Overview of RNA Interference and Related Processes
David Baulcombe1
1The Sainsbury Laboratory John Innes Center, Norwich, United Kingdom
1The Sainsbury Laboratory John Innes Center, Norwich, United Kingdom
Publication Name:
Current Protocols in Molecular Biology
Unit Number:
Unit 26.1
DOI:
10.1002/0471142727.mb2601s62
Online Posting Date:
May, 2003 Abstract
The history of RNA interference (RNAi) has unfolded rapidly since 1997 with a series of discoveries from plants, fungi, and animals. Initially, the interest was directed towards development of gene silencing technology that could be applied in research, medical therapy, and crop improvement. However, as the underlying mechanism was revealed, it became apparent that RNAi manifests a novel system of genetic regulation that was only hinted at by previous data. This overview unit gives a brief history of the field, describes the natural role of RNAi and related processes, identifies strategies for RNAi and cosuppression in plants and animals, and describes methods for detection and characterization of siRNA and miRNA.
Literature Cited
| Literature Cited | |
| 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 409:363-366. | |
| Burton, R.A., Gibeaut, D.M., Bacic, A., Findlay, K., Roberts, K., Hamilton, A., Baulcombe, D.C., and Fincher, G.B. 2000. Virus-induced silencing of a plant cellulose synthase gene. Plant Cell 12:691-705. | |
| Caudy, A.A., Myers, M., Hannon, G.J., and Hammond, S.M. 2002. Fragile X-related protein and VIG associate with the RNAi machinery. Genes Dev. 16:2491-2496. | |
| Chuang, C.-H. and Meyerowitz, E.M. 2000. Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 97:4985-4990. | |
| Cogoni, C. and Macino, G. 1999. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399:166-169. | |
| Dalmay, T., Hamilton, A.J., 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. 101:543-553. | |
| Djikeng, A., Shi, H., Tschudi, C., and Ullu, E. 2001. RNA interference in Trypanosoma brucei: Cloning of small interfering RNAs provides evidence for retroposon-derived 24-26 nucleotide RNAs. RNA. 7:1522-1530. | |
| Elbashir, S.M., Martinez, J., Patkaniowska, A., Lendeckel, W., and Tuschl, T. 2001a. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20:6877-6888. | |
| Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. 2001b. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 411:494-498. | |
| Fire, A., Albertson, D., Harrison, S., and Moerman, D. 1991. Production of antisense RNA leads to effective and specific inhibition of gene expression in C. elegans. Devel. 113:503-514. | |
| Giordano, E., Rendina, R., Peluso, I., and Furia, M. 2002. RNAi triggered by symmetrically transcribed transgenes in Drosophila melanogaster. Genetics 160:637-648. | |
| Grierson, D., Fray, R.G., Hamilton, A.J., Smith, C.J.S., and Watson, C.F. 1991. Does co-suppression of sense genes in transgenic plants involve antisense RNA Trends Biotech. 9:122-123. | |
| Guo, S. and Kemphues, K. 1995. Par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell 81:611-620. | |
| Hamilton, A.J. and Baulcombe, D.C. 1999. A novel species of small antisense RNA in post-transcriptional gene silencing. Science 286:950-952. | |
| Hamilton, A.J., Voinnet, O., Chappell, L., and Baulcombe, D.C. 2002. Two classes of short interfering RNA in RNA silencing. EMBO J. 21:4671-4679. | |
| Hammond, S.M., Bernstein, E., Beach, D., and Hannon, G. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cell extracts. Nature 404:293-296. | |
| Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R., and Hannon, G.J. 2001. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293:1146-1150. | |
| Harborth, J., Elbashir, S.M., Bechert, K., Tuschl, T., and Weber, K. 2001. Identification of essential genes in cultured mammalian cells using small interfering RNAs. J.Cell Sci. 114:4557-4565. | |
| Jorgensen, R.A. 1995. Cosuppression, flower color patterns and metastable gene expression states. Science 268:686-691. | |
| Kamath, R.S., Fraser, A.G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D.P., Zipperlen, P., and Ahringer, J. 2003. Systemic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231-237. | |
| Ketting, R., Haverkamp, T., van Luenen, H., and Plasterk, R. 1999. mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99:133-141. | |
| Kooter, J.M. and Mol, J.N.M. 1993. Trans-inactivation of gene expression in plants. Plant Biotech. 4:166-171. | |
| Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294:853-858. | |
| Lau, N.C., Lim, L.P., Weinstein, E.G., and Bartel, D.P. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858-862. | |
| Lee, R. and Ambros, V. 2001. An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862-864. | |
| Li, H., Li, W.X., and Ding, S.W. 2002. Induction and suppression of RNA silencing by an animal virus. Science 296:1319-1321. | |
| Llave, C., Xie, Z., Kasschau, K.D., and Carrington, J.C. 2002a. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053-2056. | |
| Llave, C., Kasschau, K.D., Rector, M.A., and Carrington, J.C. 2002b. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14:1-15. | |
| McCaffrey, A.P., Meuse, L., Pham, T.T.T., Conklin, D.S., Hannon, G.J., and Kay, M.A. 2002. Gene expression-RNAi in adult mice. Nature 418:38-39. | |
| Mishra, K.K. and Handa, A.K. 1998. Post-transcriptional silencing of pectin methylesterase gene in transgenic tomato fruits results from impaired pre-mRNA processing. Plant J. 14:583-592. | |
| Mochizuki, K., Fine, N.A., Fujisawa, T., and Gorovsky, M.A. 2002. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110:689-699. | |
| Montgomery, M.K., Xu, S.Q., and Fire, A. 1998. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc. Natl. Acad. Sci. U.S.A. 95:15502-15507. | |
| Mourelatos, Z., Dostie, J., Paushkin, S., Sharma, A., Charroux, B., Abel, L., Rappsilber, J., Mann, M., and Dreyfuss, G. 2002. miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 16:720-728. | |
| Mourrain, P., Beclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J.-B., Jouette, D., Lacombe, A.-M., Nikic, S., Picault, N., Remoue, K., Sanial, M., Vo, T.-A., and Vaucheret, H. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101:533-542. | |
| Napoli, C., Lemieux, C., and Jorgensen, R.A. 1990. Introduction of a chimeric chalcone synthase gene into Petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279-289. | |
| Novina, C.D., Murray, M.F., Dykxhoorn, D.M., Beresford, P.J., Riess, J., Lee, S.-K., Collman, R.G., Lieberman, J., Shankar, P., and Sharp, P.A. 2002. siRNA-directed inhibition of HIV-1 infection. Nat. Med. 8:681-686. | |
| Nykanen, A., Haley, B., and Zamore, P.D. 2001. ATP requirements and small interfering RNA structure in the RNAi pathway. Cell 107:309-321. | |
| Paddison, P.J., Caudy, A.A., and Hannon, G.J. 2002. Stable suppression of gene expression by RNAi in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 99:1443-1448. | |
| Peart, J.R., Cook, G., Feys, B.J., Parker, J.E., and Baulcombe, D.C. 2002a. An EDS1 orthologue is required for N-mediated resistance against tobacco mosaic virus. Plant J. 29:569-579. | |
| Peart, J.R., Lu, R., Sadanandom, A., Malcuit, I., Moffett, P., Brice, D.C., Schauser, L., Jaggard, D.A.W., Xiao, S., Coleman, M., Dow, J.M., Jones, J.D.G., Shirasu, K., and Baulcombe, D.C. 2002b. Ubiquitin ligase-associated protein SGT1 is required for host and nonhost disease resistance in plants. Proc. Natl. Acad. Sci. U.S.A. 99:10865-10869. | |
| Rheinhart, B.J., Weinstein, E.G., Rhoades, M., Bartel, B., and Bartel, D.P. 2002. MicroRNAs in plants. Genes Dev. 16:1616-1626. | |
| Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. 2002. Prediction of plant microRNA targets. Cell 110:513-520. | |
| Ruvkun, G. 2001. Glimpses of a tiny RNA world. Science 294:797-799. | |
| Shiu, P.K.T., Raju, N.B., Zickler, D., and Metzenberg, R.L. 2001. Meiotic silencing by unpaired DNA. Cell 107:905-916. | |
| Sijen, T., Fleenor, J., Simmer, F., Thijssen, K.L., Parrish, S., Timmons, L., Plasterk, R.H.A., and Fire, A. 2001. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107:465-476. | |
| Smith, C.J.S., Watson, C.F., Ray, J., Bird, C.R., Morris, P.C., Schuch, W., and Grierson, D. 1988. Antisense RNA inhibition of polygalaturonase gene expression in transgenic tomatoes. Nature 334:724-726. | |
| Smith, C.J.S., Watson, C.F., Bird, C.R., Ray, J., Schuch, W., and Grierson, D. 1990. Expression of a truncated tomato polygalacturonase gene inhibits expression of the endogenous gene in transgenic plants. Mol.Gen.Genet. 224:447-481. | |
| Sui, G., Soohoo, C., Affar, E.B., Gay, F., Shi, Y., Forrester, W.C., and Shi, Y. 2002. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 99:5515-5520. | |
| Timmons, L. and Fire, A. 1998. Specific interference by ingested dsRNA. Nature 395:854. | |
| van der Krol, A.R., Mur, L.A., Beld, M., Mol, J.N.M., and Stuitji, A.R. 1990. Flavonoid genes in petunia: Addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2:291-299. | |
| Voinnet, O. 2001. RNA silencing as a plant immune system against viruses. Trends Genet. 17:449-459. | |
| Volpe, T., Kidner, C., Hall, I.M., Teng, G., Grewal, S.I.S., and Martienssen, R. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833-1837. | |
| Waterhouse, P.M., Graham, H.W., and Wang, M.B. 1998. Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc. Natl. Acad. Sci. U.S.A. 95:13959-13964. | |
| Wesley, S.V., Helliwell, C.A., Smith, N.A., Wang, M., Rouse, D.T., Liu, Q., Gooding, P.S., Singh, S.P., Abbott, D., Stoutjesdijk, P.A., Robinson, S.P., Gleave, A.P., Green, A.G., and Waterhouse, P. 2001. Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27:581-590. | |
| Yang, D., Buchholz, F., Huang, Z.D., 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 RNAi in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 99:9942-9947. | |
| Zamore, P.D. 2001. RNA interference: Listening to the sound of silence. Nat. Struc. Biol. 8:746-750. | |
Troubleshooting Tips
|
TOOLS & CALCULATORS |





Join the Conversation
Post new comment