Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish

Nature Protocols

Volumn 1, Issue 3, 2006, Pages 1297-1305

  Fisher, Shannon ^a   Grice, Elizabeth A ^a   Vinton, Ryan M ^a   Bessling, Seneca L ^a   Urasaki, Akihiro ^b   Kawakami, Koichi ^b   McCallion, Andrew S ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA;

ANIMAL; ARTICLE; ENHANCER REGION; GENE TRANSFER; GENETICS; GENOMICS; METHODOLOGY; POLYMERASE CHAIN REACTION; TRANSPOSON; ZEBRA FISH;

ANIMALS; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; ENHANCER ELEMENTS (GENETICS); GENE TRANSFER TECHNIQUES; GENOMICS; POLYMERASE CHAIN REACTION; ZEBRAFISH;

EID: 34347244234     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.230     Document Type: Article

References (19)

1. Kimura, M. & Ota, T. Protein polymorphism as a phase of molecular evolution. Nature 229, 467-469 (1971).
2. Pennacchio, L.A. & Rubin, E.M. Genomic strategies to identify mammalian regulatory sequences. Nature Rev. Genet. 2, 100-109 (2001).
3. Waterston, R.H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
4. Woolfe, A. et al. Highly conserved noncoding sequences are associated with vertebrate development. PLoS Biol 3, e7 (2005).
5. Koga, A., Suzuki, M., Inagaki, H., Bessho, Y. & Hori, H. Transposable element in fish. Nature 383, 30 (1996).
6. Davidson, A.E. et al. Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon. Dev. Biol. 263, 191-202 (2003).
7. Ivics, Z., Hackett, P.B., Plasterk, R.H. & Izsvak, Z. Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell 91, 501-510 (1997).
8. Thermes, V. et al. I-SceI meganuclease mediates highly efficient transgenesis in fish. Mech. Dev. 118, 91-98 (2002).
9. Kawakami K. et al. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev. Cell 7, 133-144 (2004).
10. Dorsky, R.I., Sheldahl, L.C. & Moon, R.T. A transgenic Lef1/ β-catenin-dependent reporter is expressed in spatially restricted domains throughout zebrafish development. Dev. Biol. 241, 229-237 (2002).
11. 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 312, 276-279 (2006).
12. Johnson, S.L. & Zon, L.I. Genetic backgrounds and some standard stocks and strains used in zebrafish developmental biology and genetics. Methods Cell Biol 60, 357-359 (1999).
13. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
14. Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M. & Dubchak, I. VISTA: Computational tools for comparative genomics. Nucleic Acids Res. 32, W273-W279 (2004).
15. Schwartz, S. et al. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 10, 577-586 (2000).
16. Margulies, E.H., Blanchette, M., Haussler, D., & Green, E.D. Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507-2518 (2003).
17. Kolbe, D. et al. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res. 14 706-707 (2004).
18. Brudno, M., Chapman, M., Gottgens, B., Batzoglou, S. & Morgenstern, B. Fast and sensitive multiple alignment of Large genomic sequences. BMC Bioinformatics 4, 66 (2003).
19. Westerfield, M. (ed.) The Zebrafish Book(University of Oregon Press, Eugene, OR, 1995).