Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 25, 2010, Pages 11435-11440

  Haley, Benjamin ^a,b   Foys, Bryon ^a   Levine, Michael ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b GENENTECH INC   (United States)

Author keywords

Intron; miRNA; shRNA

Indexed keywords

MESSENGER RNA; NUCLEOTIDE; RNA; SMALL INTERFERING RNA; FLUORESCENT DYE;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DROSOPHILA; GENE ACTIVITY; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENE SILENCING; GENE TARGETING; GENETIC SCREENING; GENETIC TRANSCRIPTION; IN VIVO STUDY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REPORTER GENE; RNA INTERFERENCE; SEQUENCE HOMOLOGY; ANIMAL; BIOLOGICAL MODEL; CULTURE TECHNIQUE; GENE VECTOR; GENETIC PROCEDURES; GENETICS; INTRON; METABOLISM; TRANSGENIC ANIMAL;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; CELL CULTURE TECHNIQUES; DROSOPHILA; FLUORESCENT DYES; GENE SILENCING; GENES, REPORTER; GENETIC TECHNIQUES; GENETIC VECTORS; INTRONS; MODELS, GENETIC; PHENOTYPE; RNA INTERFERENCE; RNA, MESSENGER; RNA, SMALL INTERFERING;

EID: 77954903711     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1006689107     Document Type: Article

References (35)

1. de Fougerolles A, Vornlocher HP, Maraganore J, Lieberman J (2007) Interfering with disease: A progress report on siRNA-based therapeutics. Nat Rev Drug Discov 6: 443-453.
2. Birmingham A, et al. (2006) 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3:199-204.
3. Jackson AL, et al. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21:635-637.
4. Jackson AL, et al. (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA 12:1179-1187.
5. Kulkarni MM, et al. (2006) Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays. Nat Methods 3:833-838.
6. Ma Y, Creanga A, Lum L, Beachy PA (2006) Prevalence of off-target effects in Drosophila RNA interference screens. Nature 443:359-363.
7. Dietzl G, et al. (2007) A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448:151-156.
8. Ni JQ, et al. (2009) A Drosophila resource of transgenic RNAi lines for neurogenetics. Genetics 182:1089-1100.
9. Adams MD, et al. (2000) The genome sequence of Drosophila melanogaster. Science 287:2185-2195.
10. Bischof J, Maeda RK, Hediger M, Karch F, Basler K (2007) An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc Natl Acad Sci USA 104:3312-3317.
11. Haley B, Zamore PD (2004) Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 11:599-606.
12. Martinez J, Tuschl T (2004) RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev 18:975-980.
13. Bartel DP (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116:281-297.
14. Perrimon N, Mathey-Prevot B (2007) Matter arising: Off-targets and genome-scale RNAi screens in Drosophila. Fly (Austin) 1:1-5.
15. Haley B, Hendrix D, Trang V, Levine M (2008) A simplified miRNA-based gene silencing method for Drosophila melanogaster. Dev Biol 321:482-490.
16. Tang G, Reinhart BJ, Bartel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17:49-63.
17. Spencer FA, Hoffmann FM, Gelbart WM (1982) Decapentaplegic: A gene complex affecting morphogenesis in Drosophila melanogaster. Cell 28:451-461.
18. Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401-415.
19. Du G, Yonekubo J, Zeng Y, Osisami M, Frohman MA (2006) Design of expression vectors for RNA interference based on miRNAs and RNA splicing. FEBS J 273:5421-5427.
20. Lin SL, Ying SY (2006) Gene silencing in vitro and in vivo using intronic microRNAs. Methods Mol Biol 342:295-312.
21. Kataoka N, Fujita M, Ohno M (2009) Functional association of the Microprocessor complex with the spliceosome. Mol Cell Biol 29:3243-3254.
22. Morlando M, et al. (2008) Primary microRNA transcripts are processed cotranscriptionally. Nat Struct Mol Biol 15:902-909.
23. Kim YK, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26:775-783.
24. Shaner NC, et al. (2004) Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22:1567-1572.
25. Hafen E (2009) Pushing single-gene genetic analysis up a Notch. Dev Cell 16:623-624.
26. Zieler H, Huynh CQ (2002) Intron-dependent stimulation of marker gene expression in cultured insect cells. Insect Mol Biol 11:87-95.
27. Duncker BP, Davies PL, Walker VK (1997) Introns boost transgene expression in Drosophila melanogaster. Mol Gen Genet 254:291-296.
28. Le Hir H, Nott A, Moore MJ (2003) How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci 28:215-220.
29. Iwasaki S, Kawamata T, Tomari Y (2009) Drosophila argonaute1 and argonaute2 employ distinct mechanisms for translational repression. Mol Cell 34:58-67.
30. Xu T, Rubin GM (1993) Analysis of genetic mosaics in developing and adult Drosophila tissues. Development 117:1223-1237.
31. Davidson MW, Campbell RE (2009) Engineered fluorescent proteins: Innovations and applications. Nat Methods 6:713-717.
32. Rose AB (2008) Intron-mediated regulation of gene expression. Curr Top Microbiol Immunol 326:277-290.
33. Nott A, Le Hir H, Moore MJ (2004) Splicing enhances translation in mammalian cells: An additional function of the exon junction complex. Genes Dev 18:210-222.
34. Nott A, Meislin SH, Moore MJ (2003) A quantitative analysis of intron effects on mammalian gene expression. RNA 9:607-617.
35. Markstein M, Pitsouli C, Villalta C, Celniker SE, Perrimon N (2008) Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat Genet 40:476-483.