Characterization of zebrafish polymerase III promoters for the expression of short-hairpin RNA interference molecules

Zebrafish

Volumn 10, Issue 4, 2013, Pages 472-479

  Clarke, Brian D ^a,b   Cummins, David M ^a   McColl, Ken A ^a   Ward, Alister C ^b   Doran, Tim J ^a  

^a CSIRO   (Australia)

^b DEAKIN UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; CHLOROCEBUS AETHIOPS; COMPARATIVE STUDY; GENE SILENCING; GENETICS; METABOLISM; PROMOTER REGION; VERO CELL LINE; ZEBRA FISH;

ANIMALS; CERCOPITHECUS AETHIOPS; GENE KNOCKDOWN TECHNIQUES; GREEN FLUORESCENT PROTEINS; PROMOTER REGIONS, GENETIC; RNA POLYMERASE III; RNA, SMALL INTERFERING; VERO CELLS; ZEBRAFISH;

EID: 84888401705     PISSN: 15458547     EISSN: None     Source Type: Journal    
DOI: 10.1089/zeb.2012.0782     Document Type: Article

References (54)

1. Brummelkamp TR, Bernards R, Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science 202;296:550-553
2. Roelz R, Pilz IH, Mutschler M, Pahl HL. Of mice and men: Human RNA polymerase III promoter U6 is more efficient than its murine homologue for shRNA expression from a lentiviral vector in both human and murine progenitor cells. Exp Hematol 2010;38:792-797
3. Wise TG, Schafer DJ, Lambeth LS, Tyack SG, Bruce MP, Moore RJ, Doran TJ. Characterization and comparison of chicken U6 promoters for the expression of short hairpin RNAs. Animal Biotechnol 2007;18:153-162
4. Lambeth LS, Wise TG, Moore RJ, Muralitharan MS, Doran TJ. Comparison of bovine RNA polymerase III promoters for short hairpin RNA expression. Animal Genet 2006;37: 369-372
5. Bannister S, Wise T, Cahill D, Doran T. Comparison of chicken 7SK and U6 RNA polymerase III promoters for short hairpin RNA expression. BMC Biotechnol 2007;7:79
6. Mosimann C, Kaufman CK, Li P, Pugach EK, Tamplin OJ, Zon LI. Ubiquitous transgene expression and Cre-based recombination driven by the ubiquitin promoter in zebrafish. Development 2011;138:169-177
7. Kawakami K. Tol2: A versatile gene transfer vector in vertebrates. Genome Biol 2007;8:S7
8. Nasevicius A, Ekker SC. Effective targeted gene/ 'knockdown/' in zebrafish. Nature Genet 2000;26:216-220
9. Dong M, Fu YF, Du TT, Jing CB, Fu CT, Chen Y, et al. Heritable and lineage-specific gene knockdown in zebrafish embryo. PLoS ONE 2009;4:e6125
10. Boonanuntanasarn S, Panyim S, Yoshizaki G. Usage of putative zebrafish U6 promoters to express shRNA in Nile tilapia and shrimp cell extracts. Transgen Res 2009;18: 323-325
11. Oates AC, Bruce AE, Ho RK. Too much interference: Injection of double-stranded RNA has nonspecific effects in the zebrafish embryo. Develop Biol 2000;224:20-28
12. Wargelius A, Ellingsen S, Fjose A. Double-stranded RNA induces specific developmental defects in zebrafish embryos. Biochem Biophys Res Commun 1999;263:156-161
13. Zhao X-F, Fjose A, Larsen N, Helvik JV, Drivenes Ø. Treatment with small interfering RNA affects the microRNA pathway and causes unspecific defects in zebrafish embryos. FEBS J 2008;275:2177-2184
14. Liu, W-Y, Wang Y, Sun YH, Want Y, Wang UP, Chen SP, Zhy ZY. Efficient RNA interference in zebrafish embryos using siRNA synthesized with SP6 RNA polymerase. Develop Growth Different 2005;47:323-331
15. Boonanuntanasarn S, Yoshizaki G, Takeuchi T. Specific gene silencing using small interfering RNAs in fish embryos. Biochem Biophys Res Commun 2003;310:1089-1095
16. Bohle H, Lorenzen N, Schyth BD. Species specific inhibition of viral replication using dicer substrate siRNAs (DsiRNAs) targeting the viral nucleoprotein of the fish pathogenic rhabdovirus viral hemorrhagic septicemia virus (VHSV). Antiviral Res 2011;90:187-194
17. Kim M, Jee BY, Cho MY, Kim JW, Jeong HD, Kim KH. Fugu double U6 promoter-driven long double-stranded RNA inhibits proliferation of viral hemorrhagic septicemia virus (VHSV) in fish cell lines. Arch Virol 1-10 (2012).doi:10.1007/ s00705-012-1275-1
18. Ruiz S, Schyth BD, Encinas P, Tafalla C, Estepa A, Lorenzen N, Coll JM. New tools to study RNA interference to fish viruses: Fish cell lines permanently expressing siRNAs targeting the viral polymerase of viral hemorrhagic septicemia virus. Antiviral Res 2009;82:148-156
19. Kim Y-S, Ke F, Lei X-Y, Zhu R, Zhang Q-Y. Viral envelope protein 53R gene highly specific silencing and iridovirus resistance in fish cells by AmiRNA. PLoS ONE 2010;5:e10308
20. Schyth BD, Lorenzen N, Pedersen F.S. A high throughput in vivo model for testing delivery and antiviral effects of siRNAs in vertebrates. Mol Ther 2007;15:1366-1372
21. Schyth BD, Lorenzen N, Pedersen FS. Antiviral activity of small interfering RNAs: Specificity testing using heterologous virus reveals interferon-related effects overlooked by conventional mismatch controls. Virology 2006;349: 134-141
22. Zenke K, Kim KH. Novel fugu U6 promoter driven shRNA expression vector for efficient vector based RNAi in fish cell lines. Biochem Biophys Res Commun 2008;371:480-483
23. Grimm D, Streetz JL, Jopling CL, Storm TA, Pandey K, Davis CR, et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006;441:537-541
24. Carmell MA, Zhang L, Conklin DS, Hannon GJ, Rosenquist TA. Germline transmission of RNAi in mice. Nature Struct Mol Biol 2003;10:91-92
25. McCaffrey AP, Meuse L, Pham TT, Conklin DS, Hannon GJ, Kay MA. Gene expression: RNA interference in adult mice. Nature 2002;418:38-39
26. Lyall J, Irvine RM, Sherman A, McKinley TJ, Nunez A, Purdie A, et al. Suppression of avian influenza transmission in genetically modified chickens. Science 2011;331:223-226
27. Rienzo GD, Gutzman JH, Sive H. Efficient shRNA-mediated inhibition of gene expression in zebrafish. Zebrafish 120712112605003 (2012).doi:10.1089/zeb. 2012.0770
28. Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Develop 2001;15:188-200
29. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by doublestranded RNA in caenorhabditis elegans. Nature 1998;391: 806-811
30. Gruber J, Manninga H, Tuschl T, Osborn M, Weber K. Specific RNAi mediated gene knockdown in zebrafish cell lines. RNAbiology 2005;2:101-105
31. Peng Y, Lu J-X, Shen X-F. shRNA driven by Pol II/T7 dualpromoter system effectively induce cell-specific RNA interference in mammalian cells. Biochem Biophys Res Commun 2007;360:496-500
32. Calegari F, Haubensak W, Yang D, Huttner WB, Buchholz F. Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease- prepared short interfering RNA. Proc Natl Acad Sci USA 2002;99:14236-14240
33. Ventura A, Meissner A, Dillon CP, McManus M, Sharp PA, Van Parijs L, et al. Cre-lox-regulated conditional RNA interference from transgenes. Proc Natl Acad Sci USA 2004;101:10380-10385
34. Schopman NCT, Liu YP, Konstantinova P, Brake ter O, Berkhout B. Optimization of shRNA inhibitors by variation of the terminal loop sequence. Antiviral Res 2010;86: 204-211
35. Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 2001;20:6877-6888
36. Cummins DM, Tyack SG, Doran TJ. Characterisation and comparison of the chicken H1 RNA polymerase III promoter for short hairpin RNA expression. Biochem Biophys Res Commun 2011;416:194-198
37. Danzeiser DA, Urso O, Kunkel GR. Functional characterization of elements in a human U6 small nuclear RNA gene distal control region. Mol Cell Biol 1993;13:4670-4678
38. Kunkel GR. Identification of a SPH element in the distal region of a human U6 small nuclear RNA gene promoter and characterization of the SPH binding factor in HeLa cell extracts. Gene Express 1996;6:59-72
39. Schaub M. Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III. EMBO J 1997; 16:173-181
40. Grimm, D. Wang L, Lee JS, Schumann N, Gu S, Borner K, et al. Argonaute proteins are key determinants of RNAi efficacy, toxicity, and persistence in the adult mouse liver. J Clin Invest 2010;120:3106-3119
41. Halbig KM, Lekven AC, Kunkel GR. Zebrafish U6 small nuclear RNA gene promoters contain a SPH element in an unusual location. Gene 2008;421:89-94
42. Fjose A, Zhao X-F. Exploring microRNA functions in zebrafish. New Biotechnol 2010;27:250-255
43. Zhao Z, Cao Y, Li M, Meng A. Double-stranded RNA injection produces nonspecific defects in zebrafish. Develop Biol 2001;229:215-223
44. Myslinski E, Amé J-C, Krol A, Carbon P. An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene. Nucleic Acids Res 2001;29:2502-2509
45. Mäkinen PI, Koponen JK, Karkkainen AM, Malm TM, Pulkkinen KH, Koistinaho J, et al. Stable RNA interference: Comparison of U6 and H1 promoters in endothelial cells and in mouse brain. J Gene Med 2006;8:433-441
46. Boden D, Pusch O, Lee F, Tucker L, Shank PR, Ramratnam B. Promoter choice affects the potency of HIV-1 specific RNA interference. Nucleic Acids Res 2003;31:5033-5038
47. He S, Salas-Vidal E, Rueb S, Krens SF, Meijer AH, Snaar-Jagalska BE, Spaink HP. Genetic and transcriptome characterization of model zebrafish cell lines. Zebrafish 2006;3: 441-453
48. Rangini Z, Driever W. Characterization of a cell line derived from zebrafish. In Vitro Cell Develop Biol 1993;29: 749-754
49. Wellcome Trust Sanger Institute The Danio rerio Sequencing Project. sanger.ac.uk at < http://www.sanger.ac.uk/Projects/ D-rerio/ > (accessed February 13, 2012
50. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403-410
51. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003;31:3497-3500
52. Murphy S, Pierani A, Scheidereit C, Melli M, Roeder RG. Purified octamer binding transcription factors stimulate RNA polymerase III-mediated transcription of the 7SK RNA gene. Cell 1989;59:1071-1080
53. Schramm L, Hernandez N. Recruitment of RNA polymerase III to its target promoters. Genes Devel 2002;16:2593-2620
54. Eder PS, Srinivasan A, Fishma, MC, Altman S. The RNA subunit of ribonuclease P from the zebrafish, Danio rerio. J Biol Chem 1996;271:21031-21036