Kinetic analysis of the RNAi enzyme complex (original) (raw)

References

  1. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).
    Article CAS Google Scholar
  2. Elbashir, S.M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188–200 (2001).
    Article CAS Google Scholar
  3. Nykänen, A., Haley, B. & Zamore, P.D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309–321 (2001).
    Article Google Scholar
  4. Martinez, J., Patkaniowska, A., Urlaub, H., Lührmann, R. & Tuschl, T. Single-stranded antisense siRNA guide target RNA cleavage in RNAi. Cell 110, 563–574 (2002).
    Article CAS Google Scholar
  5. 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).
    Article CAS Google Scholar
  6. Hannon, G.J. & Zamore, P.D. Small RNAs, big biology and biochemical studies of RNA interference. In RNAi: A Guide To Gene Silencing (ed. Hannon, G.J.) 87–108 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2003).
    Google Scholar
  7. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001).
    Article CAS Google Scholar
  8. Amarzguioui, M., Holen, T., Babaie, E. & Prydz, H. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res. 31, 589–595 (2003).
    Article CAS Google Scholar
  9. Elbashir, S.M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877–6888 (2001).
    Article CAS Google Scholar
  10. Holen, T., Amarzguioui, M., Babaie, E. & Prydz, H. Similar behaviour of single-strand and double-strand siRNAs suggests they act through a common RNAi pathway. Nucleic Acids Res. 31, 2401–2407 (2003).
    Article CAS Google Scholar
  11. Tang, G., Reinhart, B.J., Bartel, D.P. & Zamore, P.D. A biochemical framework for RNA silencing in plants. Genes Dev. 17, 49–63 (2003).
    Article CAS Google Scholar
  12. Phipps, K.M., Martinez, A., Lu, J., Heinz, B.A. & Zhao, G. Small interfering RNA molecules as potential anti-human rhinovirus agents: in vitro potency, specificity, and mechanism. Antiviral Res. 61, 49–55 (2004).
    Article CAS Google Scholar
  13. Ding, H. et al. Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell 2, 209–217 (2003).
    Article CAS Google Scholar
  14. Jackson, A.L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21, 635–637 (2003).
    Article CAS Google Scholar
  15. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004).
    Article CAS Google Scholar
  16. Rajewsky, N. & Socci, N.D. Computational identification of microRNA targets. Dev. Biol. 267, 529–535 (2004).
    Article CAS Google Scholar
  17. Lai, E.C. Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet. 30, 363–364 (2002).
    Article CAS Google Scholar
  18. Doench, J.G. & Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504–511 (2004).
    Article CAS Google Scholar
  19. Chiu, Y.L. & Rana, T.M. siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034–1048 (2003).
    Article CAS Google Scholar
  20. Hutvágner, G. & Zamore, P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002).
    Article Google Scholar
  21. Hutvágner, G., Simard, M.J., Mello, C.C. & Zamore, P.D. Sequence-specific inhibition of small RNA function. PLoS Biol. 2, 1–11 (2004).
    Article Google Scholar
  22. Schwarz, D.S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).
    Article CAS Google Scholar
  23. Lewis, B., Shih, I., Jones-Rhoades, M., Bartel, D. & Burge, C. Prediction of mammalian microRNA targets. Cell 115, 787–798 (2003).
    Article CAS Google Scholar
  24. Rhoades, M.W. et al. Prediction of plant microRNA targets. Cell 110, 513–520 (2002).
    Article CAS Google Scholar
  25. Stark, A., Brennecke, J., Russel, R. & Cohen, S. Identification of Drosophila microRNA targets. PLoS Biol. 1, 1–13 (2003).
    Article Google Scholar
  26. Chiu, Y.-L. & Rana, T.M. RNAi in human cells: basic structural and functional features of small interfering RNA. Molecular Cell 10, 549–561 (2002).
    Article CAS Google Scholar
  27. Lima, W.F. & Crooke, S.T. Binding affinity and specificity of Escherichia coli RNase H1: impact on the kinetics of catalysis of antisense oligonucleotide-RNA hybrids. Biochemistry 36, 390–398 (1997).
    Article CAS Google Scholar
  28. Meister, G., Landthaler, M., Dorsett, Y. & Tuschl, T. Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA 10, 544–550 (2004).
    Article CAS Google Scholar
  29. Tomari, Y. et al. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116, 831–841 (2004).
    Article CAS Google Scholar
  30. Reynolds, A. et al. Rational siRNA design for RNA interference. Nat. Biotechnol. 22, 326–330 (2004).
    Article CAS Google Scholar
  31. Stryer, L. Biochemistry. (W. H. Freeman and Company, San Francisco; 1981).
    Google Scholar
  32. Martinez, J. & Tuschl, T. RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev. 18, 975–980 (2004).
    Article CAS Google Scholar
  33. 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).
    Article CAS Google Scholar
  34. Enright, A. et al. MicroRNA targets in Drosophila. Genome Biol. 5, R1 (2003).
    Article Google Scholar
  35. Lee, R.C., Feinbaum, R.L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854. (1993).
    Article CAS Google Scholar
  36. Reinhart, B.J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906. (2000).
    Article CAS Google Scholar
  37. Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B. & Cohen, S.M. bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36 (2003).
    Article CAS Google Scholar
  38. Abrahante, J.E. et al. The _Caenorhabditis elegans hunchback_-like gene lin-57/hbl-1 controls developmental timing and is regulated by microRNAs. Dev. Cell 4, 625–637 (2003).
    Article CAS Google Scholar
  39. Vella, M., Choi, E., Lin, S., Reinert, K. & Slack, F. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev. 18, 132–137 (2004).
    Article CAS Google Scholar
  40. Xu, P., Vernooy, S.Y., Guo, M. & Hay, B.A. The Drosophila microRNA miR-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13, 790–795 (2003).
    Article CAS Google Scholar
  41. Johnston, R.J. & Hobert, O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845–849 (2003).
    Article CAS Google Scholar
  42. Haley, B., Tang, G. & Zamore, P.D. In vitro analysis of RNA interference in Drosophila melanogaster. Methods 30, 330–336 (2003).
    Article CAS Google Scholar
  43. Schwarz, D.S., Tomari, Y. & Zamore, P.D. The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr. Biol. 14, 787–791 (2004).
    Article CAS Google Scholar
  44. Voet, D. & Voet, J.G. Biochemistry. (John Wiley & Sons, Hoboken, NJ; 2004).
    Google Scholar
  45. Wu, H., Lima, W.F. & Crooke, S.T. Investigating the structure of human RNase H1 by site-directed mutagenesis. J. Biol. Chem. 276, 23547–23553. (2001).
    Article CAS Google Scholar

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