Genome editing using artificial site-specific nucleases in zebrafish

Development Growth and Differentiation

Volumn 56, Issue 1, 2014, Pages 26-33

  Hisano, Yu ^a   Ota, Satoshi ^a   Kawahara, Atsuo ^a  

^a RIKEN Center for Biosystems Dynamics Research   (Japan)

Author keywords

clustered regularly interspaced short palindromic repeats Cas9; Genome editing; Heteroduplex mobility assay; transcription activator like effector nucleases

Indexed keywords

BETA GALACTOSIDASE; HETERODUPLEX; NUCLEASE; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR NUCLEASE; UNCLASSIFIED DRUG; RESTRICTION ENDONUCLEASE;

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DNA MODIFICATION; ENZYME ACTIVITY; GENE DISRUPTION; GENE FUNCTION; GENE LOCUS; GENE MAPPING; GENE MUTATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC PROCEDURES; GENOME EDITING; HETERODUPLEX ANALYSIS; IN VIVO STUDY; MUTANT; NONHUMAN; REVIEW; ZEBRA FISH; ANIMAL; CRISPR CAS SYSTEM; ENZYME SPECIFICITY; GENETIC ENGINEERING; GENETICS; GENOME; METABOLISM; PROCEDURES;

DANIO RERIO; MUS; VERTEBRATA;

ANIMALS; CRISPR-CAS SYSTEMS; DNA RESTRICTION ENZYMES; GENETIC ENGINEERING; GENOME; SUBSTRATE SPECIFICITY; ZEBRAFISH;

EID: 84892670711     PISSN: 00121592     EISSN: 1440169X     Source Type: Journal    
DOI: 10.1111/dgd.12094     Document Type: Review

References (38)

1. Ansai, S., Sakuma, T., Yamamoto, T., Ariga, H., Uemura, N., Takahashi, R. & Kinoshita, M. 2013. Efficient targeted mutagenesis in medaka using custom-designed transcription activator-like effector nucleases. Genetics 193, 739-749.
2. Bedell, V. M., Wang, Y., Campbell, J. M., Poshusta, T.L., Starker, C.G., Krug, R.G. 2nd., Tan, W., Penheiter, S.G., Ma, A.C., Leung, A.Y., Fahrenkrug, S.C., Carlson, D.F., Voytas, D.F., Clark, K.J., Essner, J.J. & Ekker, S.C. 2012. In vivo genome editing using a high-efficiency TALEN system. Nature 491, 114-118.
3. Ben Shoham, A., Malkinson, G., Krief, S., Shwartz, Y., Ely, Y., Ferrara, N., Yaniv, K. & Zelzer, E. 2012. S1P1 inhibits sprouting angiogenesis during vascular development. Development 139, 3859-3869.
4. Beumer, K. J., Trautman, J. K., Bozas, A., Liu, J.L., Rutter, J., Gall, J.G. & Carroll, D. 2008. Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc. Natl Acad. Sci. USA 105, 19821-19826.
5. Carroll, D. 2011. Genome engineering with zinc-finger nucleases. Genetics 188, 773-782.
6. Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., Baller, J.A., Somia, N.V., Bogdanove, A.J. & Voytas, D.F. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39, e82.
7. Chen, J., Zhang, X., Wang, T., Li, Z., Guan, G. & Hong, Y. 2012. Efficient detection, quantification and enrichment of subtle allelic alterations. DNA Res. 19, 423-433.
8. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A. & Zhang, F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823.
9. Cradick, T. J., Fine, E. J., Antico, C. J. & Bao, G. 2013. CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. doi: 10.1093/nar/gkt714.
10. Dahlem, T. J., Hoshijima, K., Jurynec, M. J., Gunther, D., Starker, C.G., Locke, A.S., Weis, A.M., Voytas, D.F. & Grunwald, D.J. 2012. Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genet. 8, e1002861.
11. Dawid, I. B. 2004. Developmental biology of zebrafish. Ann. N. Y. Acad. Sci. 1038, 88-93.
12. Fukui, H., Hanaoka, R. & Kawahara, A. 2009. Noncanonical activity of seryl-tRNA synthetase is involved in vascular development. Circ. Res. 104, 1253-1259.
13. 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. & Nüsslein-Volhard, C. 1996. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123, 1-36.
14. Hisano, Y., Kobayashi, N., Yamaguchi, A. & Nishi, T. 2012a. Mouse SPNS2 functions as a sphingosine-1-phosphate transporter in vascular endothelial cells. PLoS ONE 7, e38941.
15. Hisano, Y., Nishi, T. & Kawahara, A. 2012b. The functional roles of S1P in immunity. J. Biochem. 152, 305-311.
16. Hisano, Y., Ota, S., Arakawa, K., Kono, N., Oshita, K., Sakuma, T., Tomita, M., Yamamoto, T., Okada, Y. & Kawahara, A. 2013a. Quantitative assay for TALEN activity at endogenous genomic loci. Biol. Open 2, 363-367.
17. Hisano, Y., Ota, S., Takada, S. & Kawahara, A. 2013b. Functional cooperation of spns2 and fibronectin in cardiac and lower jaw development. Biol. Open 2, 789-794.
18. Hla, T., Venkataraman, K. & Michaud, J. 2008. The vascular S1P gradient-cellular sources and biological significance. Biochim. Biophys. Acta 1781, 477-482.
19. Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., Collins, J.E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G.J., White, S., Chow, W., Kilian, B., Quintais, L.T., Guerra-Assunção, J.A., Zhou, Y., Gu, Y., Yen, J., Vogel, J.H., Eyre, T., Redmond, S., Banerjee, R., Chi, J., Fu, B., Langley, E., Maguire, S.F., Laird, G.K., Lloyd, D., Kenyon, E., Donaldson, S., Sehra, H., Almeida-King, J., Loveland, J., Trevanion, S., Jones, M., Quail, M., Willey, D., Hunt, A., Burton, J., Sims, S., McLay, K., Plumb, B., Davis, J., Clee, C., Oliver, K., Clark, R., Riddle, C., Eliott, D., Threadgold, G., Harden, G., Ware, D., Mortimer, B., Kerry, G., Heath, P., Phillimore, B., Tracey, A., Corby, N., Dunn, M., Johnson, C., Wood, J., Clark, S., Pelan, S., Griffiths, G., Smith, M. & Glithero, R., Howden, P., Barker, N., Stevens, C., Harley, J., Holt, K., Panagiotidis, G., Lovell, J., Beasley, H., Henderson, C., Gordon, D., Auger, K., Wright, D., Collins, J., Raisen, C., Dyer, L., Leung, K., Robertson, L., Ambridge, K., Leongamornlert, D., McGuire, S., Gilderthorp, R., Griffiths, C., Manthravadi, D., Nichol, S., Barker, G., Whitehead, S., Kay, M., Brown, J., Murnane, C., Gray, E., Humphries, M., Sycamore, N., Barker, D., Saunders, D., Wallis, J., Babbage, A., Hammond, S., Mashreghi-Mohammadi, M., Barr, L., Martin, S., Wray, P., Ellington, A., Matthews, N., Ellwood, M., Woodmansey, R., Clark, G., Cooper, J., Tromans, A., Grafham, D., Skuce, C., Pandian, R., Andrews, R., Harrison, E., Kimberley, A., Garnett, J., Fosker, N., Hall, R., Garner, P., Kelly, D., Bird, C., Palmer, S., Gehring, I., Berger, A., Dooley, C.M., Ersan-Ürün, Z., Eser, C., Geiger, H., Geisler, M., Karotki, L., Kirn, A., Konantz, J., Konantz, M., Oberländer, M., Rudolph-Geiger, S., Teucke, M., Osoegawa, K., Zhu, B., Rapp, A., Widaa, S., Langford, C., Yang, F., Carter, N.P., Harrow, J., Ning, Z., Herrero, J., Searle, S.M., Enright, A., Geisler, R., Plasterk, R.H., Lee, C., Westerfield, M., de Jong, P.J., Zon, L.I., Postlethwait, J.H., Nüsslein-Volhard, C., Hubbard, T.J., Roest Crollius, H., Rogers, J. & Stemple, D.L. 2013. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498-503.
20. Joung, J. K. & Sander, J. D. 2013. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 14, 49-55.
21. Kawahara, A., Nishi, T., Hisano, Y., Fukui, H., Yamaguchi, A. & Mochizuki, N. 2009. The sphingolipid transporter spns2 functions in migration of zebrafish myocardial precursors. Science 323, 524-527.
22. Kim, H. J., Lee, H. J., Kim, H., Cho, S.W. & Kim, J.S. 2009. Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res. 19, 1279-1288.
23. Kupperman, E., An, S., Osborne, N., Waldron, S. & Stainier, D. Y. 2000. A sphingosine-1-phosphate receptor regulates cell migration during vertebrate heart development. Nature 406, 192-195.
24. Li, T., Liu, B., Spalding, M. H., Weeks, D. P. & Yang, B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat. Biotechnol. 30, 390-392.
25. Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J.E., Norville, J.E. & Church, G.M. 2013. RNA-guided human genome engineering via Cas9. Science, 339, 823-826.
26. Mashimo, T., Kaneko, T., Sakuma, T., Kobayashi, J., Kunihiro, Y., Voigt, B., Yamamoto, T. & Serikawa, T. 2013. Efficient gene targeting by TAL effector nucleases coinjected with exonucleases in zygotes. Sci. Rep. 3, 1253.
27. Mendelson, K., Zygmunt, T., Torres-Vazquez, J., Evans, T. & Hla, T. 2013. Sphingosine 1-phosphate receptor signaling regulates proper embryonic vascular patterning. J. Biol. Chem. 288, 2143-2156.
28. Nasevicius, A. & Ekker, S. C. 2000. Effective targeted gene 'knockdown' in zebrafish. Nat. Genet. 26, 216-220.
29. Nishi, T., Kobayashi, N., Hisano, Y., Kawahara, A. & Yamaguchi, A. 2013. Molecular and physiological functions of sphingosine 1-phosphate transporters. Biochim. Biophys. Acta. (in press).
30. Osborne, N., Brand-Arzamendi, K., Ober, E. A., Jin, S.W., Verkade, H., Holtzman, N.G., Yelon, D. & Stainier, D.Y. 2008. The spinster homolog, two of hearts, is required for sphingosine 1-phosphate signaling in zebrafish. Curr. Biol. 18, 1882-1888.
31. Ota, S., Hisano, Y., Muraki, M., Hoshijima, K., Dahlem, T.J., Grunwald, D.J., Okada, Y. & Kawahara, A. 2013. Efficient identification of TALEN-mediated genome modifications using heteroduplex mobility assays. Genes Cells 18, 450-458.
32. Robu, M. E., Larson, J. D., Nasevicius, A., Beiraghi, S., Brenner, C., Farber, S.A. & Ekker, S.C. 2007. P53 activation by knockdown technologies. PLoS Genet. 3, e78.
33. Sakuma, T., Hosoi, S., Woltjen, K., Suzuki, K., Kashiwagi, K., Wada, H., Ochiai, H., Miyamoto, T., Kawai, N., Sasakura, Y., Matsuura, S., Okada, Y., Kawahara, A., Hayashi, S. & Yamamoto, T. 2013. Efficient TALEN construction and evaluation methods for human cell and animal applications. Genes Cells 18, 315-326.
34. Spiegel, S. & Milstien, S. 2011. The outs and the ins of sphingosine-1-phosphate in immunity. Nat. Rev. Immunol. 11, 403-415.
35. Thisse, C. & Zon, L. I. 2002. Organogenesis-heart and blood formation from the zebrafish point of view. Science 295, 457-462.
36. Tobia, C., Chiodelli, P., Nicoli, S., Dell'era, P., Buraschi, S., Mitola, S., Foglia, E., van Loenen, P.B., Alewijnse, A.E. & Presta, M. 2012. Sphingosine-1-phosphate receptor-1 controls venous endothelial barrier integrity in zebrafish. Arterioscler. Thromb. Vasc. Biol. 32, e104-e116.
37. Wienholds, E., Schulte-Merker, S., Walderich, B. & Plasterk, R. H. 2002. Target-selected inactivation of the zebrafish rag1 gene. Science, 297, 99-102.
38. Zu, Y., Tong, X., Wang, Z., Liu, D., Pan, R., Li, Z., Hu, Y., Luo, Z., Huang, P., Wu, Q., Zhu, Z., Zhang, B. & Lin, S. 2013. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat. Methods 10, 329-331.