Dicer in RNAi: Its roles <span class='italic'>in vivo</span> and utility <span class='italic'>in vitro</span>

doi:10.1017/CBO9780511546402.005

2 - Dicer in RNAi: Its roles in vivo and utility in vitro

Published online by Cambridge University Press: 31 July 2009

Jason W. Myers and

James E. Ferrell Jr.

Edited by

Krishnarao Appasani

Foreword by

Andrew Fire and

Marshall Nirenberg

Show author details

Jason W. Myers: Affiliation:
Department of Molecular Pharmacology, Stanford University School of Medicine
James E. Ferrell Jr.: Affiliation:
Department of Molecular Pharmacology, Stanford University School of Medicine
Krishnarao Appasani: Affiliation:
GeneExpression Systems, Inc., Massachusetts
Andrew Fire: Affiliation:
Stanford University, California

Book contents

Get access

Summary

Introduction

In its infancy, RNA interference (RNAi) was simply an intriguing curiosity; now it has leapt to the forefront of science (Couzin, 2002). The growth spurt of RNAi-related studies has been partly pragmatic – RNAi clearly had the potential to evolve into an incredibly powerful technology for manipulating gene expression in diverse cell types, and to a great extent this potential has been realized. Moreover, as a physiological phenomenon, RNAi represents a fascinating and previously unrecognized level of cellular regulation. RNAi is essential for silencing of heterochromatin (Reinhart and Bartel, 2002; Volpe et al., 2002; Schramke and Allshire, 2003; Volpe et al., 2003) and gene expression via methylation (Grant, 1999; Jones et al., 1999), for antiviral defense, at least in plants (Baulcombe, 1999; Grant, 1999; Ratcliff et al., 1999), for controlling the expression of transposable elements and repetitive sequences (Ketting et al., 1999; Tabara et al., 1999; Ambros et al., 2003a&b; Sijen and Plasterk, 2003), and for proper embryonic development (Grishok et al., 2001; Hütvagner et al., 2001; Ketting et al., 2001; Knight and Bass, 2001; Bernstein et al., 2003; Houbaviy et al., 2003).

This chapter focuses on Dicer, an RNAse III family enzyme essential for sequence-specific gene suppression. We begin with an overview of the discovery of Dicer and its implication in RNAi, followed by a discussion of its hypothesized roles in vivo.

Type: Chapter
Information: RNA Interference Technology
From Basic Science to Drug Development
, pp. 29 - 54

DOI: https://doi.org/10.1017/CBO9780511546402.005 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2005

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Book purchase

Temporarily unavailable

References

Abbas-Terki, T., Blanco-Bose, W., Deglon, N., Pralong, W. and Aebischer, P. (2002). Lentiviral-mediated RNA interference. Human Gene Therapy, 13, 2197–2201CrossRef Google Scholar PubMed

Ambros, V., Bartel, B., Bartel, D. P., Burge, C. B., Carrington, J. C., Chen, X., Dreyfuss, G., Eddy, S. R., Griffiths-Jones, S., Marshall, M., Matzke, M., Ruvkun, G. and Tuschl, T. (2003a). A uniform system for microRNA annotation. RNA, 9, 277–279CrossRef Google Scholar

Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. and Jewell, D. (2003b). microRNAs and other tiny endogenous RNAs in C. elegans. Current Biology, 13, 807–818CrossRef Google Scholar

An, D. S., Xie, Y., Mao, S. H., Morizono, K., Kung, S. K. and Chen, I. S. (2003). Efficient lentiviral vectors for short hairpin RNA delivery into human cells. Human Gene Therapy, 14, 1207–1212CrossRef Google Scholar PubMed

Andino, R. (2003). RNAi puts a lid on virus replication. Nature Biotechnology, 21, 629–630CrossRef Google Scholar PubMed

Angell, S. M. and Baulcombe, D. C. (1997). Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA. European Molecular Biology Organization Journal, 16, 3675–3684CrossRef Google Scholar PubMed

Arasu, P., Wightman, B. and Ruvkun, G. (1991). Temporal regulation of lin-14 by the antagonistic action of two other heterochronic genes, lin-14 by the antagonistic action of two other heterochronic genes, lin-4 and lin-28. Genes & Development, 5, 1825–1833CrossRef Google Scholar PubMed

Aravin, A. A., Naumova, N. M., Tulin, A. V., Vagin, V. V., Rozovsky, Y. M. and Gvozdev, V. A. (2001). Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Current Biology, 11, 1017–1027CrossRef Google Scholar PubMed

Ashrafi, K., Chang, F. Y., Watts, J. L., Fraser, A. G., Kamath, R. S., Ahringer, J. and Ruvkun, G. (2003). Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature, 421, 268–272CrossRef Google Scholar PubMed

Bartel, B. and Bartel, D. P. (2003). microRNAs: at the root of plant development?Plant Physiology, 132, 709–717CrossRef Google Scholar PubMed

Barton, G. M. and Medzhitov, R. (2002). Retroviral delivery of small interfering RNA into primary cells. Proceedings of the National Academy of Sciences USA, 99, 14943–14945CrossRef Google Scholar PubMed

Baulcombe, D. C. (1999). Fast forward genetics based on virus-induced gene silencing. Current Opinion in Plant Biology, 2, 109–113CrossRef Google Scholar PubMed

Bernstein, E., Caudy, A. A., Hammond, S. M. and Hannon, G. J. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366CrossRef Google Scholar PubMed

Bernstein, E., Kim, S. Y., Carmell, M. A., Murchison, E. P., Alcorn, H., Li, M. Z., Mills, A. A., Elledge, S. J., Anderson, K. V. and Hannon, G. J. (2003). Dicer is essential for mouse development. Nature Genetics, 35, 215–217CrossRef Google Scholar PubMed

Bohula, E. A., Salisbury, A. J., Sohail, M., Playford, M. P., Riedemann, J., Southern, E. M. and Macaulay, V. M. (2003). The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R. Journal of Biological Chemistry, 278, 15991–15997CrossRef Google Scholar PubMed

Bridge, A. J., Pebernard, S., Ducraux, A., Nicoulaz, A. L. and Iggo, R. (2003). Induction of an interferon response by RNAi vectors in mammalian cells. Nature Genetics, 34, 263–264CrossRef Google Scholar PubMed

Brummelkamp, T. R., Bernards, R. and Agami, R. (2002a). Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell, 2, 243–247CrossRef Google Scholar

Brummelkamp, T. R., Bernards, R. and Agami, R. (2002b). A system for stable expression of short interfering RNAs in mammalian cells. Science, 296, 550–553CrossRef Google Scholar

Brummelkamp, T. R., Nijman, S. M., Dirac, A. M. and Bernards, R. (2003). Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-kappaB. Nature, 424, 797–801CrossRef Google Scholar PubMed

Carthew, R. W. (2001). Gene silencing by double-stranded RNA. Current Opinion in Cell Biology, 13, 244–248CrossRef Google Scholar PubMed

Castanotto, D., Li, H. and Rossi, J. J. (2002). Functional siRNA expression from transfected PCR products. RNA, 8, 1454–1460CrossRef Google Scholar PubMed

Castle, L. A., Errampalli, D., Atherton, T. L., Franzmann, L. H., Yoon, E. S. and Meinke, D. W. (1993). Genetic and molecular characterization of embryonic mutants identified following seed transformation in Arabidopsis. Molecular and General Genetics, 241, 504–514CrossRef Google Scholar PubMed

Chi, J. T., Chang, H. Y., Wang, N. N., Chang, D. S., Dunphy, N. and Brown, P. O. (2003). Genomewide view of gene silencing by small interfering RNAs. Proceedings of the National Academy of Sciences USA, 100, 6343–6346CrossRef Google Scholar PubMed

Cogoni, C., Irelan, J. T., Schumacher, M., Schmidhauser, T. J., Selker, E. U. and Macino, G. (1996). Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA-DNA interactions or DNA methylation. European Molecular Biology Organization Journal, 15, 3153–3163Google Scholar PubMed

Couzin, J. (2002). Breakthrough of the year. Small RNAs make big splash. Science, 298, 2296–2297CrossRef Google Scholar PubMed

Dalmay, T., Hamilton, A., Rudd, S., Angell, S. and Baulcombe, D. C. (2000). An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell, 101, 543–553CrossRef Google Scholar

Denli, A. M. and Hannon, G. J. (2003). RNAi: An ever-growing puzzle. Trends in Biochemical Sciences, 28, 196–201CrossRef Google Scholar PubMed

Dirac, A. M. and Bernards, R. (2003). Reversal of senescence in mouse fibroblasts through lentiviral suppression of p53. Journal of Biological Chemistry, 278, 11731–11734CrossRef Google Scholar PubMed

Doench, J. G., Petersen, C. P. and Sharp, P. A. (2003). siRNAs can function as can function as miRNAs. Genes & Development, 17, 438–442CrossRef Google Scholar PubMed

Doi, N., Zenno, S., Ueda, R., Ohki-Hamazaki, H., Ui-Tei, K. and Saigo, K. (2003). Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors. Current Biology, 13, 41–46CrossRef Google Scholar PubMed

Dougherty, W. G., Lindbo, J. A., Smith, H. A., Parks, T. D., Swaney, S. and Proebsting, W. M. (1994). RNA-mediatedvirus resistance in transgenic plants: Exploitation of a cellular pathway possibly involved in RNA degradation. Mol Plant Microbe Interact, 7, 544–552CrossRef Google Scholar PubMed

Dunn, J. J. (1982). Ribonuclease III. In The Enzymes, P. D. Boyer, ed. (New York, Academic Press), pp. 485–499

Dykxhoorn, D. M., Novina, C. D. and Sharp, P. A. (2003). Killing the messenger: Short RNAs that silence gene expression. Nature Reviews Molecular Cell Biology, 4, 457–467CrossRef Google Scholar PubMed

Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K. and Tuschl, T. (2001a). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494–498CrossRef Google Scholar

Elbashir, S. M., Lendeckel, W. and Tuschl, T. (2001b). RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes & Development, 15, 188–200CrossRef Google Scholar

Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. and Tuschl, T. (2001c). Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. European Molecular Biology Organization Journal, 20, 6877–6888CrossRef Google Scholar

Elbashir, S. M., Harborth, J., Weber, K. and Tuschl, T. (2002). Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods, 26, 199–213CrossRef Google Scholar PubMed

Errampalli, D., Patton, D., Castle, L., Mickelson, L., Hansen, K., Schnall, J., Feldmann, K. and Meinke, D. (1991). Embryonic lethals and T-DNA insertional mutagenesis in Arabidopsis. Plant Cell, 3, 149–157CrossRef Google Scholar PubMed

Feinberg, E. H. and Hunter, C. P. (2003). Transport of dsRNA into cells by the transmembrane protein SID-1. Science, 301, 1545–1547CrossRef Google Scholar PubMed

Fink, C. C., Bayer, K. U., Myers, J. W., Ferrell, J. E. Jr., Schulman, H. and Meyer, T. (2003). Selective regulation of neurite extension and synapse formation by the beta but not the alpha isoform of CaMKII. Neuron, 39, 283–297CrossRef Google Scholar

Finnegan, E. J., Margis, R. and Waterhouse, P. M. (2003). Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) mutant, a homolog of Dicer-1 from DrosophilaCurrent Biology, 13, 236–240CrossRef Google Scholar

Fire, A. (1999). RNA-triggered gene silencing. Trends in Genetics, 15, 358–363CrossRef Google Scholar PubMed

Fire, A., Albertson, D., Harrison, S. W. and Moerman, D. G. (1991). Production of antisense RNA leads to effective and specific inhibition of gene expression in C. elegans muscle. Development, 113, 503–514Google Scholar PubMed

Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E. and Mello, C. C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811CrossRef Google Scholar PubMed

Gitlin, L., Karelsky, S. and Andino, R. (2002). Short interfering RNA confers intracellular antiviral immunity in human cells. Nature, 418, 430–434CrossRef Google Scholar PubMed

Golden, T. A., Schauer, S. E., Lang, J. D., Pien, S., Mushegian, A. R., Grossniklaus, U., Meinke, D. W. and Ray, A. (2002). SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis. Plant Physiology, 130, 808–822CrossRef Google Scholar PubMed

Gonczy, P., Echeverri, C., Oegema, K., Coulson, A., Jones, S. J., Copley, R. R., Duperon, J., Oegema, J., Brehm, M., Cassin, E., Hannak, E., Kirkham, M., Pichler, S., Flohrs, K., Goessen, A., Leidel, S., Alleaume, A. M., Martin, C., Ozlu, N., Bork, P. and Hyman, A. A. (2000). Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature, 408, 331–336CrossRef Google Scholar

Grant, S. R. (1999). Dissecting the mechanisms of posttranscriptional gene silencing: Divide and conquer. Cell, 96, 303–306CrossRef Google Scholar PubMed

Grishok, A. and Mello, C. C. (2002). RNAi (Nematodes: Caenorhabditis elegans). Advances in Genetics, 46, 339–360Google Scholar

Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish, S., Ha, I., Baillie, D. L., Fire, A., Ruvkun, G. and Mello, C. C. (2001). Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23–34CrossRef Google Scholar PubMed

Guo, S. and Kemphues, K. J. (1995). par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell, 81, 611–620CrossRef Google Scholar

Hamilton, A., Voinnet, O., Chappell, L. and Baulcombe, D. (2002). Two classes of short interfering RNA in RNA silencing. European Molecular Biology Organization Journal, 21, 4671–4679CrossRef Google Scholar PubMed

Hamilton, A. J. and Baulcombe, D. C. (1999). A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950–952CrossRef Google Scholar PubMed

Hammond, S. M., Bernstein, E., Beach, D. and Hannon, G. J. (2000). An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature, 404, 293–296CrossRef Google Scholar PubMed

Hammond, S. M., Caudy, A. A. and Hannon, G. J. (2001). PostPost-transcriptional gene silencing by double-stranded RNA. Nature Reviews Genetics, 2, 110–119CrossRef Google Scholar PubMed

Hannon, G. J. (2002). RNA interference. Nature, 418, 244–251CrossRef Google Scholar PubMed

Hemann, M. T., Fridman, J. S., Zilfou, J. T., Hernando, E., Paddison, P. J., Cordon-Cardo, C., Hannon, G. J. and Lowe, S. W. (2003). An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivoNature Genetics, 33, 396–400CrossRef Google Scholar PubMed

Houbaviy, H. B., Murray, M. F. and Sharp, P. A. (2003). Embryonic stem cell-specific Micro-RNAs. Developmental Cell, 5, 351–358CrossRef Google Scholar

Hunter, C. P. (2000). Gene silencing: shrinking the black box of RNAi. Current Biology, 10, R137–140CrossRef Google Scholar PubMed

Hütvagner, G., McLachlan, J., Pasquinelli, A. E., Balint, E., Tuschl, T. and Zamore, P. D. (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science, 293, 834–838CrossRef Google Scholar PubMed

Hütvagner, G. and Zamore, P. D. (2002a). A microRNA in a multiple-turnover RNAi enzyme complex. Science, 297, 2056–2060CrossRef Google Scholar

Hütvagner, G. and Zamore, P. D. (2002b). RNAi: Nature abhors a double-strand. Current Opinion in Genetics and Development, 12, 225–232CrossRef Google Scholar

Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V., Burchard, J., Mao, M., Li, B., Cavet, G. and Linsley, P. S. (2003). Expression profiling reveals off-target gene regulation by RNAi. Nature Biotechnology, 21, 635–637CrossRef Google Scholar PubMed

Jacobsen, S. E., Running, M. P. and Meyerowitz, E. M. (1999). Disruption of an RNA helicase/RNase III gene in Arabidopsis causes unregulated cell division in floral meristems. Development, 126, 5231–5243Google Scholar PubMed

Jones, L., Hamilton, A. J., Voinnet, O., Thomas, C. L., Maule, A. J. and Baulcombe, D. C. (1999). RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell, 11, 2291–2301CrossRef Google Scholar PubMed

Jorgensen, R. (1990). Altered gene expression in plants due to trans-interactions between homologous genes. Trends in Biotechnology, 8, 340–344CrossRef Google Scholar PubMed

Kamath, R. S. and Ahringer, J. (2003). Genome-wide RNAi screening in Caenorhabditis elegans. Methods, 30, 313–321CrossRef Google Scholar PubMed

Kamath, R. S., Fraser, A. G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Bot, N., Moreno, S., Sohrmann, M., Welchman, D. P., Zipperlen, P. and Ahringer, J. (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231–237CrossRef Google Scholar

Kawasaki, H., Suyama, E., Iyo, M. and Taira, K. (2003). siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cells. Nucleic Acids Research, 31, 981–987CrossRef Google Scholar PubMed

Kennerdell, J. R. and Carthew, R. W. (1998). Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled 2 act in the wingless pathway. Cell, 95, 1017–1026CrossRef Google Scholar PubMed

Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T., Hannon, G. J. and Plasterk, R. H. (2001). Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Development, 15, 2654–2659CrossRef Google Scholar PubMed

Ketting, R. F., Haverkamp, T. H., Luenen, H. G. and Plasterk, R. H. (1999). Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNAseD. Cell, 99, 133–141CrossRef Google Scholar PubMed

Khvorova, A., Reynolds, A. and Jayasena, S. D. (2003). Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209–216CrossRef Google Scholar PubMed

Kiger, A., Baum, B., Jones, S., Jones, M., Coulson, A., Echeverri, C. and Perrimon, N. (2003). A functional genomic analysis of cell morphology using RNA interference. Journal of Biology, 2, 27CrossRef Google Scholar PubMed

Knight, S. W. and Bass, B. L. (2001). A role for the RNAse III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science, 293, 2269–2271CrossRef Google Scholar PubMed

Kostura, M. and Mathews, M. B. (1989). Purification and activation of the double-stranded RNA-dependent eIF-2 kinase DAI. Molecular and Cellular Biology, 9, 1576–1586CrossRef Google Scholar PubMed

Kumagai, M. H., Donson, J., della-Cioppa, G., Harvey, D., Hanley, K. and Grill, L. K. (1995). Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proceedings of the National Academy of Sciences USA, 92, 1679–1683CrossRef Google Scholar PubMed

Lang, J. D., Ray, S. and Ray, A. (1994). sin 1, a mutation affecting female fertility in Arabidopsis, interacts with mod 1, its recessive modifier. Genetics, 137, 1101–1110Google Scholar

Lassus, P., Opitz-Araya, X. and Lazebnik, Y. (2002). Requirement for caspase-2 in stress-induced apoptosis before mitochondrial permeabilization. Science, 297, 1352–1354CrossRef Google Scholar PubMed

Lassus, P., Rodriguez, J. and Lazebnik, Y. (2002). Confirming specificity of RNAi in mammalian cells. Science's STKE: Signal Transduction Knowledge Environment, 2002, PL13Google Scholar PubMed

Lee, N. S., Dohjima, T., Bauer, G., Li, H., Li, M. J., Ehsani, A., Salvaterra, P. and Rossi, J. (2002a). Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnology, 20, 500–505CrossRef Google Scholar

Lee, Y., Jeon, K., Lee, J. T., Kim, S. and Kim, V. N. (2002b). microRNA maturation: Stepwise processing and subcellular localization. European Molecular Biology Organization Journal, 21, 4663–4670CrossRef Google Scholar

Lee, R. C., Feinbaum, R. L. and Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843–854CrossRef Google Scholar

Lee, S. S., Lee, R. Y., Fraser, A. G., Kamath, R. S., Ahringer, J. and Ruvkun, G. (2003a). A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nature Genetics, 33, 40–48CrossRef Google Scholar

Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S. and Kim, V. N. (2003b). The nuclear RNAse III Drosha initiates microRNA processing. Nature, 425, 415–419CrossRef Google Scholar

Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. and Bartel, D. P. (2003). Vertebrate microRNA genes. Science, 299, 1540CrossRef Google Scholar PubMed

Lingel, A., Simon, B., Izaurralde, E. and Sattler, M. (2003). Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature, 426, 465–469CrossRef Google Scholar PubMed

Lingel, A., Simon, B., Izaurralde, E. and Sattler, M. (2004). Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nature, Structural and Molecular Biology, 11, 576–577CrossRef Google Scholar PubMed

Llave, C., Kasschau, K. D., Rector, M. A. and Carrington, J. C. (2002a). Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14, 1605–1619CrossRef Google Scholar

Llave, C., Xie, Z., Kasschau, K. D. and Carrington, J. C. (2002b). Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053–2056CrossRef Google Scholar

Lum, L., Yao, S., Mozer, B., Rovescalli, A., Kessler, D., Nirenberg, M. and Beachy, P. A. (2003). Identification of hedgehog pathway components by RNAi in Drosophila cultured cells. Science, 299, 2039–2045CrossRef Google Scholar PubMed

Lustig, K. D., Stukenberg, P. T., McGarry, T. J., King, R. W., Cryns, V. L., Mead, P. E., Zon, L. I., Yuan, J. and Kirschner, M. W. (1997). Small pool expression screening: Identification of genes involved in cell cycle control, apoptosis, and early development. Methods in Enzymolgy, 283, 83–99CrossRef Google Scholar PubMed

Ma, J. B., Ye, K. and Patel, D. J. (2004). Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature, 429, 318–322CrossRef Google Scholar PubMed

Manche, L., Green, S. R., Schmedt, C. and Mathews, M. B. (1992). Interactions between double-stranded RNA regulators and the protein kinase DAI. Molecular and Cellular Biology, 12, 5238–5248CrossRef Google Scholar PubMed

Matta, H., Hozayev, B., Tomar, R., Chugh, P. and Chaudhary, P. M. (2003). Use of lenti-viral vectors for delivery of small interfering RNA. Cancer Biology and Therapy, 2, 206–210CrossRef Google Scholar

McElver, J., Tzafrir, I., Aux, G., Rogers, R., Ashby, C., Smith, K., Thomas, C., Schetter, A., Zhou, Q., Cushman, M. A., Tossberg, J., Nickle, T., Levin, J. Z., Law, M., Meinke, D. and Patton, D. (2001). Insertional mutagenesis of genes required for seed development in Arabidopsis thaliana. Genetics, 159, 1751–1763Google Scholar PubMed

Mette, M. F., Aufsatz, W., Winden, J., Matzke, M. A. and Matzke, A. J. (2000). Transcriptional silencing and promoter methylation triggered by double-stranded RNA. European Molecular Biology Organization Journal, 19, 5194–5201CrossRef Google Scholar PubMed

Minks, M. A., West, D. K., Benvin, S. and Baglioni, C. (1979). Structural requirements of double-stranded RNA for the activation of 2′,5′-oligo(A) polymerase and proteins kinase of interferon-treated HeLa cells. Journal of Biological Chemistry, 254, 10180–10183Google Scholar PubMed

Miyagishi, M. and Taira, K. (2002). U6 promoter-driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells. Nature Biotechnology, 20, 497–500CrossRef Google Scholar PubMed

Moss, E. G. (2000). Non-coding RNAs: lightning strikes twice. Current Biology, 10, R436–439CrossRef Google Scholar PubMed

Myers, J. W., Jones, J. T., Meyer, T. and Ferrell, J. E. Jr. (2003). Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nature Biotechnology, 21, 324–328CrossRef Google Scholar PubMed

Oefner, P. J. (2002). Sequence variation and the biological function of genes: Methodological and biological considerations Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences, 782, 3–25CrossRef Google Scholar

Olsen, P. H. and Ambros, V. (1999). The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Developmental Biology, 216, 671–680CrossRef Google Scholar PubMed

Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J. and Conklin, D. S. (2002a). Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes & Development, 16, 948–958CrossRef Google Scholar

Paddison, P. J., Caudy, A. A. and Hannon, G. J. (2002b). Stable suppression of gene expression by RNAi in mammalian cells. Proceedings of the National Academy of Sciences USA, 99, 1443–1448CrossRef Google Scholar

Paddison, P. J. and Hannon, G. J. (2002). RNA interference: The new somatic cell genetics? Cancer Cell, 2, 17–23CrossRef Google Scholar PubMed

Papp, I., Mette, M. F., Aufsatz, W., Daxinger, L., Schauer, S. E., Ray, A., Winden, J., Matzke, M. and Matzke, A. J. (2003). Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiology, 132, 1382–1390CrossRef Google Scholar PubMed

Park, W., Li, J., Song, R., Messing, J. and Chen, X. (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology, 12, 1484–1495CrossRef Google Scholar PubMed

Parrish, S., Fleenor, J., Xu, S., Mello, C. and Fire, A. (2000). Functional anatomy of a dsRNA trigger. Differential requirement for the two trigger strands in RNA interference. Molecular Cell, 6, 1077–1087CrossRef Google Scholar PubMed

Pasquinelli, A. E. and Ruvkun, G. (2002). Control of developmental timing by microRNAs and their targets. Annual Review of Cell and Developmental Biology, 18, 495–513CrossRef Google Scholar PubMed

Paul, C. P., Good, P. D., Winer, I. and Engelke, D. R. (2002). Effective expression of small interfering RNA in human cells. Nature Biotechnology, 20, 505–508CrossRef Google Scholar PubMed

Pothof, J., Haaften, G., Thijssen, K., Kamath, R. S., Fraser, A. G., Ahringer, J., Plasterk, R. H. and Tijsterman, M. (2003). Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Genes & Development, 17, 443–448CrossRef Google Scholar

Provost, P., Dishart, D., Doucet, J., Frendewey, D., Samuelsson, B. and Radmark, O. (2002a). Ribonuclease activity and RNA binding of recombinant human Dicer. European Molecular Biology Organization Journal, 21, 5864–5874CrossRef Google Scholar

Provost, P., Silverstein, R. A., Dishart, D., Walfridsson, J., Djupedal, I., Kniola, B., Wright, A., Samuelsson, B., Radmark, O. and Ekwall, K. (2002b). Dicer is required for chromosome segregation and gene silencing in fission yeast cells. Proceedings of the National Academy of Sciences USA, 99, 16648–16653CrossRef Google Scholar

Ratcliff, F. G., MacFarlane, S. A. and Baulcombe, D. C. (1999). Gene silencing without DNA. RNA-mediated cross-protection between viruses. Plant Cell, 11, 1207–1216CrossRef Google Scholar PubMed

Ray, A., Lang, J. D., Golden, T. and Ray, S. (1996a). SHORT INTEGUMENT (SIN1), a gene required for ovule development in Arabidopsis, also controls flowering time. Development, 122, 2631–2638Google Scholar

Ray, S., Golden, T. and Ray, A. (1996b). Maternal effects of the short integument mutation on embryo development in Arabidopsis. Developmental Biology, 180, 365–369CrossRef Google Scholar

Reinhart, B. J. and Bartel, D. P. (2002a). Small RNAs correspond to centromere heterochromatic repeats. Science, 297, 1831CrossRef Google Scholar

Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B. and Bartel, D. P. (2002b). Micro-RNAs in plants. Genes & Development, 16, 1616–1626CrossRef Google Scholar

Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W. S. and Khvorova, A. (2004). Rational siRNA design for RNA interference. Nature Biotechnology, 22, 326–330CrossRef Google Scholar PubMed

Robertson, H. D. and Hunter, T. (1975). Sensitive methods for the detection and characterization of double helical ribonucleic acid. Journal of Biological Chemistry, 250, 418–425Google Scholar PubMed

Robinson-Beers, K., Pruitt, R. E. and Gasser, C. S. (1992). Ovule development in wild-type Arabidopsis and two female-sterile mutants. Plant Cell, 4, 1237–1249CrossRef Google Scholar PubMed

Rubinson, D. A., Dillon, C. P., Kwiatkowski, A. V., Sievers, C., Yang, L., Kopinja, J., Rooney, D. L., Ihrig, M. M., McManus, M. T., Gertler, F. B., Scott, M. L. and Parijs, L. (2003). A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference. Nature Genetics, 33, 401–406CrossRef Google Scholar PubMed

Ruiz, M. T., Voinnet, O. and Baulcombe, D. C. (1998). Initiation and maintenance of virus-induced gene silencing. Plant Cell, 10, 937–946CrossRef Google Scholar PubMed

Samuel, C. E. (2001). Antiviral actions of interferons. Clinical Microbiology Reviews, 14, 778–809CrossRef Google Scholar PubMed

Schauer, S. E., Jacobsen, S. E., Meinke, D. W. and Ray, A. (2002). DICER-LIKE1: Blind men and elephants in Arabidopsis development. Trends in Plant Sciences, 7, 487–491CrossRef Google Scholar PubMed

Scherr, M., Battmer, K., Ganser, A. and Eder, M. (2003). Modulation of gene expression by lentiviral-mediated delivery of small interfering RNA. Cell Cycle, 2, 251–257CrossRef Google Scholar PubMed

Schramke, V. and Allshire, R. (2003). Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science, 301, 1069–1074CrossRef Google Scholar PubMed

Schwarz, D. S., Hütvagner, G., Du, T., Xu, Z., Aronin, N. and Zamore, P. D. (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199–208CrossRef Google Scholar PubMed

Schwarz, D. S., Hütvagner, G., Haley, B. and Zamore, P. D. (2002). Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Molecular Cell, 10, 537–548CrossRef Google Scholar

Semizarov, D., Frost, L., Sarthy, A., Kroeger, P., Halbert, D. N. and Fesik, S. W. (2003). Specificity of short interfering RNA determined through gene expression signatures. Proceedings of the National Academy of Sciences USA, 100, 6347–6352CrossRef Google Scholar PubMed

Sharp, P. A. (2001). RNA interference – 2001. Genes & Development, 15, 485–490CrossRef Google Scholar PubMed

Shen, C., Buck, A. K., Liu, X., Winkler, M. and Reske, S. N. (2003). Gene silencing by adenovirus-delivered siRNA. Federation of European Biochemical Society Letters, 539, 111–114CrossRef Google Scholar PubMed

Sijen, T. and Plasterk, R. H. (2003). Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature, 426, 310–314CrossRef Google Scholar PubMed

Simmer, F., Moorman, C., Linden, A. M., Kuijk, E., Berghe, P. V., Kamath, R., Fraser, A. G., Ahringer, J. and Plasterk, R. H. (2003). Genome-wide RNAi of C. of C. elegans using the hypersensitive rrf-3 strain reveals novel Gene Functions. Public Library of Science Biology, 1, E12Google Scholar PubMed

Sledz, C. A., Holko, M., Veer, M. J., Silverman, R. H. and Williams, B. R. (2003). Activation of the interferon system by short-interfering RNAs. Nature Cell Biology, 5, 834–839CrossRef Google Scholar PubMed

Smith, W. C. and Harland, R. M. (1992). Expression cloning of noggin, a new dorsalizing factor localized to the Spemann organizer in Xenopus embryos. Cell, 70, 829–840CrossRef Google Scholar PubMed

Song, J. J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J. and Joshua-Tor, L. (2003). The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Structural Biology, 10, 1026–1032CrossRef Google Scholar PubMed

Stark, G. R., Kerr, I. M., Williams, B. R., Silverman, R. H. and Schreiber, R. D. (1998). How cells respond to interferons. Annual Review of Biochemistry, 67, 227–264CrossRef Google Scholar PubMed

Tabara, H., Sarkissian, M., Kelly, W. G., Fleenor, J., Grishok, A., Timmons, L., Fire, A. and Mello, C. C. (1999). The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell, 99, 123–132CrossRef Google Scholar PubMed

Tang, G., Reinhart, B. J., Bartel, D. P. and Zamore, P. D. (2003). A biochemical framework for RNA silencing in plants. Genes & Development, 17, 49–63CrossRef Google Scholar PubMed

Thoma, C., Hasselblatt, P., Kock, J., Chang, S. F., Hockenjos, B., Will, H., Hentze, M. W., Blum, H. E., Weizsacker, F. and Offensperger, W. B. (2001). Generation of stable mRNA fragments and translation of N-truncated proteins induced by antisense oligodeoxynucleotides. Molecular Cell, 8, 865–872CrossRef Google Scholar PubMed

Tijsterman, M., Ketting, R. F. and Plasterk, R. H. (2002). The genetics of RNA silencing. Annual Review of Genetics, 36, 489–519CrossRef Google Scholar PubMed

Timmons, L. and Fire, A. (1998). Specific interference by ingested dsRNA. Nature, 395, 854CrossRef Google Scholar PubMed

Tomar, R. S., Matta, H. and Chaudhary, P. M. (2003). Use of adeno-associated viral vector for delivery of small interfering RNA. Oncogene, 22, 5712–5715CrossRef Google Scholar PubMed

Tuschl, T., Zamore, P. D., Lehmann, R., Bartel, D. P. and Sharp, P. A. (1999). Targeted mRNA degradation by double-stranded RNA in vitro. Genes & Development, 13, 3191–3197CrossRef Google Scholar PubMed

Vastenhouw, N. L., Fischer, S. E., Robert, V. J., Thijssen, K. L., Fraser, A. G., Kamath, R. S., Ahringer, J. and Plasterk, R. H. (2003). A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans. Current Biology, 13, 1311–1316CrossRef Google Scholar PubMed

Vaucheret, H., Beclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J. B., Mourrain, P., Palauqui, J. C. and Vernhettes, S. (1998). Transgene-induced gene silencing in plants. Plant Journal, 16, 651–659CrossRef Google Scholar PubMed

Vickers, T. A., Koo, S., Bennett, C. F., Crooke, S. T., Dean, N. M. and Baker, B. F. (2003). Efficient reduction of target RNAs by small interfering RNA and RNAse H-dependent antisense agents. A comparative analysis. Journal of Biological Chemistry, 278, 7108–7118CrossRef Google Scholar PubMed

Volpe, T., Schramke, V., Hamilton, G. L., White, S. A., Teng, G., Martienssen, R. A. and Allshire, R. C. (2003). RNA interference is required for normal centromere function in fission yeast. Chromosome Research, 11, 137–146CrossRef Google Scholar PubMed

Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I. and Martienssen, R. A. (2002). Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297, 1833–1837CrossRef Google Scholar PubMed

Winston, W. M., Molodowitch, C. and Hunter, C. P. (2002). Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science, 295, 2456–2459CrossRef Google Scholar

Yan, K. S., Yan, S., Farooq, A., Han, A., Zeng, L. and Zhou, M. M. (2003). Structure and conserved RNA binding of the PAZ domain. Nature, 426, 468–474CrossRef Google Scholar PubMed

Yang, D., Buchholz, F., Huang, Z., Goga, A., Chen, C. Y., Brodsky, F. M. and Bishop, J. M. (2002). Short RNA duplexes produced by hydrolysis with Escherichia coli RNAse III mediate effective RNA interference in mammalian cells. Proceedings of the National Academy of Sciences USA, 99, 9942–9947CrossRef Google Scholar PubMed

Yang, D., Lu, H. and Erickson, J. W. (2000). Evidence that processed small dsRNAs may mediate sequence-specific mRNA degradation during RNAi in Drosophila embryos. Current Biology, 10, 1191–1200CrossRef Google Scholar PubMed

Yu, J. Y., DeRuiter, S. L. and Turner, D. L. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proceedings of the National Academy of Sciences USA, 99, 6047–6052CrossRef Google Scholar PubMed

Zamore, P. D. (2002). Ancient pathways programmed by small RNAs. Science, 296, 1265–1269CrossRef Google Scholar PubMed

Zamore, P. D., Tuschl, T., Sharp, P. A. and Bartel, D. P. (2000). RNAi: Double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25–33CrossRef Google Scholar PubMed

Zhang, H., Kolb, F. A., Brondani, V., Billy, E. and Filipowicz, W. (2002). Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. European Molecular Biology Organization Journal, 21, 5875–5885CrossRef Google Scholar PubMed

Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. and Filipowicz, W. (2004). Single processing center models for human Dicer and bacterial RNAse III. Cell, 118, 57–68CrossRef Google Scholar PubMed