A systematic analysis of the effect of target RNA structure on RNA interference

Nucleic Acids Research

Volumn 35, Issue 13, 2007, Pages 4322-4330

  Westerhout, Ellen M ^a   Berkhout, Ben ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

LENTIVIRUS VECTOR; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; MESSENGER RNA;

ARTICLE; CANCER CELL CULTURE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE CASSETTE; GENE EXPRESSION; GENE MUTATION; GENE TARGETING; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; PRIORITY JOURNAL; REPRODUCIBILITY; RNA BINDING; RNA INTERFERENCE; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; THERMODYNAMICS; UTERINE CERVIX CARCINOMA; VIRAL GENE DELIVERY SYSTEM; CHEMISTRY; CONFORMATION; METABOLISM; NUCLEOTIDE SEQUENCE; TUMOR CELL LINE;

BASE SEQUENCE; CELL LINE, TUMOR; HUMANS; NUCLEIC ACID CONFORMATION; RNA INTERFERENCE; RNA, MESSENGER; RNA, SMALL INTERFERING;

EID: 34547843654     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm437     Document Type: Article

References (59)

1. Fire,A., Xu,S., Montgomery,M.K., Kostas,S.A., Driver,S.E. and Mello,C.C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806-811.
2. Vance,V. and Vaucheret,H. (2001) RNA silencing in plants-defense and counterdefense. Science, 292, 2277-2280.
3. Waterhouse,P.M., Wang,M.B. and Lough,T. (2001) Gene silencing as an adaptive defence against viruses. Nature, 411, 834-842.
4. Galiana-Arnoux,D., Dostert,C., Schneemann,A., Hoffmann,J.A. and Imler,J.L. (2006) Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila. Nat. Immunol., 7, 590-597.
5. Kalmykova,A.I., Klenov,M.S. and Gvozdev,V.A. (2005) Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline. Nucleic Acids Res., 33, 2052-2059.
6. Ketting,R.F., Haverkamp,T.H., van Luenen,H.G. and Plasterk,R.H. (1999) Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell, 99, 133-141.
7. Elbashir,S.M., Lendeckel,W. and Tuschl,T. (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev., 15, 188-200.
8. Hammond,S.M., Bernstein,E., Beach,D. and Hannon,G.J. (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature, 404, 293-296.
9. Zamore,P.D., Tuschl,T., Sharp,P.A. and Bartel,D.P. (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25-33.
10. Hammond,S.M., Caudy,A.A. and Hannon,G.J. (2001) Post-transcriptional gene silencing by double-stranded RNA. Nat. Rev. Genet., 2, 110-119.
11. Martinez,J., Patkaniowska,A., Urlaub,H., Luhrmann,R. and Tuschl,T. (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563-574.
12. Filipowicz,W. (2005) RNAi: The nuts and bolts of the RISC machine. Cell, 122, 17-20.
13. Brummelkamp,T.R., Bernards,R. and Agami,R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science, 296, 550-553.
14. Elbashir,S.M., Harborth,J., Lendeckel,W., Yalcin,A., Weber,K. and Tuschl,T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494-498.
15. Paul,C.P., Good,P.D., Winer,I. and Engelke,D.R. (2002) Effective expression of small interfering RNA in human cells. Nat. Biotechnol. 20, 505-508.
16. Holen,T., Amarzguioui,M., Wiiger,M.T., Babaie,E. and Prydz,H. (2002) Positional effect of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res., 30, 1757-1766.
17. Khvorova,A., Reynolds,A. and Jayasena,S.D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209-216.
18. Schwarz,D.S., Hutvagner,G., Du,T., Xu,Z., Aronin,N. and Zamore,P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208.
19. Reynolds,A., Leake,D., Boese,Q., Scaringe,S., Marshall,W.S. and Khvorova,A. (2004) Rational siRNA design for RNA interference. Nat. Biotechnol., 22, 326-330.
20. Ui-Tei,K., Naito,Y., Takahashi,F., Haraguchi,T., Ohki-Hamazaki,H., Juni,A., Ueda,R. and Saigo,K. (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res., 32, 936-948.
21. Patzel,V., Rutz,S., Dietrich,I., Koberle,C., Scheffold,A. and Kaufmann,S.H. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat. Biotechnol., 23, 1440-1444.
22. Bohula,E.A., Salisbury,A.J., Sohail,M., Playford,M.P., Riedemann,J., Southern,E.M. and Macaulay,V.M. (2003) The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGFIR) is influenced by secondary structure in the IGFIR transcript. J. Biol. Chem., 278, 15991-15997.
23. Kretschmer-Kazemi,F.R. and Sczakiel,G. (2003) The activity of siRNA in mammalian cells is related to structural target accessibility: A comparison with antisense oligonucleotides. Nucleic Acids Res., 31, 4417-4424.
24. Haasnoot,P.C.J. and Berkhout.B. (2006) RNA interference: Its use as antiviral therapy. Handbook of Experimental Pharmacology Springer-Verlag Berlin Heidelberg, Heidelberg, Vol. 173, pp. 117-150.
25. Coburn,G.A. and Cullen,B.R. (2002) Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J. Virol., 76, 9225-9231.
26. Jacque,J.M., Triques,K. and Stevenson,M. (2002) Modulation of HIV-1 replication by RNA interference. Nature, 418, 435-438.
27. Lee,N.S., Dohjima,T., Bauer,G., Li,H., Li,M.J., Ehsani,A., Salvaterra,P. and Rossi,J. (2002) Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat. Biotechnol., 20, 500-505.
28. Novina,C.D., Murray,M.F., Dykxhoorn,D.M., Beresford,P.J., Riess,J., Lee,S.K., Collman,R.G., Lieberman,J., Shankar,P. et al. (2002) siRNA-directed inhibition of HIV-1 infection. Nat. Med., 8, 681-686.
29. Banerjea,A., Li,M.J., Bauer,G., Remling,L., Lee,N.S., Rossi,J. and Akkina,R. (2003) Inhibition of HIV-1 by lentiviral vector-transduced siRNAs in T lymphocytes differentiated in SCID-hu mice and CD34 + progenitor cell-derived macrophages. Mol. Ther., 8, 62-71.
30. Boden,D., Pusch,O., Lee,F., Tucker,L. and Ramratnam,B. (2004) Efficient gene transfer of HIV-1-specific short hairpin RNA into human lymphocytic cells using recombinant adeno-associated virus vectors. Mol. Ther. 9, 396-402.
31. Das.A.T., Brummelkamp,T.R., Westerhout,E.M., Vink.M., Madiredjo,M., Bernards,R. and Berkhout,B. (2004) Human immunodeficiency virus-type 1 escapes from RNA interference-mediated inhibition. J. Virol., 78, 2601-2605.
32. Lee,M.T., Coburn,G.A., McClure,M.O. and Cullen,B.R. (2003) Inhibition of human immunodeficiency virus type 1 replication in primary macrophages by using Tat- or CCR5-specific small interfering RNAs expressed from a lentivirus vector. J. Virol., 77, 11964-11972.
33. Lee,S.K., Dykxhoorn,D.M., Kumar,P., Ranjbar,S., Song,E., Maliszewski,L.E., Francois-Bongarcon,V., Goldfeld,A., Swamy,N.M. et al. (2005) Lentiviral delivery of short hairpin RNAs protects CD4T cells from multiple clades and primary isolates of HIV. Blood, 106, 818-826.
34. Ter Brake,O., Konstantinova,P., Ceylan,M. and Berkhout,B. (2006) Silencing of HIV-1 with RNA interference: A multiple shRNA approach. Mol. Ther., 14, 883-892.
35. Boden,D., Pusch,O., Lee,F., Tucker,L. and Ramratnam,B. (2003) Human immunodeficiency virus type 1 escape from RNA interference. J. Virol. 77, 11531-11535.
36. Westerhout,E.M., Ooms,M., Vink,M., Das,A.T. and Berkhout,B. (2005) HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res., 33, 796-804.
37. Berkhout,B. (2004) RNA interference as an antiviral approach: Targeting HIV-1. Curr. Opin. Mol. Ther., 6, 141-145.
38. Westerhout,E.M., Ter Brake,O. and Berkhout,B. (2006) The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference. Retrovirology, 3, 57-65.
39. Luo,K.Q. and Chang,D.C. (2004) The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region. Biochem. Biophys. Res. Commun., 318, 303-310.
40. Yoshinari,K., Miyagishi,M. and Taira,K. (2004) Effects on RNAi of the tight structure, sequence and position of the targeted region. Nucleic Acids Res., 32, 691-699.
41. Schubert,S., Grunweller,A., Erdmann,V.A. and Kurreck,J. (2005) Local RNA target structure influences siRNA efficacy: Systematic analysis of intentionally designed binding regions. J. Mol. Biol., 348, 883-893.
42. Doench,J.G. and Sharp,P.A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504-511.
43. Haley,B. and Zamore,P.D. (2004) Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol., 11, 599-606.
44. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
45. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
46. Lingel,A., Simon,B., Izaurralde,E. and Sattler,M. (2004) Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nat. Struct. Mol. Biol., 11, 576-577.
47. Ma,J.B., Yuan,Y.R., Meister,G., Pei,Y., Tuschl,T. and Patel,D.J. (2005) Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature, 434, 666-670.
48. Parker,J.S., Roe,S.M. and Barford,D. (2005) Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature, 434, 663-666.
49. Nykanen,A., Haley,B. and Zamore,P.D. (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309-321.
50. Brown,K.M., Chu,C.Y. and Rana,T.M. (2005) Target accessibility dictates the potency of human RISC. Nat. Struct. Mol. Biol., 12, 469-470.
51. Mittal,V. (2004) Improving the efficiency of RNA interference in mammals. Nat. Rev. Genet., 5, 355-365.
52. Nishitsuji,H., Ikeda,T., Miyoshi,H., Ohashi,T., Kannagi,M. and Masuda,T. (2004) Expression of small hairpin RNA by lentivirus-based vector confers efficient and stable gene-suppression of HIV-1 on human cells including primary non-dividing cells. Microbes Infect., 6, 76-85.
53. Van den Haute,C., Eggermont,K., Nuttin,B., Debyser,Z. and Baekelandt,V. (2003) Lentiviral vector-mediated delivery of short hairpin RNA results in persistent knockdown of gene expression in mouse brain. Hum. Gene Ther., 14, 1799-1807.
54. Beerens,N., Groot,F. and Berkhout,B. (2000) Stabilization of the U5-leader stem in the HIV-1 RNA genome affects initiation and elongation of reverse transcription. Nucleic Acids Res., 28, 4130-4137.
55. Hay,N. and Aloni,Y. (1984) Attenuation in SV40 as a mechanism of transcription-termination by RNA polymerase B. Nucleic Acids Res., 12, 1401-1414.
56. Miyagishi,M., Sumimoto,H., Miyoshi,H., Kawakami,Y. and Taira K. (2004) Optimization of an siRNA-expression system with an improved hairpin and its significant suppressive effects in mammalian cells. J. Gene Med. 6, 715-723.
57. Du,Q., Thonberg,H., Wang,J., Wahlestedt,C. and Liang,Z. (2005) A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites. Nucleic Acids Res., 33, 1671-1677.
58. Holen,T., Moe,S.E., Sorbo,J.G., Meza,T.J., Ottersen,O.P. and Klungland,A. (2005) Tolerated wobble mutations in siRNAs decrease specificity, but can enhance activity in vivo. Nucleic Acids Res., 33, 4704-4710.
59. ter Brake, O., Berkhout B., Journal of Gene Medicine 2007 (in press). Lentiviral vectors that carry anti-HIV shRNAs: Problems and solutions.