Kinetic analysis of the RNAi enzyme complex (original) (raw)
References
Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature391, 806–811 (1998). ArticleCAS Google Scholar
Elbashir, S.M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev.15, 188–200 (2001). ArticleCAS Google Scholar
Nykänen, A., Haley, B. & Zamore, P.D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell107, 309–321 (2001). Article Google Scholar
Martinez, J., Patkaniowska, A., Urlaub, H., Lührmann, R. & Tuschl, T. Single-stranded antisense siRNA guide target RNA cleavage in RNAi. Cell110, 563–574 (2002). ArticleCAS Google Scholar
Hammond, S.M., Bernstein, E., Beach, D. & Hannon, G.J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature404, 293–296 (2000). ArticleCAS Google Scholar
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
Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature411, 494–498 (2001). ArticleCAS Google Scholar
Amarzguioui, M., Holen, T., Babaie, E. & Prydz, H. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res.31, 589–595 (2003). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Ding, H. et al. Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell2, 209–217 (2003). ArticleCAS Google Scholar
Jackson, A.L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol.21, 635–637 (2003). ArticleCAS Google Scholar
Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116, 281–297 (2004). ArticleCAS Google Scholar
Rajewsky, N. & Socci, N.D. Computational identification of microRNA targets. Dev. Biol.267, 529–535 (2004). ArticleCAS Google Scholar
Lai, E.C. Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet.30, 363–364 (2002). ArticleCAS Google Scholar
Doench, J.G. & Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev.18, 504–511 (2004). ArticleCAS Google Scholar
Chiu, Y.L. & Rana, T.M. siRNA function in RNAi: a chemical modification analysis. RNA9, 1034–1048 (2003). ArticleCAS Google Scholar
Hutvágner, G. & Zamore, P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science297, 2056–2060 (2002). Article Google Scholar
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
Schwarz, D.S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell115, 199–208 (2003). ArticleCAS Google Scholar
Lewis, B., Shih, I., Jones-Rhoades, M., Bartel, D. & Burge, C. Prediction of mammalian microRNA targets. Cell115, 787–798 (2003). ArticleCAS Google Scholar
Rhoades, M.W. et al. Prediction of plant microRNA targets. Cell110, 513–520 (2002). ArticleCAS Google Scholar
Stark, A., Brennecke, J., Russel, R. & Cohen, S. Identification of Drosophila microRNA targets. PLoS Biol.1, 1–13 (2003). Article Google Scholar
Chiu, Y.-L. & Rana, T.M. RNAi in human cells: basic structural and functional features of small interfering RNA. Molecular Cell10, 549–561 (2002). ArticleCAS Google Scholar
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. Biochemistry36, 390–398 (1997). ArticleCAS Google Scholar
Meister, G., Landthaler, M., Dorsett, Y. & Tuschl, T. Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA10, 544–550 (2004). ArticleCAS Google Scholar
Tomari, Y. et al. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell116, 831–841 (2004). ArticleCAS Google Scholar
Reynolds, A. et al. Rational siRNA design for RNA interference. Nat. Biotechnol.22, 326–330 (2004). ArticleCAS Google Scholar
Stryer, L. Biochemistry. (W. H. Freeman and Company, San Francisco; 1981). Google Scholar
Martinez, J. & Tuschl, T. RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev.18, 975–980 (2004). ArticleCAS Google Scholar
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. Cell117, 83–94 (2004). ArticleCAS Google Scholar
Enright, A. et al. MicroRNA targets in Drosophila. Genome Biol.5, R1 (2003). Article Google Scholar
Lee, R.C., Feinbaum, R.L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell75, 843–854. (1993). ArticleCAS Google Scholar
Reinhart, B.J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature403, 901–906. (2000). ArticleCAS Google Scholar
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. Cell113, 25–36 (2003). ArticleCAS Google Scholar
Abrahante, J.E. et al. The _Caenorhabditis elegans hunchback_-like gene lin-57/hbl-1 controls developmental timing and is regulated by microRNAs. Dev. Cell4, 625–637 (2003). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Johnston, R.J. & Hobert, O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature426, 845–849 (2003). ArticleCAS Google Scholar
Haley, B., Tang, G. & Zamore, P.D. In vitro analysis of RNA interference in Drosophila melanogaster. Methods30, 330–336 (2003). ArticleCAS Google Scholar
Schwarz, D.S., Tomari, Y. & Zamore, P.D. The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr. Biol.14, 787–791 (2004). ArticleCAS Google Scholar
Voet, D. & Voet, J.G. Biochemistry. (John Wiley & Sons, Hoboken, NJ; 2004). Google Scholar
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). ArticleCAS Google Scholar