Synthetic shRNAs as potent RNAi triggers

Nature Biotechnology

Volumn 23, Issue 2, 2005, Pages 227-231

  Siolas, Despina ^a,b   Lerner, Cara ^c   Burchard, Julja ^c   Ge, Wei ^c   Linsley, Peter S ^c   Paddison, Patrick J ^b   Hannon, Gregory J ^b   Cleary, Michele A ^c  

^a STONY BROOK UNIVERSITY   (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c ROSETTA INPHARMATICS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; CELLS; COMPLEXATION; OPTIMIZATION; SUBSTRATES; SYNTHESIS (CHEMICAL);

CLEAVAGES; DICERS; NUCLEOTIDES; TRANSFECTION;

RNA;

DICER; RECOMBINANT ENZYME; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; ENZYME SUBSTRATE COMPLEX; GENE SILENCING; GENE TARGETING; GENETIC TRANSFECTION; PRIORITY JOURNAL; PROTEIN DEGRADATION; RNA INTERFERENCE;

GENE EXPRESSION REGULATION; GENE SILENCING; GENE TARGETING; GENETIC ENGINEERING; RNA, SMALL INTERFERING; TRANSFECTION;

MAMMALIA;

EID: 13844280638     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1052     Document Type: Article

References (30)

1. Zamore, P.D., Tuschl, T., Sharp, P.A. & Bartel, D.P. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25-33 (2000).
2. Hammond, S.M., Bernstein, E., Beach, D. & Hannon, G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293-296 (2000).
3. Bernstein, E., Caudy, A.A., Hammond, S.M. & Hannon, G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363-366 (2001).
4. Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R. & Hannon, G.J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146-1150 (2001).
5. Song, J.J., Smith, S.K., Hannon, G.J. & Joshua-Tor, L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305, 1434-1437 (2004).
6. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437-1441 (2004).
7. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498 (2001).
8. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
9. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415-419 (2003).
10. Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834-838 (2001).
11. Ketting, R.F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654-2659 (2001).
12. Grishok A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23-34 (2001).
13. Brummelkamp, T.R., Bernards, R. & Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550-553 (2002).
14. Paddison, P.J., Caudy, A.A., Bernstein, E., Hannon, G.J. & Conklin, D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948-958 (2002).
15. Zeng, Y., Wagner, E.J. & Cullen, B.R. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell 9, 1327-1333 (2002).
16. Schwarz, D.S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208 (2003).
17. Khvorova, A., Reynolds, A. & Jayasena, S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216 (2003).
18. Lee, Y.S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69-81 (2004).
19. Pham, J.W., Pellino, J.L., Lee, Y.S., Carthew, R.W. & Sontheimer, E.J. A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117, 83-94 (2004).
20. Tomari, Y. et al. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116, 831-841 (2004).
21. Zhang, H., Kolb, F.A., Brondani, V., Billy, E. & Filipowicz, W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875-5885 (2002).
22. Lund, E., Guttinger, S., Calado, A., Dahlberg, J.E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95-98 (2004).
23. Ma, J.B., Ye, K. & Patel, D.J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318-322 (2004).
24. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426, 465-469 (2003).
25. Song, J.J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10, 1026-1032 (2003).
26. Yan, K.S. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468-474 (2003).
27. Zhang, H., Kolb, F.A., Jaskiewicz, L., Westhof, E. & Filipowicz, W. Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57-68 (2004).
28. Jackson, A.L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21, 635-637 (2003).
29. Rossi, J.J. et al. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat. Biotechnol. 23, in the press (2005).
30. Doi, N. et al. Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and elF2C translation initiation factors. Curr. Biol. 13, 41-46 (2003).