser M. Neural crest diversification. Curr Top Dev Biol 1999;43:221-258
24. Vaglia JL, Hall BK. Regulation of neural crest cell populations: occurrence, distribution and underlying mechanisms. Int J Dev Biol 1999;43:95-110
25. Raible DW, Eisen JS. Restriction of neural crest cell fate in the trunk of the embryonic zebrafish. Development 1994;120:495-503
26. Raible DW, Eisen JS. Regulative interactions in zebrafish neural crest. Development 1996;122:501-507
27. Raible DW, Wood A, Hodsdon W, Henion PD, Weston JA, Eisen JS. Segregation and early dispersal of neural crest cells in the embryonic zebrafish. Dev Dyn 1992;195:29-42
28. Schilling TF, Kimmel CB. Segment and cell type lineage restrictions during pharyngeal arch development in the zebrafish embryo. Development 1994;120:483-494
29. Kelsh RN, Brand M, Jiang YJ, Heisenberg CP, Lin S, Haffter P, Odenthal J, Mullins MC, van Eeden FJ, Furutani-Seiki M, Granato M, Hammerschmidt M, Kane DA, Warga RM, Beuchle D, Vogelsang L, Nusslein-Volhard C. Zebrafish pigmentation mutations and the processes of neural crest development. Development 1996;123:369-389
30. Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. Stages of embryonic development of the zebrafish. Dev Dyn 1995;203:253-310
31. Ekker M. Saving zebrafish mutants. Bioessays 1999;21:94-98
32. Patton EE, Zon LI. The art and design of genetic screens: zebrafish. Nat Rev Genet 2001;2:956-966
33. Udvadia AJ, Linney E. Windows into development: historic, current, and future perspectives on transgenic zebrafish. Dev Biol 2003;256:1-17
34. Haffter P, Odenthal J, Mullins MC, Lin S, Farrel MJ, Vogelsang E, Hass F, Brand M, van Eeden FJ, Furutani-Seiki M, Granato M, Hammerschmidt M, Heisenberg CP, Jiang YJ, Kane DA, Kelsh RN, Hopkins N, Nusslein-Volhard C. Mutations affecting pigmentation and shape of adult zebrafish. Dev Genes Evol 1996;206:260-276
35. Kirschbaum F. Investigations on the colour pattern of the zebrafish Brachydanio rerio (Cyprinidae, Teleostei). Roux's Arch Dev Biol 1975;177:129-152
36. Johnson SL, Africa D, Walker C, Weston JA. Genetic control of adult pigment stripe development in zebrafish. Dev Biol 1995;167:27-33
37. Streisinger G, Singer F, Walker C, Knauber D, Dower N. Segregation analyses and gene-centromere distances in zebrafish. Genetics 1986;112:311-319
38. Haffter P, Granato M, Brand M, Mullins MC, Hammerschmidt M, Kane DA, Odenthal J, van Eeden FJ, Jiang YJ, Heisenberg CP, Kelsh RN, Furutani-Seiki M, Vogelsang E, Beuchle D, Schach U, Fabian C, Nusslein-Volhard C. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 1996;123:1-36
39. Camp E, Lardelli M. Tyrosinase gene expression in zebrafish embryos. Dev Genes Evol 2001;211:150-153
40. Camp E, Badhwar P, Mann GJ, Lardelli M. Expression analysis of a tyrosinase promoter sequence in zebrafish. Pigment Cell Res 2003;16:117-126
41. Pelletier I, Bally-Cuif L, Ziegler I. Cloning and developmental expression of zebrafish GTP cyclohydrolase I. Mech Dev 2001;109:99-103
42. Koga A, Suzuki M, Inagaki H, Bessho Y, Hori H. Transposable element in fish. Nature 1996;383:30.
43. Spritz RA, Chiang PW, Oiso N, Alkhateeb A. Human and mouse disorders of pigmentation. Curr Opin Genet Dev 2003;13:284-289
44. Fukamachi S, Shimada A, Shima A. Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka. Nat Genet 2001;28:381-385
45. Kawakami K, Shima A, Kawakami N. 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 2000;97:11403-11408
46. van Eeden FJ, Granato M, Odenthal J, Haffter P. Developmental mutant screens in the zebrafish. Methods Cell Biol 1999;60:21-41
47. Hrabe de Angelis MH, Flaswinkel H, Fuchs H, Rathkolb B, Soewarto D, Marschall S, Heffner S, Pargent W, Wuensch K, Jung M, Reis A, Richter T, Alessandrini F, Jakob T, Fuchs E, Kolb H, Kremmer E, Schaeble K, Rollinski B, Roscher A, Peters C, Meitinger T, Strom T, Steckler T, Holsboer F, Klopstock T, Gekeler F, Schindewolf C, Jung T, Avraham K, Behrendt H, Ring J, Zimmer A, Schughart K, Pfeffer K, Wolf E, Balling R. Genome-wide, large-scale production of mutant mice by ENU mutagenesis. Nat Genet 2000;25:444-447
48. Nolan PM, Peters J, Strivens M, Rogers D, Hagan J, Spurr N, Gray IC, Vizor L, Brooker D, Whitehill E, Washbourne R, Hough T, Greenaway S, Hewitt M, Liu X, McCormack S, Pickford K, Selley R, Wells C, Tymowska-Lalanne Z, Roby P, Glenister P, Thornton C, Thaung C, Stevenson JA, Arkell R, Mburu P, Hardisty R, Kiernan A, Erven A, Steel KP, Voegeling S, Guenet JL, Nickols C, Sadri R, Nasse M, Isaacs A, Davies K, Browne M, Fisher EM, Martin J, Rastan S, Brown SD, Hunter J. A systematic, genome-wide, phenotype-driven mutagenesis programme for gene function studies in the mouse. Nat Genet 2000;25:440-443
49. Nusslein-Volhard C, Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature 1980;287:795-801
50. Kemphues KJ, Priess JR, Morton DG, Cheng NS. Identification of genes required for cytoplasmic localization in early C. elegans embryos. Cell 1988;52:311-320
51. Mayer U, Torres Ruiz RA, Berleth T, Miseéra S, Juürgens G. Mutations affecting body organization in the Arabidopsis embryo. Nature 1991;353:402-407
52. Driever W, Solnica-Krezel L, Schier AF, Neuhauss SC, Malicki J, Stemple DL, Stainier DY, Zwartkruis F, Abdelilah S, Rangini Z, Belak J, Boggs C. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 1996;123:37-46
53. Haffter P, Nusslein-Volhard C. Large scale genetics in a small vertebrate, the zebrafish. Int J Dev Biol 1996;40:221-227
54. Henion PD, Raible DW, Beattie CE, Stoesser KL, Weston JA, Eisen JS. Screen for mutations affecting development of Zebrafish neural crest. Dev Genet 1996;18:11-17
55. Lister JA, Robertson CP, Lepage T, Johnson SL, Raible DW. nacre encodes a zebrafish microphthalmia-related protein that regulates neural-crest-derived pigment cell fate. Development 1999;126:3757-3767
56. Johnson SL, Zon LI. Genetic backgrounds and some standard stocks and strains used in zebrafish developmental biology and genetics. Methods Cell Biol 1999;60:357-359
57. Talbot WS, Schier AF. Positional cloning of mutated zebrafish genes. Methods Cell Biol 1999;60:259-286
58. Zhang J, Talbot WS, Schier AF. Positional cloning identifies zebrafish one-eyed pinhead as a permissive EGF-related ligand required during gastrulation. Cell 1998;92:241-251
59. Amsterdam A, Burgess S, Golling G, Chen W, Sun Z, Townsend K, Farrington S, Haldi M, Hopkins N. A large-scale insertional mutagenesis screen in zebrafish. Genes Dev 1999;13:2713-2724
60. Golling G, Amsterdam A, Sun Z, Antonelli M, Maldonado E, Chen W, Burgess S, Haldi M, Artzt K, Farrington S, Lin SY, Nissen RM, Hopkins N. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat Genet 2002;31:135-140
61. Dias N, Stein CA. Antisense oligonucleotides: basic concepts and mechanisms. Mol Cancer Ther 2002;1:347-355
62. Kurreck J. Antisense technologies. Improvement through novel chemical modifications. Eur J Biochem 2003;270:1628-1644
63. Urtishak KA, Choob M, Tian X, Sternheim N, Talbot WS, Wickstrom E, Farber SA. Targeted gene knockdown in zebrafish using negatively charged peptide nucleic acid mimics. Dev Dyn 2003;228:405-413
64. Summerton J, Weller D. Morpholino antisense oligomers: design, preparation, and properties. Antisense Nucleic Acid Drug Dev 1997;7:187-195
65. Corey DR, Abrams JM. Morpholino antisense oligonucleotides: tools for investigating vertebrate development. Genome Biol 2001;2:1015(reviews)
66. Ekker SC, Larson JD. Morphant technology in model developmental systems. Genesis 2001;30:89-93
67. Heasman J. Morpholino oligos: making sense of antisense? Dev Biol 2002;243:209-214
68. Summerton J. Morpholino antisense oligomers: the case for an RNase H-independent structural type. Biochim Biophys Acta 1999;1489:141-518
69. Kang SH, Cho MJ, Kole R. Up-regulation of luciferase gene expression with antisense oligonucleotides: implications and applications in functional assay development. Biochemistry 1998;37:6235-6239
70. Lacerra G, Sierakowska H, Carestia C, Fucharoen S, Summerton J, Weller D, Kole R. Restoration of hemoglobin A synthesis in erythroid cells from peripheral blood of thalassemic patients. Proc Natl Acad Sci USA 2000;97:9591-9596
71. Qin G, Taylor M, Ning YY, Iversen P, Kobzik L. In vivo evaluation of a morpholino antisense oligomer directed against tumor necrosis factor-alpha. Antisense Nucleic Acid Drug Dev 2000;10:11-16
72. Arora V, Knapp DC, Reddy MT, Weller DD, Iversen PL. Bioavailability and efficacy of antisense morpholino oligomers targeted to c-myc and cytochrome P-450 3A2 following oral administration in rats. J Pharm Sci 2002;91:1009-1018
73. Heasman J, Kofron M, Wylie C. Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach. Dev Biol 2000;222:124-134
74. Chen E, Hackett PB, Ekker SC. Gene 'knockdown' approaches using unconventional antisense oligonucleotides. In: Gong Z, Korzh V, eds. Molecular Aspects of Fish and Marine Biology. Fish Developmental Biology: Zebrafish and Medaka. Singapore: World Scientific, (in press)
75. Myers KJ, Dean NM. Sensible use of antisense: how to use oligonucleotides as research tools. Trends Pharmacol Sci 2000;21:19-23
76. Stein CA. The experimental use of antisense oligonucleotides: a guide for the perplexed. J Clin Invest 2001;108:641-644
77. Ekker SC. non-conventional antisense in zebrafish for functional genomics applications. In: Detrich HW, Westerfield M, Zon LI, eds. Methods in Cell Biology. The Zebrafish: Genetics, Genomics and Informatics. 2nd edn, San Diego: Elsevier Press (in press).
78. Ekker SC. Morphants: a new systematic vertebrate functional genomics approach. Yeast 2000;17:302-306
79. Dutton K, Dutton JR, Pauliny A, Kelsh RN. A morpholino phenocopy of the colourless mutant. Genesis 2001;30:188-189
80. Malicki J, Schier AF, Solnica-Krezel L, Stemple DL, Neuhauss SC, Stainier DY, Abdelilah S, Rangini Z, Zwartkruis F, Driever W. Mutations affecting development of the zebrafish ear. Development 1996;123:275-283
81. Knight RD, Nair S, Nelson SS, Afshar A, Javidan Y, Geisler R, Rauch GJ, Schilling TF. lockjaw encodes a zebrafish tfap2a required for early neural crest development. Development 2003;130:5755-5768
82. O'Brien EK, d'Alencon C, Bonde G, Li W, Schoenebeck J, Allende ML, Gelb BD, Yelon D, Eisen JS, Cornell RA. Transcription factor Ap-2alpha is necessary for development of embryonic melanophores, autonomic neurons and pharyngeal skeleton in zebrafish. Dev Biol 2004;265:246-261
83. Klee EW, Ekker SC, Ellis LB. Target selection for Danio rerio functional genomics. Genesis 2001;30:123-125
84. Klee EW, Carlson DF, Fahrenkrug SC, Ekker SC, Ellis LB. Identifying secretomes in people, pufferfish and pigs. Nucleic Acids Res 2004;32:1414-1421
85. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J. An optimized protocol for analysis of EST sequences. Nucleic Acids Res 2000;28:3657-3665
86. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000;300:1005-1016
87. Basrur V, Yang F, Kushimoto T, Higashimoto Y, Yasumoto K, Valencia J, Muller J, Vieira WD, Watabe H, Shabanowitz J, Hearing VJ, Hunt DF, Appella E. Proteomic analysis of early melanosomes: identification of novel melanosomal proteins. J Proteome Res 2003;2:69-79
88. Koga A, Inagaki H, Bessho Y, Hori H. Insertion of a novel transposable element in the tyrosinase gene is responsible for an albino mutation in the medaka fish, Oryzias latipes. Mol Gen Genet 1995;249:400-405
89. Iida A, Inagaki H, Suzuki M, Wakamatsu Y, Hori H, Koga A. The tyrosinase gene of the i(b) albino mutant of the medaka fish carries a transposable element insertion in the promoter region. Pigment Cell Res 2004;17:158-164
90. Davidson AE, Balciunas D, Mohn D, Shaffer J, Hermanson S, Sivasubbu S, Cliff MP, Hackett PB, Ekker SC. Efficient gene delivery and gene expression in zebrafish using the sleeping beauty transposon. Dev Biol 2003;263:191-202
91. Plasterk RH. The Tcl/mariner transposon family. Curr Top Microbiol Immunol 1996;204:125-143
92. Spradling AC, Stern DM, Kiss I, Roote J, Laverty T, Rubin GM. Gene disruptions using P transposable elements: an integral component of the drosophila genome project. Proc Natl Acad Sci USA 1995;92:10824-10830
93. Kawakami K, Takeda H, Kawakami N, Kobayashi M, Matsuda N, Mishina M. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev Cell 2004;7:133-144
94. Lister JA, Close J, Raible DW. Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential. Dev Biol 2001;237:333-344
95. Parichy DM, Ransom DG, Paw B, Zon LI, Johnson SL. An orthologue of the kit-related gene fms is required for development of neural crest-derived xanthophores and a subpopulation of adult melanocytes in the zebrafish, Danio rerio. Development 2000;127:3031-3044
96. Dutton KA, Pauliny A, Lopes SS, Elworthy S, Carney TJ, Rauch J, Geisler R, Haffter P, Kelsh RN. Zebrafish colourless encodes sox10 and specifies non-ectomesenchymal neural crest fates. Development 2001;128:4113-4125
97. Cretekos CJ, Grunwald DJ. Alyron, an insertional mutation affecting early neural crest development in zebrafish. Dev Biol 1999;210:322-338
98. Knight RD, Javidan Y, Nelson S, Zhang T, Schilling T. Skeletal and pigment cell defects in the lockjaw mutant reveal multiple roles for zebrafish tfap2a in neural crest development. Dev Dyn 2004;229:87-98
99. Jackson IJ. Evolution and expression of tyrosinase-related proteins. Pigment Cell Res 1994;7:241-242
100. Sprague J, Doerry E, Douglas S, Westerfield M. The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. Nucleic Acids Res 2001;29:87-90