Zebrafish: An integrative system for neurogenomics and neurosciences

Progress in Neurobiology

Volumn 93, Issue 2, 2011, Pages 231-243

  Rinkwitz, Silke ^a   Mourrain, Philippe ^b,c   Becker, Thomas S ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b ECOLE NORMALE SUPÉRIEURE   (France)

^c STANFORD UNIVERSITY   (United States)

Author keywords

Animal models; Optogenetics; Transgenes

Indexed keywords

4 AMINOBUTYRIC ACID; ADRENALIN; CARTASTEINE; CASPASE 6; DICKKOPF 1 PROTEIN; DOPAMINE; GHRELIN; GLUTAMIC ACID; GLYCINE; GONADORELIN; HISTAMINE; LEPTIN; LIVER RECEPTOR HOMOLOG 1; LYMPHOID ENHANCER FACTOR 1; MELANOCORTIN; MELATONIN; MICRORNA; NEUROPEPTIDE; NEUROTRANSMITTER; NORADRENALIN; OREXIN; SEROTONIN; TRANSCRIPTION FACTOR GAL4; WNT1 PROTEIN; AGENTS INTERACTING WITH TRANSMITTER, HORMONE OR DRUG RECEPTORS;

BACTERIAL ARTIFICIAL CHROMOSOME; CHEMICAL MUTAGENESIS; EMBRYO DEVELOPMENT; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; GENETIC ANALYSIS; HUMAN; IN VIVO STUDY; MOLECULAR GENETICS; NERVOUS SYSTEM DEVELOPMENT; NEUROSCIENCE; NONHUMAN; PRIORITY JOURNAL; REVIEW; TELENCEPHALON; TRANSGENE; ZEBRA FISH; ANIMAL; GENETICS; GENOMICS; GROWTH, DEVELOPMENT AND AGING; HISTOLOGY; METABOLISM; NERVE CELL NETWORK; NERVOUS SYSTEM; NEUROBIOLOGY; PHYSIOLOGY; PRENATAL DEVELOPMENT; TRANSGENIC ANIMAL;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; GENE EXPRESSION; GENOMICS; HUMANS; NERVE NET; NERVOUS SYSTEM; NEUROBIOLOGY; NEUROTRANSMITTER AGENTS; TRANSGENES; ZEBRAFISH;

EID: 78650607495     PISSN: 03010082     EISSN: 18735118     Source Type: Journal    
DOI: 10.1016/j.pneurobio.2010.11.003     Document Type: Review

References (185)

1. Abraham E., Palevitch O., Gothilf Y., Zohar Y. The zebrafish as a model system for forebrain GnRH neuronal development. Gen. Comp. Endocrinol. 2009, 164:151-160.
2. Akalin A., Fredman D., Arner E., Dong X., Bryne J.C., Suzuki H., Daub C.O., Hayashizaki Y., Lenhard B. Transcriptional features of genomic regulatory blocks. Genome Biol. 2009, 10:R38.
3. Allende M.L., Amsterdam A., Becker T., Kawakami K., Gaiano N., Hopkins N. Insertional mutagenesis in zebrafish identifies two novel genes, pescadillo and dead eye, essential for embryonic development. Genes Dev. 1996, 10:3141-3155.
4. Amaral P.P., Mattick J.S. Noncoding RNA in development. Mamm. Genome 2008, 19:454-492.
5. Amsterdam A. Insertional mutagenesis in zebrafish: genes for development, genes for disease. Brief Funct. Genomic Proteomic 2006, 5:19-23.
6. Amsterdam A., Becker T.S. Transgenes as screening tools to probe and manipulate the zebrafish genome. Dev. Dyn. 2005, 234:255-268.
7. 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.
8. Amsterdam A., Nissen R.M., Sun Z., Swindell E.C., Farrington S., Hopkins N. Identification of 315 genes essential for early zebrafish development. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:12792-12797.
9. Antonellis A., Huynh J.L., Lee-Lin S.Q., Vinton R.M., Renaud G., Loftus S.K., Elliot G., Wolfsberg T.G., Green E.D., McCallion A.S., Pavan W.J. Identification of neural crest and glial enhancers at the mouse Sox10 locus through transgenesis in zebrafish. PLoS Genet. 2008, 4:e1000174.
10. Appelbaum L., Wang G.X., Maro G.S., Mori R., Tovin A., Marin W., Yokogawa T., Kawakami K., Smith S.J., Gothilf Y., Mignot E., Mourrain P. Sleep-wake regulation and hypocretin-melatonin interaction in zebrafish. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:21942-21947.
11. Arrenberg A.B., Del Bene F., Baier H. Optical control of zebrafish behavior with halorhodopsin. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:17968-17973.
12. Asakawa K., Kawakami K. Targeted gene expression by the Gal4-UAS system in zebrafish. Dev. Growth Differ. 2008, 50:391-399.
13. Baier H. Zebrafish on the move: towards a behavior-genetic analysis of vertebrate vision. Curr. Opin. Neurobiol. 2000, 10:451-455.
14. Baier H., Scott E.K. Genetic and optical targeting of neural circuits and behaviour-zebrafish in the spotlight. Curr. Opin. Neurobiol. 2009, 19:553-560.
15. Baier H., Klostermann S., Trowe T., Karlstrom R.O., Nusslein-Volhard C., Bonhoeffer F. Genetic dissection of the retinotectal projection. Development 1996, 123:415-425.
16. Balciunas D., Davidson A.E., Sivasubbu S., Hermanson S.B., Welle Z., Ekker S.C. Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics 2004, 5:62.
17. Becker C.G., Becker T. Adult zebrafish as a model for successful central nervous system regeneration. Restor. Neurol. Neurosci. 2008, 26:71-80.
18. Bellen H.J. Ten years of enhancer detection: lessons from the fly. Plant Cell 1999, 11:2271-2281.
19. Berman J.R., Skariah G., Maro G.S., Mignot E., Mourrain P. Characterization of two melanin-concentrating hormone genes in zebrafish reveals evolutionary and physiological links with the mammalian MCH system. J. Comp. Neurol. 2009, 517:695-710.
20. Bertrand S., Thisse B., Tavares R., Sachs L., Chaumot A., Bardet P.L., Escriva H., Duffraisse M., Marchand O., Safi R., Thisse C., Laudet V. Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression. PLoS Genet. 2007, 3:e188.
21. Biran J., Ben-Dor S., Levavi-Sivan B. Molecular identification and functional characterization of the kisspeptin/kisspeptin receptor system in lower vertebrates. Biol. Reprod. 2008, 79:776-786.
22. Blow M.J., McCulley D.J., Li Z., Zhang T., Akiyama J.A., Holt A., Plajzer-Frick I., Shoukry M., Wright C., Chen F., Afzal V., Bristow J., Ren B., Black B.L., Rubin E.M., Visel A., Pennacchio L.A. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 2010, 42:806-810.
23. Brand M., Heisenberg C.P., Jiang Y.J., Beuchle D., Lun K., Furutani-Seiki M., Granato M., Haffter P., Hammerschmidt M., Kane D.A., Kelsh R.N., Mullins M.C., Odenthal J., van Eeden F.J., Nusslein-Volhard C. Mutations in zebrafish genes affecting the formation of the boundary between midbrain and hindbrain. Development 1996, 123:179-190.
24. Burgess H.A., Granato M. The neurogenetic frontier-lessons from misbehaving zebrafish. Brief Funct. Genomic Proteomic 2008, 7:474-482.
25. Burne T., Scott E., van Swinderen B., Hilliard M., Reinhard J., Claudianos C., Eyles D., McGrath J. Big ideas for small brains: what can psychiatry learn from worms, flies, bees and fish?. Mol. Psychiatry 2010, epub 30 March 2010.
26. Cahill G.M. Circadian regulation of melatonin production in cultured zebrafish pineal and retina. Brain Res. 1996, 708:177-181.
27. Canestro C., Yokoi H., Postlethwait J.H. Evolutionary developmental biology and genomics. Nat. Rev. Genet. 2007, 8:932-942.
28. Chambers D., Fishell G. Functional genomics of early cortex patterning. Genome Biol. 2006, 7:202.
29. Choi W.Y., Giraldez A.J., Schier A.F. Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430. Science 2007, 318:271-274.
30. Coolen M., Bally-Cuif L. MicroRNAs in brain development and physiology. Curr. Opin. Neurobiol. 2009, 19:461-470.
31. Danesin C., Peres J.N., Johansson M., Snowden V., Cording A., Papalopulu N., Houart C. Integration of telencephalic Wnt and hedgehog signaling center activities by Foxg1. Dev. Cell 2009, 16:576-587.
32. de Lecea L., Sutcliffe J.G. The hypocretins and sleep. FEBS J. 2005, 272:5675-5688.
33. de Martino S., Yan Y.L., Jowett T., Postlethwait J.H., Varga Z.M., Ashworth A., Austin C.A. Expression of sox11 gene duplicates in zebrafish suggests the reciprocal loss of ancestral gene expression patterns in development. Dev. Dyn. 2000, 217:279-292.
34. Distel M., Wullimann M.F., Koster R.W. Optimized Gal4 genetics for permanent gene expression mapping in zebrafish. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:13365-13370.
35. Dong X., Fredman D., Lenhard B. Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol. 2009, 10:R86.
36. Dong X., Navratilova P., Fredman D., Drivenes O., Becker T.S., Lenhard B. Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic Acids Res. 2009, 38(4):1071-1085.
37. Douglass A.D., Kraves S., Deisseroth K., Schier A.F., Engert F. Escape behavior elicited by single, channelrhodopsin-2-evoked spikes in zebrafish somatosensory neurons. Curr. Biol. 2008, 18:1133-1137.
38. Doyon Y., McCammon J.M., Miller J.C., Faraji F., Ngo C., Katibah G.E., Amora R., Hocking T.D., Zhang L., Rebar E.J., Gregory P.D., Urnov F.D., Amacher S.L. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol. 2008, 26:702-708.
39. Driever W., Solnica-Krezel L., Schier A.F., Neuhauss S.C., Malicki J., Stemple D.L., Stainier D.Y., Zwartkruis F., Abdelilah S., Rangini Z., Belak J., Boggs C. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 1996, 123:37-46.
40. Dugas J.C., Cuellar T.L., Scholze A., Ason B., Ibrahim A., Emery B., Zamanian J.L., Foo L.C., McManus M.T., Barres B.A. Dicer1 and miR-219 are required for normal oligodendrocyte differentiation and myelination. Neuron 2010, 65:597-611.
41. Ellingsen S., Laplante M.A., Konig M., Kikuta H., Furmanek T., Hoivik E.A., Becker T.S. Large-scale enhancer detection in the zebrafish genome. Development 2005, 132:3799-3811.
42. Elsalini O.A., Rohr K.B. Phenylthiourea disrupts thyroid function in developing zebrafish. Dev. Genes Evol. 2003, 212:593-598.
43. Engstrom P.G., Fredman D., Lenhard B. Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol. 2008, 9:R34.
44. Esain V., Postlethwait J.H., Charnay P., Ghislain J. FGF-receptor signalling controls neural cell diversity in the zebrafish hindbrain by regulating olig2 and sox9. Development 2010, 137:33-42.
45. Faraco J.H., Appelbaum L., Marin W., Gaus S.E., Mourrain P., Mignot E. Regulation of hypocretin (orexin) expression in embryonic zebrafish. J. Biol. Chem. 2006, 281:29753-29761.
46. Felip A., Zanuy S., Pineda R., Pinilla L., Carrillo M., Tena-Sempere M., Gomez A. Evidence for two distinct KiSS genes in non-placental vertebrates that encode kisspeptins with different gonadotropin-releasing activities in fish and mammals. Mol. Cell. Endocrinol. 2009, 312:61-71.
47. Fisher S., Grice E.A., Vinton R.M., Bessling S.L., McCallion A.S. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 2006, 312:276-279.
48. Foley J.E., Maeder M.L., Pearlberg J., Joung J.K., Peterson R.T., Yeh J.R. Targeted mutagenesis in zebrafish using customized zinc-finger nucleases. Nat. Protoc. 2009, 4:1855-1867.
49. Foley J.E., Yeh J.R., Maeder M.L., Reyon D., Sander J.D., Peterson R.T., Joung J.K. Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN). PLoS One 2009, 4(2):e4348.
50. Fredman D., Engstrom P.G., Lenhard B. Web-based tools and approaches to study long-range gene regulation in Metazoa. Brief Funct. Genomic Proteomic 2009, 8:231-242.
51. Gaiano N., Amsterdam A., Kawakami K., Allende M., Becker T., Hopkins N. Insertional mutagenesis and rapid cloning of essential genes in zebrafish. Nature 1996, 383:829-832.
52. Garaschuk O., Milos R.I., Grienberger C., Marandi N., Adelsberger H., Konnerth A. Optical monitoring of brain function in vivo: from neurons to networks. Pflugers Arch. 2006, 453:385-396.
53. Gehrig J., Reischl M., Kalmar E., Ferg M., Hadzhiev Y., Zaucker A., Song C., Schindler S., Liebel U., Muller F. Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos. Nat. Methods 2009, 6:911-916.
54. Giraldez A.J., Cinalli R.M., Glasner M.E., Enright A.J., Thomson J.M., Baskerville S., Hammond S.M., Bartel D.P., Schier A.F. MicroRNAs regulate brain morphogenesis in zebrafish. Science 2005, 308:833-838.
55. Giraldez A.J., Mishima Y., Rihel J., Grocock R.J., Van Dongen S., Inoue K., Enright A.J., Schier A.F. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006, 312:75-79.
56. Golling G., Amsterdam A., Sun Z., Antonelli M., Maldonado E., Chen W., Burgess S., Haldi M., Artzt K., Farrington S., Lin S.Y., Nissen R.M., Hopkins N. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat. Genet. 2002, 31:135-140.
57. Gomez-Skarmeta J.L., Lenhard B., Becker T.S. New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Dev. Dyn. 2006, 235:870-885.
58. Granato M., van Eeden F.J., Schach U., Trowe T., Brand M., Furutani-Seiki M., Haffter P., Hammerschmidt M., Heisenberg C.P., Jiang Y.J., Kane D.A., Kelsh R.N., Mullins M.C., Odenthal J., Nusslein-Volhard C. Genes controlling and mediating locomotion behavior of the zebrafish embryo and larva. Development 1996, 123:399-413.
59. Griffond B., Baker B.I. Cell and molecular cell biology of melanin-concentrating hormone. Int. Rev. Cytol. 2002, 213:233-277.
60. Guan C., Ye C., Yang X., Gao J. A review of current large-scale mouse knockout efforts. Genesis 2010, 48:73-85.
61. Guo S. Using zebrafish to assess the impact of drugs on neural development and function. Expert Opin. Drug Discov. 2009, 4:715-726.
62. Haffter P., Granato M., Brand M., Mullins M.C., Hammerschmidt M., Kane D.A., Odenthal J., van Eeden F.J., Jiang Y.J., Heisenberg C.P., Kelsh R.N., 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.
63. Hanashima C., Fernandes M., Hebert J.M., Fishell G. The role of Foxg1 and dorsal midline signaling in the generation of Cajal-Retzius subtypes. J. Neurosci. 2007, 27:11103-11111.
64. Hebert J.M., Fishell G. The genetics of early telencephalon patterning: some assembly required. Nat. Rev. Neurosci. 2008, 9:678-685.
65. Heintz N. Gene expression nervous system atlas (GENSAT). Nat. Neurosci. 2004, 7:483.
66. Heisenberg C.P., Brand M., Jiang Y.J., Warga R.M., Beuchle D., van Eeden F.J., Furutani-Seiki M., Granato M., Haffter P., Hammerschmidt M., Kane D.A., Kelsh R.N., Mullins M.C., Odenthal J., Nusslein-Volhard C. Genes involved in forebrain development in the zebrafish, Danio rerio. Development 1996, 123:191-203.
67. Heisenberg C.P., Houart C., Take-Uchi M., Rauch G.J., Young N., Coutinho P., Masai I., Caneparo L., Concha M.L., Geisler R., Dale T.C., Wilson S.W., Stemple D.L. A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon. Genes Dev. 2001, 15:1427-1434.
68. Higashijima S., Hotta Y., Okamoto H. Visualization of cranial motor neurons in live transgenic zebrafish expressing green fluorescent protein under the control of the islet-1 promoter/enhancer. J. Neurosci. 2000, 20:206-218.
69. Higashijima S., Mandel G., Fetcho J.R. Distribution of prospective glutamatergic, glycinergic, and GABAergic neurons in embryonic and larval zebrafish. J. Comp. Neurol. 2004, 480:1-18.
70. Hoppmann V., Wu J.J., Soviknes A.M., Helvik J.V., Becker T.S. Expression of the eight AMPA receptor subunit genes in the developing central nervous system and sensory organs of zebrafish. Dev. Dyn. 2008, 237:788-799.
71. Houart C., Caneparo L., Heisenberg C., Barth K., Take-Uchi M., Wilson S. Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling. Neuron 2002, 35:255-265.
72. Ito H., Yamamoto N. Non-laminar cerebral cortex in teleost fishes?. Biol. Lett. 2009, 5:117-121.
73. Janovjak H., Szobota S., Wyart C., Trauner D., Isacoff E.Y. A light-gated, potassium-selective glutamate receptor for the optical inhibition of neuronal firing. Nat. Neurosci. 2010, 13:1027-1032.
74. Kapsimali M., Kloosterman W.P., de Bruijn E., Rosa F., Plasterk R.H., Wilson S.W. MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system. Genome Biol. 2007, 8:R173.
75. Karlstrom R.O., Trowe T., Klostermann S., Baier H., Brand M., Crawford A.D., Grunewald B., Haffter P., Hoffmann H., Meyer S.U., Muller B.K., Richter S., van Eeden F.J., Nusslein-Volhard C., Bonhoeffer F. Zebrafish mutations affecting retinotectal axon pathfinding. Development 1996, 123:427-438.
76. Kaslin J., Panula P. Comparative anatomy of the histaminergic and other aminergic systems in zebrafish (Danio rerio). J. Comp. Neurol. 2001, 440:342-377.
77. Kaslin J., Nystedt J.M., Ostergard M., Peitsaro N., Panula P. The orexin/hypocretin system in zebrafish is connected to the aminergic and cholinergic systems. J. Neurosci. 2004, 24:2678-2689.
78. Kastenhuber E., Kratochwil C.F., Ryu S., Schweitzer J., Driever W. Genetic dissection of dopaminergic and noradrenergic contributions to catecholaminergic tracts in early larval zebrafish. J. Comp. Neurol. 2010, 518:439-458.
79. 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.
80. Kawauchi H. Functions of melanin-concentrating hormone in fish. J. Exp. Zool. A Comp. Exp. Biol. 2006, 305:751-760.
81. Kawauchi H., Kawazoe I., Tsubokawa M., Kishida M., Baker B.I. Characterization of melanin-concentrating hormone in chum salmon pituitaries. Nature 1983, 305:321-323.
82. Keller P.J., Schmidt A.D., Wittbrodt J., Stelzer E.H. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 2008, 322:1065-1069.
83. Kikuta H., Kawakami K. Transient and stable transgenesis using tol2 transposon vectors. Methods Mol. Biol. 2009, 546:69-84.
84. Kikuta H., Fredman D., Rinkwitz S., Lenhard B., Becker T.S. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks-a fundamental feature of vertebrate genomes. Genome Biol. 2007, 8(Suppl. 1):S4.
85. Kikuta H., Laplante M., Navratilova P., Komisarczuk A.Z., Engstrom P.G., Fredman D., Akalin A., Caccamo M., Sealy I., Howe K., Ghislain J., Pezeron G., Mourrain P., Ellingsen S., Oates A.C., Thisse C., Thisse B., Foucher I., Adolf B., Geling A., Lenhard B., Becker T.S. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 2007, 17:545-555.
86. Kim C.H., Oda T., Itoh M., Jiang D., Artinger K.B., Chandrasekharappa S.C., Driever W., Chitnis A.B. Repressor activity of Headless/Tcf3 is essential for vertebrate head formation. Nature 2000, 407:913-916.
87. Kim J., Inoue K., Ishii J., Vanti W.B., Voronov S.V., Murchison E., Hannon G., Abeliovich A. A MicroRNA feedback circuit in midbrain dopamine neurons. Science 2007, 317:1220-1224.
88. King A. Researchers find their Nemo. Cell 2009, 139:843-846.
89. Kitahashi T., Ogawa S., Parhar I.S. Cloning and expression of kiss2 in the zebrafish and medaka. Endocrinology 2009, 150:821-831.
90. Kokel D., Bryan J., Laggner C., White R., Cheung C.Y., Mateus R., Healey D., Kim S., Werdich A.A., Haggarty S.J., Macrae C.A., Shoichet B., Peterson R.T. Rapid behavior-based identification of neuroactive small molecules in the zebrafish. Nat. Chem. Biol. 2010, 6(3):231-237.
91. Komisarczuk A.Z., Topp S., Stigloher C., Kapsimali M., Bally-Cuif L., Becker T.S. Enhancer detection and developmental expression of zebrafish sprouty1, a member of the fgf8 synexpression group. Dev. Dyn. 2008, 237:2594-2603.
92. Komisarczuk A.Z., Kawakami K., Becker T.S. Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split. Dev. Biol. 2009, 336:301-312.
93. Lagutin O.V., Zhu C.C., Kobayashi D., Topczewski J., Shimamura K., Puelles L., Russell H.R., McKinnon P.J., Solnica-Krezel L., Oliver G. Six3 repression of Wnt signaling in the anterior neuroectoderm is essential for vertebrate forebrain development. Genes Dev. 2003, 17:368-379.
94. Laplante M., Kikuta H., Konig M., Becker T.S. Enhancer detection in the zebrafish using pseudotyped murine retroviruses. Methods 2006, 39:189-198.
95. Lettice L.A., Heaney S.J., Purdie L.A., Li L., de Beer P., Oostra B.A., Goode D., Elgar G., Hill R.E., de Graaff E. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 2003, 12:1725-1735.
96. Leucht C., Stigloher C., Wizenmann A., Klafke R., Folchert A., Bally-Cuif L. MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary. Nat. Neurosci. 2008, 11:641-648.
97. Li J., Mack J.A., Souren M., Yaksi E., Higashijima S., Mione M., Fetcho J.R., Friedrich R.W. Early development of functional spatial maps in the zebrafish olfactory bulb. J. Neurosci. 2005, 25:5784-5795.
98. Lieschke G.J., Currie P.D. Animal models of human disease: zebrafish swim into view. Nat. Rev. Genet. 2007, 8:353-367.
99. Lillesaar C., Tannhauser B., Stigloher C., Kremmer E., Bally-Cuif L. The serotonergic phenotype is acquired by converging genetic mechanisms within the zebrafish central nervous system. Dev. Dyn. 2007, 236:1072-1084.
100. Lin L., Faraco J., Li R., Kadotani H., Rogers W., Lin X., Qiu X., de Jong P.J., Nishino S., Mignot E. The sleep disorder canine narcolepsy is caused by a mutation in the hypocretin (orexin) receptor 2 gene. Cell 1999, 98:365-376.
101. Lopez-Patino M.A., Yu L., Cabral H., Zhdanova I.V. Anxiogenic effects of cocaine withdrawal in zebrafish. Physiol. Behav. 2008, 93:160-171.
102. Low S.E., Ryan J., Sprague S.M., Hirata H., Cui W.W., Zhou W., Hume R.I., Kuwada J.Y., Saint-Amant L. touche Is required for touch-evoked generator potentials within vertebrate sensory neurons. J. Neurosci. 2010, 30:9359-9367.
103. Loya C.M., Lu C.S., Van Vactor D., Fulga T.A. Transgenic microRNA inhibition with spatiotemporal specificity in intact organisms. Nat. Methods 2009, 6:897-903.
104. Ma L.H., Punnamoottil B., Rinkwitz S., Baker R. Mosaic hoxb4a neuronal pleiotropism in zebrafish caudal hindbrain. PLoS One 2009, 4:e5944.
105. Manuel M., Martynoga B., Yu T., West J.D., Mason J.O., Price D.J. The transcription factor Foxg1 regulates the competence of telencephalic cells to adopt subpallial fates in mice. Development 2010, 137:487-497.
106. Martynoga B., Morrison H., Price D.J., Mason J.O. Foxg1 is required for specification of ventral telencephalon and region-specific regulation of dorsal telencephalic precursor proliferation and apoptosis. Dev. Biol. 2005, 283:113-127.
107. Mathur P., Guo S. Use of zebrafish as a model to understand mechanisms of addiction and complex neurobehavioral phenotypes. Neurobiol. Dis. 2010, 40(1):66-72.
108. Mattick J.S. Deconstructing the dogma: a new view of the evolution and genetic programming of complex organisms. Ann. N.Y. Acad. Sci. 2009, 1178:29-46.
109. Megason S.G. In toto imaging of embryogenesis with confocal time-lapse microscopy. Methods Mol. Biol. 2009, 546:317-332.
110. Megason S.G., Fraser S.E. Imaging in systems biology. Cell 2007, 130:784-795.
111. Meng X., Noyes M.B., Zhu L.J., Lawson N.D., Wolfe S.A. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat. Biotechnol. 2008, 26:695-701.
112. Mueller T., Wullimann M.F. An evolutionary interpretation of teleostean forebrain anatomy. Brain Behav. Evol. 2009, 74:30-42.
113. Mueller T., Vernier P., Wullimann M.F. The adult central nervous cholinergic system of a neurogenetic model animal, the zebrafish Danio rerio. Brain Res. 2004, 1011:156-169.
114. Muzio L., Mallamaci A. Foxg1 confines Cajal-Retzius neuronogenesis and hippocampal morphogenesis to the dorsomedial pallium. J. Neurosci. 2005, 25:4435-4441.
115. Nagayoshi S., Hayashi E., Abe G., Osato N., Asakawa K., Urasaki A., Horikawa K., Ikeo K., Takeda H., Kawakami K. Insertional mutagenesis by the Tol2 transposon-mediated enhancer trap approach generated mutations in two developmental genes: tcf7 and synembryn-like. Development 2008, 135:159-169.
116. Nasevicius A., Ekker S.C. Effective targeted gene 'knockdown' in zebrafish. Nat. Genet. 2000, 26:216-220.
117. Naumann E.A., Kampff A.R., Prober D.A., Schier A.F., Engert F. Monitoring neural activity with bioluminescence during natural behavior. Nat. Neurosci. 2010, 13:513-520.
118. Navratilova P., Becker T.S. Genomic regulatory blocks in vertebrates and implications in human disease. Brief Funct. Genomic Proteomic 2009, 8:333-342.
119. Navratilova P., Fredman D., Hawkins T.A., Turner K., Lenhard B., Becker T.S. Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev. Biol. 2009, 327:526-540.
120. Navratilova P., Fredman D., Lenhard B., Becker T.S. Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol. Genet. Genomics 2010, 283:171-184.
121. Niell C.M., Smith S.J. Functional imaging reveals rapid development of visual response properties in the zebrafish tectum. Neuron 2005, 45:941-951.
122. Ninkovic J., Bally-Cuif L. The zebrafish as a model system for assessing the reinforcing properties of drugs of abuse. Methods 2006, 39:262-274.
123. Ninkovic J., Folchert A., Makhankov Y.V., Neuhauss S.C., Sillaber I., Straehle U., Bally-Cuif L. Genetic identification of AChE as a positive modulator of addiction to the psychostimulant D-amphetamine in zebrafish. J. Neurobiol. 2006, 66:463-475.
124. Norton W., Bally-Cuif L. Adult zebrafish as a model organism for behavioural genetics. BMC Neurosci. 2010, 11:90.
125. Oakley A.E., Clifton D.K., Steiner R.A. Kisspeptin signaling in the brain. Endocr. Rev. 2009, 30:713-743.
126. Osorio J., Mueller T., Retaux S., Vernier P., Wullimann M.F. Phylotypic expression of the bHLH genes Neurogenin2, Neurod, and Mash1 in the mouse embryonic forebrain. J. Comp. Neurol. 2010, 518:851-871.
127. Owens K.N., Santos F., Roberts B., Linbo T., Coffin A.B., Knisely A.J., Simon J.A., Rubel E.W., Raible D.W. Identification of genetic and chemical modulators of zebrafish mechanosensory hair cell death. PLoS Genet. 2008, 4:e1000020.
128. Parinov S., Kondrichin I., Korzh V., Emelyanov A. Tol2 transposon-mediated enhancer trap to identify developmentally regulated zebrafish genes in vivo. Dev. Dyn. 2004, 231:449-459.
129. Petzold A.M., Balciunas D., Sivasubbu S., Clark K.J., Bedell V.M., Westcot S.E., Myers S.R., Moulder G.L., Thomas M.J., Ekker S.C. Nicotine response genetics in the zebrafish. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:18662-18667.
130. Pissios P., Bradley R.L., Maratos-Flier E. Expanding the scales: the multiple roles of MCH in regulating energy balance and other biological functions. Endocr. Rev. 2006, 27:606-620.
131. Pologruto T.A., Yasuda R., Svoboda K. Monitoring neural activity and [Ca2+] with genetically encoded Ca2+ indicators. J. Neurosci. 2004, 24:9572-9579.
132. Portugues R., Engert F. The neural basis of visual behaviors in the larval zebrafish. Curr. Opin. Neurobiol. 2009, 19:644-647.
133. Prober D.A., Rihel J., Onah A.A., Sung R.J., Schier A.F. Hypocretin/orexin overexpression induces an insomnia-like phenotype in zebrafish. J. Neurosci. 2006, 26:13400-13410.
134. Puelles L., Rubenstein J.L. Forebrain gene expression domains and the evolving prosomeric model. Trends Neurosci. 2003, 26:469-476.
135. Punnamoottil B., Kikuta H., Pezeron G., Erceg J., Becker T.S., Rinkwitz S. Enhancer detection in zebrafish permits the identification of neuronal subtypes that express Hox4 paralogs. Dev. Dyn. 2008, 237:2195-2208.
136. Ragvin A., Moro E., Fredman D., Navratilova P., Drivenes O., Engstrom P.G., Alonso M.E., Mustienes Ede L., Skarmeta J.L., Tavares M.J., Casares F., Manzanares M., van Heyningen V., Molven A., Njolstad P.R., Argenton F., Lenhard B., Becker T.S. Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:775-780.
137. Reiff D.F., Ihring A., Guerrero G., Isacoff E.Y., Joesch M., Nakai J., Borst A. In vivo performance of genetically encoded indicators of neural activity in flies. J. Neurosci. 2005, 25:4766-4778.
138. Renier C., Faraco J.H., Bourgin P., Motley T., Bonaventure P., Rosa F., Mignot E. Genomic and functional conservation of sedative-hypnotic targets in the zebrafish. Pharmacogenet. Genomics 2007, 17:237-253.
139. Rihel J., Prober D.A., Arvanites A., Lam K., Zimmerman S., Jang S., Haggarty S.J., Kokel D., Rubin L.L., Peterson R.T., Schier A.F. Zebrafish behavioral profiling links drugs to biological targets and rest/wake regulation. Science 2010, 327:348-351.
140. Russek-Blum N., Gutnick A., Nabel-Rosen H., Blechman J., Staudt N., Dorsky R.I., Houart C., Levkowitz G. Dopaminergic neuronal cluster size is determined during early forebrain patterning. Development 2008, 135:3401-3413.
141. Sandelin A., Bailey P., Bruce S., Engstrom P.G., Klos J.M., Wasserman W.W., Ericson J., Lenhard B. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 2004, 5:99.
142. Saraswati S., Fox L.E., Soll D.R., Wu C.F. Tyramine and octopamine have opposite effects on the locomotion of Drosophila larvae. J. Neurobiol. 2004, 58:425-441.
143. Schaefer A., O'Carroll D., Tan C.L., Hillman D., Sugimori M., Llinas R., Greengard P. Cerebellar neurodegeneration in the absence of microRNAs. J. Exp. Med. 2007, 204:1553-1558.
144. Schafers C., Teigeler M., Wenzel A., Maack G., Fenske M., Segner H. Concentration- and time-dependent effects of the synthetic estrogen, 17alpha-ethinylestradiol, on reproductive capabilities of the zebrafish, Danio rerio. J. Toxicol. Environ. Health A 2007, 70:768-779.
145. Schoonheim P.J., Arrenberg A.B., Del Bene F., Baier H. Optogenetic localization and genetic perturbation of saccade-generating neurons in zebrafish. J. Neurosci. 2010, 30:7111-7120.
146. Scott E.K., Baier H. The cellular architecture of the larval zebrafish tectum, as revealed by gal4 enhancer trap lines. Front Neural Circuits 2009, 3:13.
147. Scott E.K., Mason L., Arrenberg A.B., Ziv L., Gosse N.J., Xiao T., Chi N.C., Asakawa K., Kawakami K., Baier H. Targeting neural circuitry in zebrafish using GAL4 enhancer trapping. Nat. Methods 2007, 4:323-326.
148. Shin J., Park H.C., Topczewska J.M., Mawdsley D.J., Appel B. Neural cell fate analysis in zebrafish using olig2 BAC transgenics. Methods Cell Sci. 2003, 25:7-14.
149. Shkumatava A., Stark A., Sive H., Bartel D.P. Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Dev. 2009, 23:466-481.
150. Sprague J., Bayraktaroglu L., Bradford Y., Conlin T., Dunn N., Fashena D., Frazer K., Haendel M., Howe D.G., Knight J., Mani P., Moxon S.A., Pich C., Ramachandran S., Schaper K., Segerdell E., Shao X., Singer A., Song P., Sprunger B., Van Slyke C.E., Westerfield M. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res. 2008, 36:D768-772.
151. Staudt N., Houart C. The prethalamus is established during gastrulation and influences diencephalic regionalization. PLoS Biol. 2007, 5:e69.
152. Stigloher C., Ninkovic J., Laplante M., Geling A., Tannhauser B., Topp S., Kikuta H., Becker T.S., Houart C., Bally-Cuif L. Segregation of telencephalic and eye-field identities inside the zebrafish forebrain territory is controlled by Rx3. Development 2006, 133:2925-2935.
153. Stuhmer T., Puelles L., Ekker M., Rubenstein J.L. Expression from a Dlx gene enhancer marks adult mouse cortical GABAergic neurons. Cereb. Cortex 2002, 12:75-85.
154. Suster M.L., Kikuta H., Urasaki A., Asakawa K., Kawakami K. Transgenesis in zebrafish with the tol2 transposon system. Methods Mol. Biol. 2009, 561:41-63.
155. Suster M.L., Sumiyama K., Kawakami K. Transposon-mediated BAC transgenesis in zebrafish and mice. BMC Genomics 2009, 10:477.
156. Szobota S., Gorostiza P., Del Bene F., Wyart C., Fortin D.L., Kolstad K.D., Tulyathan O., Volgraf M., Numano R., Aaron H.L., Scott E.K., Kramer R.H., Flannery J., Baier H., Trauner D., Isacoff E.Y. Remote control of neuronal activity with a light-gated glutamate receptor. Neuron 2007, 54:535-545.
157. Takacs C.M., Giraldez A.J. MicroRNAs as genetic sculptors: fishing for clues. Semin. Cell Dev. Biol. 2010, (7):760-767.
158. Thatcher E.J., Bond J., Paydar I., Patton J.G. Genomic organization of zebrafish microRNAs. BMC Genomics 2008, 9:253.
159. Thisse B., Thisse C. Functions and regulations of fibroblast growth factor signaling during embryonic development. Dev. Biol. 2005, 287:390-402.
160. Thisse C., Thisse B. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat. Protoc. 2008, 3:59-69.
161. Thisse B., Heyer V., Lux A., Alunni V., Degrave A., Seiliez I., Kirchner J., Parkhill J.P., Thisse C. Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening. Methods Cell Biol. 2004, 77:505-519.
162. Tomancak P., Berman B.P., Beaton A., Weiszmann R., Kwan E., Hartenstein V., Celniker S.E., Rubin G.M. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2007, 8:R145.
163. Trowe T., Klostermann S., Baier H., Granato M., Crawford A.D., Grunewald B., Hoffmann H., Karlstrom R.O., Meyer S.U., Muller B., Richter S., Nusslein-Volhard C., Bonhoeffer F. Mutations disrupting the ordering and topographic mapping of axons in the retinotectal projection of the zebrafish, Danio rerio. Development 1996, 123:439-450.
164. van Aerle R., Kille P., Lange A., Tyler C.R. Evidence for the existence of a functional Kiss1/Kiss1 receptor pathway in fish. Peptides 2008, 29:57-64.
165. Van de Peer Y., Maere S., Meyer A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 2009, 10:725-732.
166. Vaughan J.M., Fischer W.H., Hoeger C., Rivier J., Vale W. Characterization of melanin-concentrating hormone from rat hypothalamus. Endocrinology 1989, 125:1660-1665.
167. Wang D., Jao L.E., Zheng N., Dolan K., Ivey J., Zonies S., Wu X., Wu K., Yang H., Meng Q., Zhu Z., Zhang B., Lin S., Burgess S.M. Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:12428-12433.
168. Webb K.J., Norton W.H., Trumbach D., Meijer A.H., Ninkovic J., Topp S., Heck D., Marr C., Wurst W., Theis F.J., Spaink H.P., Bally-Cuif L. Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biol. 2009, 10:R81.
169. White R.M., Sessa A., Burke C., Bowman T., LeBlanc J., Ceol C., Bourque C., Dovey M., Goessling W., Burns C.E., Zon L.I. Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell 2008, 2:183-189.
170. Whitlock K.E., Smith K.M., Kim H., Harden M.V. A role for foxd3 and sox10 in the differentiation of gonadotropin-releasing hormone (GnRH) cells in the zebrafish Danio rerio. Development 2005, 132:5491-5502.
171. Whitlock K.E., Illing N., Brideau N.J., Smith K.M., Twomey S. Development of GnRH cells: setting the stage for puberty. Mol. Cell. Endocrinol. 2006, 254-255:39-50.
172. Wienholds E., van Eeden F., Kosters M., Mudde J., Plasterk R.H.., Cuppen E. Efficient target-selected mutagenesis in zebrafish. Genome Res. 2003, 13:2700-2707.
173. Wienholds E., Kloosterman W.P., Miska E., Alvarez-Saavedra E., Berezikov E., de Bruijn E., Horvitz H.R., Kauppinen S., Plasterk R.H. MicroRNA expression in zebrafish embryonic development. Science 2005, 309:310-311.
174. Wilson S.W., Houart C. Early steps in the development of the forebrain. Dev. Cell 2004, 6:167-181.
175. Wyart C., Del Bene F., Warp E., Scott E.K., Trauner D., Baier H., Isacoff E.Y. Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature 2009, 461:407-410.
176. Yamamoto K., Ruuskanen J.O., Wullimann M.F., Vernier P. Two tyrosine hydroxylase genes in vertebrates New dopaminergic territories revealed in the zebrafish brain. Mol. Cell. Neurosci. 2010, 43:394-402.
177. Yang Z., Jiang H., Chachainasakul T., Gong S., Yang X.W., Heintz N., Lin S. Modified bacterial artificial chromosomes for zebrafish transgenesis. Methods 2006, 39:183-188.
178. Yang L., Ho N.Y., Alshut R., Legradi J., Weiss C., Reischl M., Mikut R., Liebel U., Muller F., Strahle U. Zebrafish embryos as models for embryotoxic and teratological effects of chemicals. Reprod. Toxicol. 2009, 28:245-253.
179. Yokogawa T., Marin W., Faraco J., Pezeron G., Appelbaum L., Zhang J., Rosa F., Mourrain P., Mignot E. Characterization of sleep in zebrafish and insomnia in hypocretin receptor mutants. PLoS Biol. 2007, 5:e277.
180. Zeitzer J.M., Nishino S., Mignot E. The neurobiology of hypocretins (orexins), narcolepsy and related therapeutic interventions. Trends Pharmacol. Sci. 2006, 27:368-374.
181. Zeng Y. Regulation of the mammalian nervous system by microRNAs. Mol. Pharmacol. 2009, 75:259-264.
182. Zhao X., He X., Han X., Yu Y., Ye F., Chen Y., Hoang T., Xu X., Mi Q.S., Xin M., Wang F., Appel B., Lu Q.R. MicroRNA-mediated control of oligodendrocyte differentiation. Neuron 2010, 65:612-626.
183. Zhu P., Narita Y., Bundschuh S.T., Fajardo O., Scharer Y.P., Chattopadhyaya B., Bouldoires E.A., Stepien A.E., Deisseroth K., Arber S., Sprengel R., Rijli F.M., Friedrich R.W. Optogenetic dissection of neuronal circuits in zebrafish using viral gene transfer and the tet system. Front Neural Circuits 2009, 3:21.
184. Ziv L., Gothilf Y. Period2 expression pattern and its role in the development of the pineal circadian clock in zebrafish. Chronobiol. Int. 2006, 23:101-112.
185. Zohar Y., Munoz-Cueto J.A., Elizur A., Kah O. Neuroendocrinology of reproduction in teleost fish. Gen. Comp. Endocrinol. 2010, 165:438-455.