Building mammalian signalling pathways with RNAi screens (original) (raw)

• Brummelkamp, T. R. & Bernards, R. New tools for functional mammalian cancer genetics. Nature Rev. Cancer 3, 781?789 (2003).
  Article CAS Google Scholar
• Hannon, G. J. & Rossi, J. J. Unlocking the potential of the human genome with RNA interference. Nature 431, 371?378 (2004).
  Article CAS Google Scholar
• Sharp, P. A. RNAi and double-strand RNA. Genes Dev. 13, 139?141 (1999).
  Article CAS Google Scholar
• Novina, C. D. & Sharp, P. A. The RNAi revolution. Nature 430, 161?164 (2004).
  Article CAS Google Scholar
• Meister, G. & Tuschl, T. Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343?349 (2004).
  Article CAS Google Scholar
• Zamore, P. D. & Haley, B. Ribo-gnome: the big world of small RNAs. Science 309, 1519?1524 (2005).
  Article CAS Google Scholar
• Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806?811 (1998). First demonstration in animals that dsRNA can target gene-specific knockdown.
  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
• Kamath, R. S. et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231?237 (2003).
  Article CAS Google Scholar
• Ashrafi, K. et al. Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421, 268?272 (2003).
  Article CAS 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
• Boutros, M. et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303, 832?835 (2004).
  Article CAS Google Scholar
• Stark, G. R., Kerr, I. M., Williams, B. R., Silverman, R. H. & Schreiber, R. D. How cells respond to interferons. Annu. Rev. Biochem. 67, 227?264 (1998).
  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). Seminal discovery that short dsRNAs trigger gene silencing in mammalian cells in the absence of nonspecific responses.
  CAS Google Scholar
• McManus, M. T., Petersen, C. P., Haines, B. B., Chen, J. & Sharp, P. A. Gene silencing using micro-RNA designed hairpins. RNA 8, 842?850 (2002).
  Article CAS Google Scholar
• Brummelkamp, T. R., Bernards, R. & Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550?553 (2002). One of the first demonstrations that plasmid-based shRNAs can target gene-specific knockdown.
  Article CAS Google Scholar
• Abbas-Terki, T., Blanco-Bose, W., Deglon, N., Pralong, W. & Aebischer, P. Lentiviral-mediated RNA interference. Hum. Gene Ther. 13, 2197?2201 (2002).
  Article CAS Google Scholar
• Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J. & Conklin, D. S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948?958 (2002).
  Article CAS Google Scholar
• Stewart, S. A. et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 9, 493?501 (2003).
  Article CAS Google Scholar
• Cullen, B. R. Transcription and processing of human microRNA precursors. Mol. Cell 16, 861?865 (2004).
  Article CAS Google Scholar
• Zeng, Y., Wagner, E. J. & Cullen, B. R. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell 9, 1327?1333 (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). Describes the first shRNA-mir library that targets all human and mouse genes with 2?3 constructs per gene.
  Article CAS Google Scholar
• Manche, L., Green, S. R., Schmedt, C. & Mathews, M. B. Interactions between double-stranded RNA regulators and the protein kinase DAI. Mol. Cell. Biol. 12, 5238?5248 (1992).
  Article CAS Google Scholar
• Minks, M. A., West, D. K., Benvin, S. & Baglioni, C. Structural requirements of double-stranded RNA for the activation of 2′,5′-oligo(A) polymerase and protein kinase of interferon-treated HeLa cells. J. Biol. Chem. 254, 10180?10183 (1979).
  CAS PubMed 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). The first large-scale retroviral library that was used in a pooled infection screen.
  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
• Arts, G. J. et al. Adenoviral vectors expressing siRNAs for discovery and validation of gene function. Genome Res. 13, 2325?2332 (2003).
  Article CAS Google Scholar
• Moffat, J. et al. A lentiviral RNAi library targeting human and mouse genes: construction, characterization and application to an arrayed high-content screen. Cell (in the press). Describes the first large-scale lentiviral shRNA library and arrayed viral infection screen.
• Aza-Blanc, P. et al. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell 12, 627?637 (2003).
  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
• Pelkmans, L et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 436, 78?86 (2005). Describes the first genome-wide siRNA transfection screen of human kinases that are required for endocytosis and a systems-level analysis of the screening results.
  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
• Brummelkamp, T. R., Nijman, S. M., Dirac, A. M. & Bernards, R. Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-κB. Nature 424, 797?801 (2003).
  Article CAS Google Scholar
• Cai, X., Hagedorn, C. H. & Cullen, B. R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10, 1957?1966 (2004).
  Article CAS Google Scholar
• Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051?4060 (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
• 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
• 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
• Han, J. et al. The Drosha?DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016?3027 (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
• Yi, R., Qin, Y., Macara, I. G. & Cullen, B. R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev. 17, 3011?3016 (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
• Dickins, R. A. et al. Probing tumor phenotypes using stable and regulated synthetic microRNA precursors. Nature Genet. 37, 1289?1295 (2005). Elegant study that demonstrates the potential of shRNA-mirs in vitro and in vivo.
  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
• Paddison, P. J., Caudy, A. A. & Hannon, G. J. Stable suppression of gene expression by RNAi in mammalian cells. Proc. Natl Acad. Sci. USA 99, 1443?1448 (2002).
  Article CAS 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).
  Article CAS Google Scholar
• Shirane, D. et al. Enzymatic production of RNAi libraries from cDNAs. Nature Genet. 36, 190?196 (2004).
  Article CAS Google Scholar
• Luo, B., Heard, A. D. & Lodish, H. F. Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc. Natl Acad. Sci. USA 101, 5494?5499 (2004).
  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
• Zheng, L. et al. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc. Natl Acad. Sci. USA 101, 135?140 (2004).
  Article CAS Google Scholar
• Sandy, P., Ventura, A. & Jacks, T. Mammalian RNAi: a practical guide. Biotechniques 39, 215?224 (2005).
  Article CAS Google Scholar
• Downward, J. Use of RNA interference libraries to investigate oncogenic signalling in mammalian cells. Oncogene 23, 8376?8383 (2004).
  Article CAS Google Scholar
• Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901?906 (1999).
  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
• 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
• Wheeler, D. B., Carpenter, A. E. & Sabatini, D. M. Cell microarrays and RNA interference chip away at gene function. Nature Genet. 37, S25?S30 (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 Meth. 3, 117?122 (2006).
  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
• 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
• Bridge, A. J., Pebernard, S., Ducraux, A., Nicoulaz, A. L. & Iggo, R. Induction of an interferon response by RNAi vectors in mammalian cells. Nature Genet. 34, 263?264 (2003).
  Article CAS Google Scholar
• Jackson, A. L. & Linsley, P. S. Noise amidst the silence: off-target effects of siRNAs? Trends Genet. 20, 521?524 (2004).
  Article CAS Google Scholar
• Hoffmann, R. & Valencia, A. A gene network for navigating the literature. Nature Genet. 36, 664 (2004).
  Article CAS Google Scholar
• Hoffmann, R. et al. Text mining for metabolic pathways, signaling cascades, and protein networks. Sci. STKE 283, pe21 (2005).
  Google Scholar
• Hoffmann, R. & Valencia, A. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 (Suppl. 2), ii252?ii258 (2005).
  CAS PubMed Google Scholar
• Liebel, U., Kindler, B. & Pepperkok, R. 'Harvester': a fast meta search engine of human protein resources. Bioinformatics 20, 1962?1963 (2004).
  Article CAS Google Scholar
• Tong, A. H. et al. Global mapping of the yeast genetic interaction network. Science 303, 808?813 (2004).
  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).
  Article CAS Google Scholar
• Huang, D., Moffat, J. & Andrews, B. Dissection of a complex phenotype by functional genomics reveals roles for the yeast cyclin-dependent protein kinase Pho85 in stress adaptation and cell integrity. Mol. Cell. Biol. 22, 5076?5088 (2002).
  Article CAS Google Scholar
• Sarbassov, D. D., Ali, S. M. & Sabatini, D. M. Growing roles for the mTOR pathway. Curr. Opin. Cell Biol. 17, 596?603 (2005).
  Article CAS Google Scholar
• Sarbassov, D. D., Guertin, D. A., Ali, S. M. & Sabatini, D. M. Phosphorylation and regulation of Akt/PKB by the rictor?mTOR complex. Science 307, 1098?1101 (2005).
  Article CAS Google Scholar
• Matsuda, T. & Cepko, C. L. Electroporation and RNA interference in the rodent retina in vivo and in vitro. Proc. Natl Acad. Sci. USA 101, 16?22 (2004).
  Article CAS Google Scholar
• Hommel, J. D., Sears, R. M., Georgescu, D., Simmons, D. L. & DiLeone, R. J. Local gene knockdown in the brain using viral-mediated RNA interference. Nature Med. 9, 1539?1544 (2003).
  Article CAS Google Scholar
• Xia, H., Mao, Q., Paulson, H. L. & Davidson, B. L. siRNA-mediated gene silencing in vitro and in vivo. Nature Biotechnol. 20, 1006?1010 (2002).
  Article CAS Google Scholar
• Kishida, T. et al. Sequence-specific gene silencing in murine muscle induced by electroporation-mediated transfer of short interfering RNA. J. Gene Med. 6, 105?110 (2004).
  Article CAS 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).
  Article CAS Google Scholar
• Ventura, A. et al. Cre?lox-regulated conditional RNA interference from transgenes. Proc. Natl Acad. Sci. USA 101, 10380?10385 (2004).
  Article CAS 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. USA 100, 1844?1848 (2003).
  Article CAS 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).
  Article CAS Google Scholar
• Siolas, D. et al. Synthetic shRNAs as potent RNAi triggers. Nature Biotechnol. 23, 227?231 (2005).
  Article CAS Google Scholar
• Carpenter, A. E. & Sabatini, D. M. Systematic genome-wide screens of gene function. Nature Rev. Genet. 5, 11?22 (2004).
  Article CAS Google Scholar