High-throughput RNAi screening in cultured cells: a user's guide (original) (raw)

• Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998). Reports the discovery of RNAi that is mediated by long dsRNA in C. elegans.
  Article CAS Google Scholar
• Fraser, A. G. et al. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408, 325–330 (2000).
  Article CAS Google Scholar
• Gönczy, P. et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331–336 (2000).
  Article 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).
  Article CAS Google Scholar
• Clemens, J. C. et al. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc. Natl Acad. Sci. USA 97, 6499–6503 (2000). The first report that addition of long dsRNAs on cultured cells triggers a potent RNAi effect.
  Article CAS Google Scholar
• Hamilton, A. J. & Baulcombe, D. C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286, 950–952 (1999).
  Article CAS Google Scholar
• Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494–498 (2001). The discovery that transfection of 21-nucleotide siRNAs cells triggers a potent RNAi effect.
  Article CAS Google Scholar
• Carpenter, A. E. & Sabatini, D. M. Systematic genome-wide screens of gene function. Nature Rev. Genet. 5, 11–22 (2004). A comprehensive review of HT screens with a particularly useful overview of commercially available image-acquisition platforms.
  Article CAS Google Scholar
• Kramer, R. & Cohen, D. Functional genomics to new drug targets. Nature Rev. Drug Discov. 3, 965–972 (2004).
  Article CAS Google Scholar
• Kiger, A. A. et al. A functional genomic analysis of cell morphology using RNA interference. J. Biol. 2, 27 (2003).
  Article CAS Google Scholar
• Boutros, M. et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303, 832–835 (2004).
  Article CAS Google Scholar
• Bettencourt-Dias, M. et al. Genome-wide survey of protein kinases required for cell cycle progression. Nature 432, 980–987 (2004).
  Article CAS Google Scholar
• Eggert, U. S. et al. Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol. 2, e379 (2004). An example of how a genome-wide RNAi screen can allow drug-target identification.
  Article Google Scholar
• Lum, L. et al. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 299, 2039–2045 (2003).
  Article CAS Google Scholar
• Nybakken, K., Vokes, S. A., Lin, T. Y., McMahon, A. P. & Perrimon, N. A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nature Genet. 37, 1323–1332 (2005).
  Article CAS Google Scholar
• Baeg, G. H., Zhou, R. & Perrimon, N. Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila. Genes Dev. 19, 1861–1870 (2005).
  Article CAS Google Scholar
• Muller, P., Kuttenkeuler, D., Gesellchen, V., Zeidler, M. P. & Boutros, M. Identification of JAK/STAT signalling components by genome-wide RNA interference. Nature 436, 871–875 (2005).
  Article Google Scholar
• Foley, E. & O'Farrell, P. H. Functional dissection of an innate immune response by a genome-wide RNAi screen. PLoS Biol. 2, e203 (2004).
  Article Google Scholar
• Gesellchen, V., Kuttenkeuler, D., Steckel, M., Pelte, N. & Boutros, M. An RNA interference screen identifies inhibitor of apoptosis protein 2 as a regulator of innate immune signalling in Drosophila. EMBO Rep. 6, 979–984 (2005).
  Article CAS Google Scholar
• DasGupta, R., Kaykas, A., Moon, R. T. & Perrimon, N. Functional genomic analysis of the Wnt-wingless signaling pathway. Science 308, 826–833 (2005). An example of a genome-wide RNAi screen in D. melanogaster cells using a transcriptional reporter assay.
  Article CAS Google Scholar
• Cherry, S. et al. Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev. 19, 445–452 (2005).
  Article CAS Google Scholar
• Philips, J. A., Rubin, E. J. & Perrimon, N. Drosophila RNAi screen reveals CD36 family member required for mycobacterial infection. Science 309, 1251–1253 (2005).
  Article CAS Google Scholar
• Agaisse, H. et al. Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science 309, 1248–1251 (2005).
  Article CAS Google Scholar
• Berns, K. et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431–437 (2004).
  Article CAS Google Scholar
• Paddison, P. J. et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428, 427–431 (2004).
  Article CAS Google Scholar
• Kolfschoten, I. G. et al. A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell 121, 849–858 (2005).
  Article CAS Google Scholar
• Westbrook, T. F. et al. A genetic screen for candidate tumor suppressors identifies REST. Cell 121, 837–848 (2005).
  Article CAS Google Scholar
• Huesken, D. et al. Design of a genome-wide siRNA library using an artificial neural network. Nature Biotechnol. 23, 995–1001 (2005).
  Article CAS Google Scholar
• Rottmann, S., Wang, Y., Nasoff, M., Deveraux, Q. L. & Quon, K. C. A TRAIL receptor-dependent synthetic lethal relationship between MYC activation and GSK3β/FBW7 loss of function. Proc. Natl Acad. Sci. USA 102, 15195–15200 (2005).
  Article CAS Google Scholar
• Pelkmans, L. et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 436, 78–86 (2005).
  Article CAS Google Scholar
• Kittler, R. et al. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 432, 1036–1040 (2004).
  Article CAS Google Scholar
• Nicke, B. et al. Involvement of MINK, a Ste20 family kinase, in Ras oncogene-induced growth arrest in human ovarian surface epithelial cells. Mol. Cell 20, 673–685 (2005).
  Article CAS Google Scholar
• Echalier, G. Drosophila Cell in Culture (Academic Press, New York, 1997).
  Google Scholar
• Armknecht, S. et al. High-throughput RNA interference screens in Drosophila tissue culture cells. Methods Enzymol. 392, 55–73 (2005).
  Article CAS Google Scholar
• Ui, K. et al. Newly established cell lines from Drosophila larval CNS express neural specific characteristics. In Vitro Cell. Dev. Biol. Anim. 30A, 209–216 (1994).
  Article CAS Google Scholar
• Song, E. et al. Sustained small interfering RNA-mediated human immunodeficiency virus type 1 inhibition in primary macrophages. J. Virol. 77, 7174–7181 (2003).
  Article CAS Google Scholar
• Liu, G. & Chen, X. The ferredoxin reductase gene is regulated by the p53 family and sensitizes cells to oxidative stress-induced apoptosis. Oncogene 21, 7195–7204 (2002).
  Article CAS Google Scholar
• Ovcharenko, D., Jarvis, R., Hunicke-Smith, S., Kelnar, K. & Brown, D. High-throughput RNAi screening in vitro: from cell lines to primary cells. RNA 11, 985–993 (2005).
  Article CAS Google Scholar
• Reynolds, A. et al. Rational siRNA design for RNA interference. Nature Biotechnol. 22, 326–330 (2004).
  Article CAS Google Scholar
• Huang, F., Khvorova, A., Marshall, W. & Sorkin, A. Analysis of clathrin-mediated endocytosis of epidermal growth factor receptor by RNA interference. J. Biol. Chem. 279, 16657–16661 (2004).
  Article CAS Google Scholar
• McManus, M. T. et al. Small interfering RNA-mediated gene silencing in T lymphocytes. J. Immunol. 169, 5754–5760 (2002).
  Article CAS Google Scholar
• Yang, D. et al. Short RNA duplexes produced by hydrolysis with Escherichia coli Rnase III mediate effective RNA interference in mammalian cells. Proc. Natl Acad. Sci. USA 99, 9942–9947 (2002).
  Article CAS Google Scholar
• Silva, J. M. et al. Second-generation shRNA libraries covering the mouse and human genomes. Nature Genet. 37, 1281–1288 (2005).
  Article CAS Google Scholar
• Stegmeier, F., Hu, G., Rickles, R. J., Hannon, G. J. & Elledge, S. J. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc. Natl Acad. Sci. USA 102, 13212–13217 (2005).
  Article CAS Google Scholar
• Dickins, R. A. et al. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nature Genet. 37, 1289–1295 (2005).
  Article CAS Google Scholar
• Ziauddin, J. & Sabatini, D. M. Microarrays of cells expressing defined cDNAs. Nature 411, 107–110 (2001).
  Article CAS Google Scholar
• Mousses, S. et al. RNAi microarray analysis in cultured mammalian cells. Genome Res. 13, 2341–2347 (2003).
  Article CAS Google Scholar
• Erfle, H., Simpson, J. C., Bastiaens, P. I. & Pepperkok, R. siRNA cell arrays for high-content screening microscopy. Biotechniques 37, 454–458, 460, 462 (2004).
  Article CAS 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. USA 101, 6548–6552 (2004).
  Article CAS Google Scholar
• Wheeler, D. B. et al. RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nature Methods 1, 127–132 (2004).
  Article CAS Google Scholar
• Jackson, A. L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotechnol. 21, 635–637 (2003).
  Article CAS Google Scholar
• Birmingham, A. et al. 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nature Methods 3, 199–204 (2006).
  Article CAS Google Scholar
• Doench, J. G., Petersen, C. P. & Sharp, P. A. siRNAs can function as miRNAs. Genes Dev. 17, 438–442 (2003).
  Article CAS 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. USA 101, 1892–1897 (2004).
  Article CAS Google Scholar
• Marques, J. T. & Williams, B. R. Activation of the mammalian immune system by siRNAs. Nature Biotechnol. 23, 1399–1405 (2005).
  Article CAS Google Scholar
• Zhang, J. H., Chung, T. D. & Oldenburg, K. R. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen 4, 67–73 (1999).
  Article CAS Google Scholar
• Kim, D. H. et al. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nature Biotechnol. 23, 222–226 (2005).
  Article CAS Google Scholar
• Bailey, S. N., Ali, S. M., Carpenter, A. E., Higgins, C. O. & Sabatini, D. M. Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nature Methods 3, 117–122 (2006).
  Article CAS Google Scholar
• Sonnichsen, B. et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462–469 (2005).
  Article CAS Google Scholar
• Ohrt, T., Merkle, D., Birkenfeld, K., Echeverri, C & Schwille, P. In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by exportin 5. Nucleic Acid Res. 34, 1369–1380 (2006).
  Article CAS Google Scholar
• Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F. & Hannon, G. J. Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235 (2004).
  Article CAS Google Scholar
• Gregory, R. I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).
  Article CAS Google Scholar
• Landthaler, M., Yalcin, A. & Tuschl, T. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol. 14, 2162–2167 (2004).
  Article CAS Google Scholar
• Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).
  Article CAS Google Scholar
• Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science 303, 95–98 (2004).
  Article CAS Google Scholar
• Bohnsack, M. T., Czaplinski, K. & Gorlich, D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10, 185–191 (2004).
  Article CAS Google Scholar
• Chendrimada, T. P. et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436, 740–744 (2005).
  Article CAS Google Scholar
• Saito, K., Ishizuka, A., Siomi, H. & Siomi, M. C. Processing of pre-microRNAs by the Dicer-1–Loquacious complex in Drosophila cells. PLoS Biol. 3, e235 (2005).
  Article Google Scholar
• Forstemann, K. et al. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3, e236 (2005).
  Article Google Scholar
• Pillai, R. S. et al. Inhibition of translational initiation by Let-7 microRNA in human cells. Science 309, 1573–1576 (2005).
  Article CAS Google Scholar
• Bagga, S. et al. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122, 553–563 (2005).
  Article CAS Google Scholar
• MacKeigan, J. P., Murphy, L. O. & Blenis, J. Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nature Cell Biol. 7, 591–600 (2005).
  Article CAS Google Scholar
• Ivanov, A. I. et al. Genes required for Drosophila nervous system development identified by RNA interference. Proc. Natl Acad. Sci. USA 101, 16216–16221 (2004).
  Article CAS Google Scholar
• Schneider, I. Cell lines derived from late embryonic stages of Drosophila melanogaster. J. Embryol. Exp. Morphol. 27, 353–365 (1972).
  CAS PubMed Google Scholar
• Yanagawa, S., Lee, J. S. & Ishimoto, A. Identification and characterization of a novel line of Drosophila Schneider S2 cells that respond to wingless signaling. J. Biol. Chem. 273, 32353–32539 (1998).
  Article CAS Google Scholar
• Echalier, G. & Ohanessian, A. In vitro culture of Drosophila melanogaster embryonic cells. In Vitro 6, 162–172 (1970).
  Article CAS Google Scholar
• Peel, D. J., Johnson, S. A. & Milner, M. J. The ultrastructure of imaginal disc cells in primary cultures and during cell aggregation in continuous cell lines. Tissue Cell 22, 749–758 (1990).
  Article CAS Google Scholar
• Kittler, R. et al. RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells. Proc. Natl Acad. Sci. USA 102, 2396–2401 (2005).
  Article CAS Google Scholar