Vector-based RNAi approaches for stable, inducible and genome-wide screens

Drug Discovery Today

Volumn 11, Issue 21-22, 2006, Pages 975-982

  Fewell, Gwen D ^a   Schmitt, Karin ^a  

^a Open Biosystems   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SHORT HAIRPIN RNA;

BIOGENESIS; DNA VECTOR; GENE FUNCTION; GENE SEQUENCE; HUMAN; LIBRARY; MAMMAL; MOLECULAR EVOLUTION; NONHUMAN; REVIEW; RNA INTERFERENCE; RNA VECTOR;

ANIMALS; DATABASES, NUCLEIC ACID; DNA POLYMERASE II; DOXORUBICIN; GENE EXPRESSION REGULATION; GENETIC TECHNIQUES; GENETIC VECTORS; HUMANS; MICRORNAS; PROMOTER REGIONS (GENETICS); PROMOTER REGIONS, GENETIC; RNA; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 33750031102     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.drudis.2006.09.008     Document Type: Review

References (53)

1. Fire A., et al. Potent and specific genetic interference by double stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
2. Hannon G.J. RNA interference. Nature 418 (2002) 244-251
3. Hannon G.J., and Rossi J.J. Unlocking the potential of the human genome with RNA interference. Nature 431 (2004) 371-378
4. Hammond S.M. Dicing and slicing: the core machinery of the RNA interference pathway. FEBS Lett. 579 (2005) 5822-5829
5. Williams B.R. Role of the double stranded RNA-activated protein kinase (PKR) in cell regulation. Biochem. Soc. Trans. 25 (1997) 509-513
6. Elbashir S.M., et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411 (2001) 494-498
7. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
8. He L., and Hannon G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5 (2004) 522-531
9. Paddison P.J., et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428 (2004) 427-431
10. Brummelkamp T.R., et al. Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-κB. Nature 424 (2003) 797-801
11. Berns K., et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428 (2004) 431-437
12. Silva J.M., et al. Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. 37 (2005) 1281-1288
13. Boden D., et al. Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins. Nucleic Acids Res. 32 (2004) 1154-1158
14. Cleary M.A., et al. Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods 1 (2004) 241-248
15. Siolas D., et al. Synthetic shRNAs as potent RNAi triggers. Nat. Biotechnol. 23 (2005) 227-231
16. Gregory R.I., et al. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123 (2005) 631-640
17. Persengiev S.P., et al. Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA 10 (2004) 12-18
18. Stegmeier F., et al. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 13212-13217
19. Paddison P.J., et al. Short hairpin shRNAs induce sequence-specific silencing in mammalian cells. Genes Dev. 16 (2002) 948-958
20. Brummelkamp T.R., et al. A system for stable expression of short interfering RNAs in mammalian cells. Science 296 (2002) 550-553
21. Moffat J., et al. A Lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124 (2006) 1283-1298
22. Westbrook T.F., et al. A genetic screen for candidate tumor suppressors identifies REST. Cell 121 (2005) 837-848
23. Kolfschoten I.G., et al. A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell 121 (2005) 849-858
24. Winzeler E.A., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285 (1999) 901-906
25. Brummelkamp T.R., et al. An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors. Nat. Chem. Biol. 2 (2006) 202-206
26. Ngo V.N., et al. A loss of function RNA interference screen for molecular targets in cancer. Nature 441 (2006) 106-110
27. Hasuwa H., et al. Small interfering RNA and gene silencing in transgenic mice and rats. FEBS Lett. 532 (2002) 227-230
28. Shinagawa T., and Ishii S. Generation of Ski-knockdown mice by expressing a long double-strand RNA from an RNA polymerase II promoter. Genes Dev. 17 (2003) 1340-1345
29. Coumoul X., et al. Conditional knockdown of Fgfr2 in mice using Cre-LoxP induced RNA interference. Nucleic Acids Res. 33 (2005) e102
30. Kunath T., et al. Transgenic RNA interference in ES cell-derived embryos recapitulates a genetic null phenotype. Nat. Biotechnol. 21 (2003) 559-561
31. Carmell M.A., et al. Germline transmission of RNAi in mice. Nat. Struct. Biol. 10 (2003) 91-92
32. Rubinson D.A., et al. A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nat. Genet. 33 (2003) 401-406
33. Tiscornia G., et al. A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 1844-1848
34. Ventura A., et al. Cre-lox-regulated conditional RNA interference from transgenes. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 10380-10385
35. Szulc J., et al. A versatile tool for conditional gene expression and knockdown. Nat Methods 3 (2006) 109-116
36. Kissler S., et al. In vivo RNA interference demonstrates a role for Nrampl in modifying susceptibility to type 1 diabetes. Nat. Genet. 38 (2006) 479-483
37. Oberdoerffer P., et al. Efficiency of RNA interference in the mouse hematopoietic system varies between cell types and developmental stages. Mol. Cell. Biol. 25 (2005) 3896-3905
38. Seibler J., et al. Single copy shRNA configuration for ubiquitous gene knockdown in mice. Nucleic Acids Res. 33 (2005) e67
39. Dickins R.A., et al. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nat. Genet. 37 (2005) 1289-1295
40. Birmingham A., et al. 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3 (2006) 199-204
41. Jackson A.L., et al. Widespread siRNA off-target transcript silencing mediated by seed region sequence complementarity. RNA 12 (2006) 1179-1187
42. Echeverri C.J., and Perrimon N. High-throughput RNAi screening in cultured cells: a user's guide. Nat. Rev. Genet. 7 (2006) 373-384
43. Eason R.G. Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 11046-11051
44. Baetz K., et al. Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 4525-4530
45. DasGupta R., et al. Functional genomic analysis of the Wnt-wingless signaling pathway. Science 308 (2005) 826-833
46. Sonnichsen B., et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434 (2005) 462-469
47. Lee Y., et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23 (2004) 4051-4060
48. Lee Y., et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425 (2003) 415-419
49. Lund E., et al. Nuclear export of microRNA precursors. Science 303 (2004) 95-98
50. Yi R., et al. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17 (2003) 3011-3016
51. Chendrimada T.P., et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436 (2005) 740-744
52. Liu J., et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305 (2004) 1437-1441
53. Meister G., et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15 (2004) 185-197