Properties of gene knockdown system by vector-based siRNA in zebrafish

Development Growth and Differentiation

Volumn 55, Issue 9, 2013, Pages 755-765

  Shinya, Minori ^a,b   Kobayashi, Kayo ^a,c   Masuda, Aki ^a   Tokumoto, Mika ^a   Ozaki, Yuichi ^a,d   Saito, Kenji ^a   Kawasaki, Toshihiro ^a   Sado, Yukiko ^a,e   Sakai, Noriyoshi ^a,b  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING   (Germany)

^d FISHERIES RESEARCH AGENCY   (Japan)

^e KYUSHU UNIVERSITY   (Japan)

Author keywords

RNAi; ShRNA; SiRNA; U6 snRNA promoter

Indexed keywords

BONE MORPHOGENETIC PROTEIN; DNA DIRECTED RNA POLYMERASE III; ENHANCED GREEN FLUORESCENT PROTEIN; MESSENGER RNA; MICRORNA; RNA POLYMERASE II; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; SONIC HEDGEHOG PROTEIN; DNA DIRECTED RNA POLYMERASE; GREEN FLUORESCENT PROTEIN;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; DOWN REGULATION; EMBRYO; FEMALE; GENE EXPRESSION; GENE SILENCING; IN VITRO STUDY; MALE; MESSENGER RNA SYNTHESIS; NONHUMAN; NORTHERN BLOTTING; PHENOTYPE; POLYMERASE CHAIN REACTION; PRACTICE GUIDELINE; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; RNA INTERFERENCE; RNA VECTOR; ZEBRA FISH; ANIMAL; ANIMAL EMBRYO; GENE VECTOR; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION;

ANIMALIA; DANIO RERIO;

ANIMALS; BASE SEQUENCE; BLOTTING, NORTHERN; CLONING, MOLECULAR; DNA-DIRECTED RNA POLYMERASES; EMBRYO, NONMAMMALIAN; FEMALE; GENE KNOCKDOWN TECHNIQUES; GENETIC VECTORS; GREEN FLUORESCENT PROTEINS; MALE; MICRORNAS; MOLECULAR SEQUENCE DATA; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE; RNA, SMALL INTERFERING; ZEBRAFISH;

EID: 84890792973     PISSN: 00121592     EISSN: 1440169X     Source Type: Journal    
DOI: 10.1111/dgd.12091     Document Type: Article

References (40)

1. Agrawal, N., Dasaradhi, P. V., Mohmmed, A., Malhotra, P., Bhatnagar, R. K. & Mukherjee, S. K. 2003. RNA interference: biology, mechanism, and applications. Microbiol. Mol. Biol. Rev. 67, 657-685.
2. Asakawa, K., Suster, M. L., Mizusawa, K., Nagayoshi, S., Kotani, T., Urasaki, A., Kishimoto, Y., Hibi, M. & Kawakami, K. 2008. Genetic dissection of neural circuits by Tol2 transposon-mediated Gal4 gene and enhancer trapping in zebrafish. Proc. Natl. Acad. Sci. USA 105, 1255-1260.
3. Chang, K., Elledge, S. J. & Hannon, G. J. 2006. Lessons from Nature: microRNA-based shRNA libraries. Nat. Methods 3, 707-714.
4. De Rienzo, G., Gutzman, J. H. & Sive, H. 2012. Efficient shRNA-mediated inhibition of gene expression in zebrafish. Zebrafish 9, 97-107.
5. Dodd, A., Chambers, S. P. & Love, D. R. 2004. Short interfering RNA-mediated gene targeting in the zebrafish. FEBS Lett. 561, 89-93.
6. Dong, M., Fu, Y. F., Du, T. T., Jing, C. B., Fu, C. T., Chen, Y., Jin, Y., Deng, M. & Liu, T. X. 2009. Heritable and lineage-specific gene knockdown in zebrafish embryo. PLoS ONE 4, e6125.
7. 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. 2008. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol. 26, 702-708.
8. 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. 1996. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123, 37-46.
9. Du, G., Yonekubo, J., Zeng, Y., Osisami, M. & Frohman, M. A. 2006. Design of expression vectors for RNA interference based on miRNAs and RNA splicing. FEBS J. 273, 5421-5427.
10. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E. & Mello, C. C. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.
11. 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. 2005. MicroRNAs regulate brain morphogenesis in zebrafish. Science 308, 833-838.
12. Gruber, J., Manninga, H., Tuschl, T., Osborn, M. & Weber, K. 2005. Specific RNAi mediated gene knockdown in zebrafish cell lines. RNA Biol. 2, 101-105.
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. & Nusslein-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. Hou, X., Omi, M., Harada, H., Ishii, S., Takahashi, Y. & Nakamura, H. 2011. Conditional knockdown of target gene expression by tetracycline regulated transcription of double strand RNA. Dev. Growth Differ. 53, 69-75.
15. Huang, P., Xiao, A., Zhou, M., Zhu, Z., Lin, S. & Zhang, B. 2011. Heritable gene targeting in zebrafish using customized TALENs. Nat. Biotechnol. 29, 699-700.
16. Johnson, A. D. & Krieg, P. A. 1994. pXeX, a vector for efficient expression of cloned sequences in Xenopus embryos. Gene 147, 223-226.
17. Kane, D. A. & Kishimoto, Y. 2002. Cell labelling and transplantation techniques. In: Zebrafish (eds C. Nüsslein-Volhard & R. Dahm ), pp. 95-119, Oxford University Press, New York.
18. Katahira, T. & Nakamura, H. 2003. Gene silencing in chick embryos with a vector-based small interfering RNA system. Dev. Growth Differ. 45, 361-367.
19. Kawakami, K., Takeda, H., Kawakami, N., Kobayashi, M., Matsuda, N. & Mishina, M. 2004. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev. Cell 7, 133-144.
20. Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B. & Schilling, T. F. 1995. Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253-310.
21. Kishimoto, Y., Lee, K. H., Zon, L., Hammerschmidt, M. & Schulte-Merker, S. 1997. The molecular nature of zebrafish swirl: BMP2 function is essential during early dorsoventral patterning. Development 124, 4457-4466.
22. Li, X., Zhao, X., Fang, Y., Jiang, X., Duong, T., Fan, C., Huang, C. C. & Kain, S. R. 1998. Generation of destabilized green fluorescent protein as a transcription reporter. J. Biol. Chem. 273, 34970-34975.
23. Meng, X., Noyes, M. B., Zhu, L. J., Lawson, N. D. & Wolfe, S. A. 2008. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat. Biotechnol. 26, 695-701.
24. Mullins, M. C., Hammerschmidt, M., Kane, D. A., Odenthal, J., Brand, M., Van Eeden, F. J., Furutani-Seiki, M., Granato, M., Haffter, P., Heisenberg, C. P., Jiang, Y. J., Kelsh, R. N. & Nusslein-Volhard, C. 1996. Genes establishing dorsoventral pattern formation in the zebrafish embryo: the ventral specifying genes. Development 123, 81-93.
25. Nasevicius, A. & Ekker, S. C. 2000. Effective targeted gene 'knockdown' in zebrafish. Nat. Genet. 26, 216-220.
26. Nikaido, M., Tada, M., Saji, T. & Ueno, N. 1997. Conservation of BMP signaling in zebrafish mesoderm patterning. Mech. Dev. 61, 75-88.
27. Rupp, R. A., Snider, L. & Weintraub, H. 1994. Xenopus embryos regulate the nuclear localization of XMyoD. Genes Dev. 8, 1311-1323.
28. Sander, J. D., Cade, L., Khayter, C., Peterson, R. T., Joung, J. K. & Yeh, J. R. 2011. Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat. Biotechnol. 29, 697-698.
29. Schauerte, H. E., van Eeden, F. J., Fricke, C., Odenthal, J., Strahle, U. & Haffter, P. 1998. Sonic hedgehog is not required for the induction of medial floor plate cells in the zebrafish. Development 125, 2983-2993.
30. Shinya, M., Koshida, S., Sawada, A., Kuroiwa, A. & Takeda, H. 2001. Fgf signalling through MAPK cascade is required for development of the subpallial telencephalon in zebrafish embryos. Development 128, 4153-4164.
31. Streisinger, G., Walker, C., Dower, N., Knauber, D. & Singer, F. 1981. Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291, 293-296.
32. Ui-Tei, K., Naito, Y., Takahashi, F., Haraguchi, T., Ohki-Hamazaki, H., Juni, A., Ueda, R. & Saigo, K. 2004. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 32, 936-948.
33. Urasaki, A., Morvan, G. & Kawakami, K. 2006. Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics 174, 639-649.
34. Valoczi, A., Hornyik, C., Varga, N., Burgyan, J., Kauppinen, S. & Havelda, Z. 2004. Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res. 32, e175.
35. van Eeden, F. J., Granato, M., Schach, U., 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., Warga, R. M., Allende, M. L., Weinberg, E. S. & Nusslein-Volhard, C. 1996. Mutations affecting somite formation and patterning in the zebrafish, Danio rerio. Development 123, 153-164.
36. Ventura, A., Meissner, A., Dillon, C. P., Mcmanus, M., Sharp, P. A., Van Parijs, L., Jaenisch, R. & Jacks, T. 2004. Cre-lox-regulated conditional RNA interference from transgenes. Proc. Natl. Acad. Sci. USA 101, 10380-10385.
37. Wienholds, E., Kloosterman, W. P., Miska, E., Alvarez-Saavedra, E., Berezikov, E., De Bruijn, E., Horvitz, H. R., Kauppinen, S. & Plasterk, R. H. 2005. MicroRNA expression in zebrafish embryonic development. Science 309, 310-311.
38. Wienholds, E., Schulte-Merker, S., Walderich, B. & Plasterk, R. H. 2002. Target-selected inactivation of the zebrafish rag1 gene. Science 297, 99-102.
39. Wienholds, E., van Eeden, F., Kosters, M., Mudde, J., Plasterk, R. H. & Cuppen, E. 2003. Efficient target-selected mutagenesis in zebrafish. Genome Res. 13, 2700-2707.
40. Wiznerowicz, M., Szulc, J. & Trono, D. 2006. Tuning silence: conditional systems for RNA interference. Nat. Methods 3, 682-688.