Unlocking the potential of the human genome with RNA interference (original) (raw)
Fire, A., Albertson, D., Harrison, S. W. & Moerman, D. G. Production of antisense RNA leads to effective and specific inhibition of gene expression in C. elegans muscle. Development113, 503–514 (1991). CASPubMed Google Scholar
Guo, S. & Kemphues, K. J. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell81, 611–620 (1995). CASPubMed Google Scholar
Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature391, 806–811 (1998). ADSCASPubMed Google Scholar
Williams, B. R. Role of the double-stranded RNA-activated protein kinase (PKR) in cell regulation. Biochem. Soc. Trans.25, 509–513 (1997). CASPubMed Google Scholar
Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature409, 363–366 (2001). ADSCASPubMed Google Scholar
Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science293, 1146–1150 (2001). CASPubMed Google Scholar
Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature411, 494–498 (2001). ADSCASPubMed Google Scholar
Hutvágner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science293, 834–838 (2001). PubMed Google Scholar
Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell106, 23–34 (2001). CASPubMed Google Scholar
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). CASPubMedPubMed Central Google Scholar
Paddison, P. J., Caudy, A. A., Sachidanandam, R. & Hannon, G. J. Short hairpin activated gene silencing in mammalian cells. Methods Mol. Biol.265, 85–100 (2004). CASPubMed Google Scholar
Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell115, 209–216 (2003). CASPubMed Google Scholar
Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell115, 199–208 (2003). CASPubMed Google Scholar
Reynolds, A. et al. Rational siRNA design for RNA interference. Nature Biotechnol.22, 326–330 (2004). CAS Google Scholar
Silva, J. M., Sachidanandam, R. & Hannon, G. J. Free energy lights the path toward more effective RNAi. Nature Genet.35, 303–305 (2003). CASPubMed Google Scholar
Aza-Blanc, P. et al. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell12, 627–637 (2003). CASPubMed Google Scholar
Pebernard, S. & Iggo, R. D. Determinants of interferon-stimulated gene induction by RNAi vectors. Differentiation72, 103–111 (2004). CASPubMed Google Scholar
Persengiev, S. P., Zhu, X. & Green, M. R. Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA10, 12–18 (2004). CASPubMedPubMed Central Google Scholar
Sledz, C. A., Holko, M., de Veer, M. J., Silverman, R. H. & Williams, B. R. Activation of the interferon system by short-interfering RNAs. Nature Cell Biol.5, 834–839 (2003). CASPubMed Google Scholar
Kim, D. H. et al. Interferon induction by siRNAs and ssRNAs synthesized by phage polymerase. Nature Biotechnol.22, 321–325 (2004). CAS Google Scholar
Jackson, A. L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotechnol.21, 635–637 (2003). CAS Google Scholar
Doench, J. G. & Sharp, P. A. Specificity of microRNA target selection in translational repression. Genes Dev.18, 504–511 (2004). CASPubMedPubMed Central Google Scholar
Lai, E. C., Tomancak, P., Williams, R. W. & Rubin, G. M. Computational identification of Drosophila microRNA genes. Genome Biol.4, R42 (2003). PubMedPubMed Central Google Scholar
Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell115, 787–798 (2003). CASPubMed Google Scholar
Scacheri, P. C. et al. Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Proc. Natl Acad. Sci. USA101, 1892–1897 (2004). ADSCASPubMedPubMed Central Google Scholar
McCaffrey, A. P. et al. RNA interference in adult mice. Nature418, 38–39 (2002). ADSCASPubMed Google Scholar
Matsuda, T. & Cepko, C. L. Electroporation and RNA interference in the rodent retina in vivo and in vitro. Proc. Natl Acad. Sci. USA101, 16–22 (2004). ADSCASPubMed Google Scholar
Lewis, D. L., Hagstrom, J. E., Loomis, A. G., Wolff, J. A. & Herweijer, H. Efficient delivery of siRNA for inhibition of gene expression in postnatal mice. Nature Genet.32, 107–108 (2002). CASPubMed Google Scholar
Sorensen, D. R., Leirdal, M. & Sioud, M. Gene silencing by systemic delivery of synthetic siRNAs in adult mice. J. Mol. Biol.327, 761–766 (2003). CASPubMed Google Scholar
Brummelkamp, T. R., Bernards, R. & Agami, R. Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell2, 243–247 (2002). CASPubMed Google Scholar
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. Nature Genet.33, 401–406 (2003). CASPubMed Google Scholar
Hemann, M. T. et al. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nature Genet.33, 396–400 (2003). CASPubMed Google Scholar
Carmell, M. A., Zhang, L., Conklin, D. S., Hannon, G. J. & Rosenquist, T. A. Germline transmission of RNAi in mice. Nature Struct. Biol.10, 91–92 (2003). CASPubMed Google Scholar
Tiscornia, G., Singer, O., Ikawa, M. & Verma, I. M. A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc. Natl Acad. Sci. USA100, 1844–1848 (2003). ADSCASPubMedPubMed Central Google Scholar
Hasuwa, H., Kaseda, K., Einarsdottir, T. & Okabe, M. Small interfering RNA and gene silencing in transgenic mice and rats. FEBS Lett.532, 227–230 (2002). CASPubMed Google Scholar
Kunath, T. et al. Transgenic RNA interference in ES cell-derived embryos recapitulates a genetic null phenotype. Nature Biotechnol.21, 559–561 (2003). CAS Google Scholar
Hsieh, A. C. et al. A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res.32, 893–901 (2004). CASPubMedPubMed Central Google Scholar
Brummelkamp, T. R., Nijman, S. M., Dirac, A. M. & Bernards, R. Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-κB. Nature424, 797–801 (2003). ADSCASPubMed Google Scholar
Berns, K. et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature428, 431–437 (2004). ADSCASPubMed Google Scholar
Paddison, P. J. et al. A resource for large-scale RNA-interference-based screens in mammals. Nature428, 427–431 (2004). ADSCASPubMed Google Scholar
Zheng, L. et al. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc. Natl Acad. Sci. USA101, 135–140 (2004). ADSCASPubMed Google Scholar
Luo, B., Heard, A. D. & Lodish, H. F. Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc. Natl Acad. Sci. USA101, 5494–5499 (2004). ADSCASPubMedPubMed Central Google Scholar
Shirane, D. et al. Enzymatic production of RNAi libraries from cDNAs. Nature Genet.36, 190–196 (2004). CASPubMed Google Scholar
Sen, G., Wehrman, T. S., Myers, J. W. & Blau, H. M. Restriction enzyme-generated siRNA (REGS) vectors and libraries. Nature Genet.36, 183–189 (2004). CASPubMed Google Scholar
Silva, J. M., Mizuno, H., Brady, A., Lucito, R. & Hannon, G. J. RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. Proc. Natl Acad. Sci. USA101, 6548–6552 (2004). ADSCASPubMedPubMed Central Google Scholar
Ziauddin, J. & Sabatini, D. M. Microarrays of cells expressing defined cDNAs. Nature411, 107–110 (2001). ADSCASPubMed Google Scholar
Jacque, J. M., Triques, K. & Stevenson, M. Modulation of HIV-1 replication by RNA interference. Nature418, 435–438 (2002). ADSCASPubMed Google Scholar
Lee, N. S. et al. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnol.20, 500–505 (2002). CAS Google Scholar
Coburn, G. A. & Cullen, B. R. Potent and specific inhibition of human immunodeficiency virus type-1 replication by RNA interference. J. Virol.76, 9225–9231 (2002). CASPubMedPubMed Central Google Scholar
Surabhi, R. M. & Gaynor, R. B. RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type-1 replication. J. Virol.76, 12963–12973 (2002). CASPubMedPubMed Central Google Scholar
Novina, C. D. et al. siRNA-directed inhibition of HIV-1 infection. Nature Med.8, 681–686 (2002). CASPubMed Google Scholar
Park, W. S. et al. Prevention of HIV-1 infection in human peripheral blood mononuclear cells by specific RNA interference. Nucleic Acids Res.30, 4830–4835 (2002). CASPubMedPubMed Central Google Scholar
Boden, D., Pusch, O., Lee, F., Tucker, L. & Ramratnam, B. Human immunodeficiency virus type-1 escape from RNA interference. J. Virol.77, 11531–11535 (2003). CASPubMedPubMed Central Google Scholar
Martinez, M. A. et al. Suppression of chemokine receptor expression by RNA interference allows for inhibition of HIV-1 replication. AIDS16, 2385–2390 (2002). CASPubMed Google Scholar
Capodici, J., Kariko, K. & Weissman, D. Inhibition of HIV-1 infection by small interfering RNA-mediated RNA interference. J. Immunol.169, 5196–5201 (2002). PubMed Google Scholar
Banerjea, A. et al. 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 (2003). CASPubMed Google Scholar
Li, M. J. et al. Inhibition of HIV-1 infection by lentiviral vectors expressing Pol III-promoted anti-HIV RNAs. Mol. Ther.8, 196–206 (2003). CASPubMed Google Scholar
Eugen-Olsen, J. et al. Heterozygosity for a deletion in the CKR-5 gene leads to prolonged AIDS-free survival and slower CD4 T-cell decline in a cohort of HIV-seropositive individuals. AIDS11, 305–310 (1997). CASPubMed Google Scholar
Samson, M. et al. Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature382, 722–725 (1996). ADSCASPubMed Google Scholar
Qin, X. F., An, D. S., Chen, I. S. & Baltimore, D. Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc. Natl Acad. Sci. USA100, 183–188 (2003). ADSCASPubMed Google Scholar
Dell'Agnola, C. et al. In vitro and in vivo hematopoietic potential of human stem cells residing in muscle tissue. Exp. Hematol.30, 905–914 (2002). CASPubMed Google Scholar
Davis, B. M., Humeau, L. & Dropulic, B. In vivo selection for human and murine hematopoietic cells transduced with a therapeutic MGMT lentiviral vector that inhibits HIV replication. Mol. Ther.9, 160–172 (2004). CASPubMed Google Scholar
Amado, R. G. et al. Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a phase I study: myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients. Hum. Gene Ther.15, 251–262 (2004). CASPubMed Google Scholar
Michienzi, A. et al. RNA-mediated inhibition of HIV in a gene therapy setting. Ann. NY Acad. Sci.1002, 63–71 (2003). ADSCASPubMed Google Scholar
McCaffrey, A. P. et al. Inhibition of hepatitis B virus in mice by RNA interference. Nature Biotechnol.6, 639–644 (2003). Google Scholar
Blight, K. J., Kolykhalov, A. A. & Rice, C. M. Efficient initiation of HCV RNA replication in cell culture. Science290, 1972–1974 (2000). ADSCASPubMed Google Scholar
Lohmann, V. et al. Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science285, 110–113 (1999). CASPubMed Google Scholar
Ikeda, M., Yi, M., Li, K. & Lemon, S. M. Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells. J. Virol.76, 2997–3006 (2002). CASPubMedPubMed Central Google Scholar
Pietschmann, T., Lohmann, V., Rutter, G., Kurpanek, K. & Bartenschlager, R. Characterization of cell lines carrying self-replicating hepatitis C virus RNAs. J. Virol.75, 1252–1264 (2001). CASPubMedPubMed Central Google Scholar
Randall, G., Grakoui, A. & Rice, C. M. Clearance of replicating hepatitis C virus replicon RNAs in cell culture by small interfering RNAs. Proc. Natl Acad. Sci. USA100, 235–240 (2003). ADSCASPubMed Google Scholar
Wilson, J. A. et al. RNA interference blocks gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells. Proc. Natl Acad. Sci. USA100, 2783–2788 (2003). ADSCASPubMedPubMed Central Google Scholar
Kapadia, S. B., Brideau-Andersen, A. & Chisari, F. V. Interference of hepatitis C virus RNA replication by short interfering RNAs. Proc. Natl Acad. Sci. USA100, 2014–2018 (2003). ADSCASPubMedPubMed Central Google Scholar
Song, E. et al. RNA interference targeting Fas protects mice from fulminant hepatitis. Nature Med.9, 347–351 (2003). CASPubMed Google Scholar
Eastman, S. J. et al. Development of catheter-based procedures for transducing the isolated rabbit liver with plasmid DNA. Hum. Gene Ther.13, 2065–2077 (2002). CASPubMed Google Scholar
Kittler, R. & Buchholz, F. RNA interference: gene silencing in the fast lane. Semin. Cancer Biol.13, 259–265 (2003). CASPubMed Google Scholar
Wall, N. R. & Shi, Y. Small RNA: can RNA interference be exploited for therapy? Lancet362, 1401–1403 (2003). CASPubMed Google Scholar
Lu, P. Y., Xie, F. Y. & Woodle, M. C. siRNA-mediated antitumorigenesis for drug target validation and therapeutics. Curr. Opin. Mol. Ther.5, 225–234 (2003). CASPubMed Google Scholar
Buchele, T. Proapoptotic therapy with oblimersen (bcl-2 antisense oligonucleotide)—review of preclinical and clinical results. Onkologie26, (Suppl. 7), 60–69 (2003). PubMed Google Scholar
Czauderna, F. et al. Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res.31, 2705–2716 (2003). CASPubMedPubMed Central Google Scholar
Wang, L., Prakash, R. K., Stein, C. A., Koehn, R. K. & Ruffner, D. E. Progress in the delivery of therapeutic oligonucleotides: organ/cellular distribution and targeted delivery of oligonucleotides in vivo. Antisense Nucleic Acid Drug Dev.13, 169–189 (2003). CASPubMed Google Scholar
Holtz, M. S. & Bhatia, R. Effect of imatinib mesylate on chronic myelogenous leukemia hematopoietic progenitor cells. Leuk. Lymphoma45, 237–245 (2004). CASPubMed Google Scholar
Tauchi, T. & Ohyashiki, K. Molecular mechanisms of resistance of leukemia to imatinib mesylate. Leuk. Res.28 (Suppl. 1), 39–45 (2004). Google Scholar
Cowan-Jacob, S. W. et al. Imatinib (STI571) resistance in chronic myelogenous leukemia: molecular basis of the underlying mechanisms and potential strategies for treatment. Mini Rev. Med. Chem.4, 285–299 (2004). CASPubMed Google Scholar
Marcucci, G., Perrotti, D. & Caligiuri, M. A. Understanding the molecular basis of imatinib mesylate therapy in chronic myelogenous leukemia and the related mechanisms of resistance. Commentary. Clin. Cancer Res., 9: 1333–1337, 2003. Clin. Cancer Res.9, 1248–1252 (2003). Google Scholar
Li, M. J., McMahon, R., Snyder, D. S., Yee, J. K. & Rossi, J. J. Specific killing of Ph+ chronic myeloid leukemia cells by a lentiviral vector-delivered anti-bcr/abl small hairpin RNA. Oligonucleotides13, 401–409 (2003). CASPubMed Google Scholar
Wohlbold, L. et al. Inhibition of bcr-abl gene expression by small interfering RNA sensitizes for imatinib mesylate (STI571). Blood102, 2236–2239 (2003). CASPubMed Google Scholar
Scherr, M. et al. Specific inhibition of bcr-abl gene expression by small interfering RNA. Blood101, 1566–1569 (2003). CASPubMed Google Scholar
Miller, V. M., Gouvion, C. M., Davidson, B. L. & Paulson, H. L. Targeting Alzheimer's disease genes with RNA interference: an efficient strategy for silencing mutant alleles. Nucleic Acids Res.32, 661–668 (2004). CASPubMedPubMed Central Google Scholar
Ding, H. et al. Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell2, 209–217 (2003). CASPubMed Google Scholar
Davidson, B. L. & Paulson, H. L. Molecular medicine for the brain: silencing of disease genes with RNA interference. Lancet Neurol.3, 145–149 (2004). CASPubMed Google Scholar
Pasquinelli, A. E. MicroRNAs: deviants no longer. Trends Genet.18, 171–173 (2002). CASPubMed Google Scholar
Moss, E. G. MicroRNAs: hidden in the genome. Curr. Biol.12, R138–R140 (2002). CASPubMed Google Scholar
Hutvágner, G., Simard, M. J., Mello, C. C. & Zamore, P. D. Sequence-specific inhibition of small RNA function. PLoS Biol.2, E98 (2004). PubMedPubMed Central Google Scholar
Saxena, S., Jonsson, Z. O. & Dutta, A. Small RNAs with imperfect match to endogenous mRNA repress translation. Implications for off-target activity of small inhibitory RNA in mammalian cells. J. Biol. Chem.278, 44312–44319 (2003). CASPubMed Google Scholar