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COMMENTARY Lasker basic Medical research award

Of maize and men, or and people: case histories to justify and other model systems

One of the byproducts of molecular cork is altogether filled with air, and that air is has been support for the ‘model system’ con- perfectly enclosed in little boxes or cells distinct cept. All living organisms are based on the same from one another.”)2 (Fig. 1). Two hundred fifty genetic code, they have similar subcellular years later, Beijerinck discovered a contagium structures and they use homologous metabolic vivum fluidum in extracts of diseased tobacco pathways. So, mechanisms can be investigated plants that he later referred to as a virus3. using organisms other than those in which In contemporary , a green alga— the knowledge will be exploited for practical Chlamydomonas reinhardtii—is a useful model benefit. Model systems are particularly use- in the analysis of kidney disease4. However, ful in the early discovery phase of a scientific in this article, I refer to the contribution of endeavor, and recent progress in biomedical biology to a family of mechanisms that I science has fully vindicated their use. Jacques refer to as RNA silencing. This topic has been Monod, for example, famously justified his reviewed comprehensively elsewhere5,6, so here work on a bacterial model system by stating I focus on personal experience and my view of that “what is true for Escherichia coli is also future potential from this work. true for elephants.” My fellow laureates, and , can defend the use The early history of RNA silencing in of the worm as a good plants model system and so I will focus . The most important development in plant Probably the best example I could use is biology in the 1980s was the introduction of that of Barbara McClintock, who used corn methods for transfer of DNA into the nuclear in her –winning work1. Her iden- genome7. Transgenic techniques were devel- tification of mobile genetic elements has been oped as a routine research tool, and the new enormously influential in and technology prompted the introduction of Figure 1 ’s micrograph of cells immunology, and continues to bear on the genetic manipulation for crop improvement. in a sample of cork. Downloaded from http:// field of that I refer to again below. The first generation of genetically modified www.nlm.nih.gov/exhibition/historicalanatomies/ She could have adapted Monod’s aphorism to plants used bacterial for herbicide tol- Images/1200_pixels/hooke_t11.jpg. refer to maize and men. Gregor Mendel would, erance or insect resistance8,9. There were also of course, have referred to peas and people. attempts from several laboratories, including structure would be formed between the mRNA There are many other historical examples, in my own, to develop virus resistance by trans- of the target and a transgenic antisense addition to McClintock’s and Mendel’s work, genic expression of virus-derived genes in the RNA. This duplex structure would then either that could justify the use of plants as models. host organism10–12. We were testing a concept block translation of the mRNA or initiate its Robert Hooke used his newly developed micro- known as parasite-derived resistance in which degradation by a nuclease specific for double- scope in 1664 to show that cork comprises the replication or spread of a disease agent stranded RNA. structures that he referred to as cells (“Our could be reduced by transgenic expression of Many of the early transgenic plants had the microscope informs us that the substance of its genes in a host. A third category of these desired traits, and they were the progenitors of early transgenic crops exploited an antisense transgenic crops that are now grown in large David Baulcombe is Royal Society Research approach to block expression of an endoge- areas of different countries. However, there Professor and Professor of , Department of nous plant gene13. Crops were to be improved were anomalous in some of the Plant , University of , Downing in this approach by specific suppression of an transgenic lines. For example, the bacterial and Street, Cambridge CB2 3EA, UK. endogenous gene that limited agronomic per- viral transgenes were not always expressed8,9. e-mail: [email protected] formance. The idea was simple: a duplex RNA In the ‘antisense plants’, the suppression effect

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that operates in a sequence–specific ous now. My failure to make the connection manner. The silencing in cis would explain why was probably because the mechanism in worms the transgenes in certain lines were not abun- involved suppression of translation, whereas, dantly expressed. Correspondingly, the silenc- in plants, we were dealing with a process that ing in trans would account for the ability of decreased stability of the targeted RNA. these transgenes to silence endogenous genes Andrew Hamilton’s experiments further or viruses20,21. demonstrated that the production of small The hypothesis further proposed that the antisense RNA required transcription of the silencing mechanism operates at the RNA corresponding sense strand. This involvement level because the targeted viruses had an RNA of both RNA strands provided an obvious and did not have a DNA phase in their connection between RNA silencing in plants replication cycle. Originally, many of the silenc- and RNA interference in worms as revealed ing-related phenomena in transgenic plants by the famous and 29 Richard Jorgensen Richard were referred to as ‘’. However, 1998 paper in Nature . Once this connection Figure 2 Variegation of silencing in flowers at a seminar in Switzerland, I was interrupted was recognized, there was an opportunity for of petunia. The target of silencing by a sense by Ingo Potrykus—the inventor of ‘golden discoveries in plants to catalyze our under- transgene is chalcone synthase. The silencing rice’22—who pointed out that I was not talk- standing of animal systems and vice versa. It effect manifested as the absence of pigment ing about ‘gene silencing’; it was ‘RNA silenc- has been enormously satisfying to witness this is present in only part of the flower. Reprinted with permission of the American Society of ing’. I agreed and have since promoted ‘RNA exchange of information and the elucidation Plant . silencing’ as a generic term to cover a family of of variations on a molecular theme associated mechanisms involving silencing and RNA. with different types of silencing mechanism in was sometimes variegated—it was present on Support for the model came from a series diverse organisms5,6. some branches of the plant and not in others, of tests carried out by Jim English with geneti- Much current RNA silencing research inter- or it was absent in localized parts of a flower14. cally modified viruses20, and the remaining est is focused on endogenous small . In There was also a problem with some of the challenges were to find out about the details of plants, there are thousands of loci that produce sense RNA controls in these antisense experi- the mechanism and its biological role. We were these small RNAs30–32. A small proportion of ments. There was a silencing effect even when also interested in finding out whether the var- the endogenous small RNAs are similar to the transgene was designed to generate sense iegated silencing of transgenes and transcrip- the microRNAs of worms that were first dis- RNA that would not form a duplex with the tional silencing of promoter sequences could covered as short temporal RNAs by Ruvkun target mRNA15–17. In some examples, there was be accommodated in the model. and Ambros27,28. Most microRNAs are nega- variegation of this sense suppression as with the A central mystery in RNA silencing was its tive regulators, although a positive regulatory antisense plants (Fig. 2). Another strange pro- ability to act in a nucleotide sequence–specific microRNA has been recently described33. cess occurred when two transgenes carried the manner. The simplest explanation required The other small RNAs in plants are siRNAs, same promoter sequence: one of these trans- an antisense RNA that would guide a silenc- the double-stranded RNA precursors, which genes could silence the other through a process ing machinery to its target. In the transgenic are produced in various ways, including the operating at the transcriptional level18. experiments described above, this antisense annealing of complementary RNA, foldback In retrospect, I can see that these anomalies RNA would be present irrespective of whether of long inverted repeats and the action of challenged the existing paradigm of genetic the transgene was in a sense or an antisense RNA-dependent RNA polymerases on a single- regulation, but initially, I made the mistake of orientation. Andrew Hamilton, who had been stranded RNA30,31. thinking that they were due to multiple dis- interested in antisense RNA ever since his PhD It could be said that, now that we have the tinct mechanisms and that they were artifacts work on transgenic tomatoes23, joined the lab understanding of multiple variations on silenc- of transgenes. However, I became more inter- to carry out the search for this elusive molecu- ing mechanisms, RNA silencing research with ested when we characterized transgenic plants lar . It is testimony to his persistence and a biomedical target should focus exclusively on manifesting parasite-derived resistance. The talent as a that he eventually found people or at least on vertebrate experimental plants with the strongest viral resistance were them24. He tried several different methods, and systems. However, for this view to be valid, those in which the transgene RNA was present his early successes used a sensitive but impre- the discovery phase of RNA silencing research at a low abundance, whereas plants expressing cise RNase protection method that generated would have to be played out. I do not consider the same gene at a high level were fully suscep- rather ugly looking smears instead of the neat this to be the case just yet because there are at tible19. It seemed that the transgene silencing electropherograms that were eventually pub- least two areas—virus resistance and epigenet- in this example of ‘less is more’ could not be lished in Science (Fig. 3). Our first estimate was ics—in which there is much to be discovered dismissed as a side effect or artifact. that these antisense RNAs were 25 and in which RNA silencing in plants has the A new model to explain some of the coun- long, but later, we refined this to 21–24 nucle- potential to inform biomedical research. terintuitive properties of the virus-resistant otides25. They are now known as small interfer- plants was attractive—at least to us—because ing RNAs (siRNAs)26. RNA silencing and virus resistance it could account for the anomalous results The initial convergence of our work with that of virus resistance was with many other transgenic plants, although of Ambros and Ruvkun was because the meth- my introduction to RNA silencing, and there it could not explain the variegation or trans- ods we used to detect siRNAs were the same is a nice irony from the subsequent discover- inactivation effects. The model proposed that as those used to detect small temporal RNAs ies that plants are naturally protected from certain transgenes, irrespective of whether from lin-4 in worms27,28. However, we did not viruses by RNA silencing. Frank Ratcliff, they were designed to be expressed in sense or immediately make the biological connection. Tamas Dalmay and Olivier Voinnet joined antisense orientation, have a silencing property In retrospect, I cannot say why—it seems obvi- my group to investigate these aspects of RNA

nature medicine volume 14 | number 10 | october 2008 xxi commentary silencing together with Andrew Hamilton. intracellular efficacy of antiviral siRNAs. Nature Their work, alongside that of the Covey, has already done the experiments in plants to Carrington and Vance groups, revealed a find out which regions of viral are the picture in which virus-specific siRNAs are most effective targets of siRNAs and whether produced using a viral RNA template in the antiviral potential is influenced by base infected plant cells34–40. These siRNAs then composition or other chemical characteristics GUS transgene target an RNA silencing effector protein to of the siRNAs. Given the structural and genetic Transcription? the viral RNA so that the replication cycle of similarities of various groups of plant and ani- Silenced the virus is blocked. Inevitably, in the arms mal viruses, it is likely that the understanding of race of defense and counter-defense between these plant systems will facilitate development viruses and their hosts, plant viral genomes of novel antiviral therapy in medicine. encode pathogenicity or virulence factors that are suppressors of silencing. Olivier’s work, RNA silencing and epigenetics together with the work of those other groups, The final anomaly in the original transgenic 22 nt revealed that there are many different types of experiments—promoter silencing at the tran- viral suppressor protein36–40. scriptional level—was finally resolved by the Associated with antiviral silencing, there is Matzke group and others. They demonstrated Anti-GUS RNA probe a mobile signal that mediates antiviral effects that double-stranded RNA and siRNAs have the of silencing beyond the infected regions of the potential to guide epigenetic modification of plant and that prevents or delays spread of the DNA or the associated chromatin proteins in Figure 3 One of Andrew Hamilton’s early RNase virus in the infected plant. The discovery of plants and other organisms25,46,47. The silencer protection assays showing that small antisense signaling41,42 was particularly satisfying because, transgene evidently produces siRNAs that can RNA—the black smear corresponding to 22 in addition to virus resistance, it explained the target the promoter of the silenced gene. nucleotides (nt)—was only present in plants that were silencing the target RNA. Production of the variegation anomaly in the early transgenic There is now a good understanding of this GUS reporter gene antisense RNA was suppressed 48 antisense and sense RNA experiments: signal epigenetic RNA silencing mechanism , and we if the sense transcription was blocked. One of produced in one part of the plant spread also know that many endogenous siRNAs are Andrew Hamilton’s early RNase protection assays unevenly so that the silencing effect was associated with epigenetic modification of the showing that small antisense RNA was only present manifested only in the parts in which it was corresponding DNA30,49. The siRNA associated in plants that were silencing the target RNA. received. with epigenetic modification is 24 nucleotides Production of the GUS reporter gene antisense RNA, detected by the anti-GUS RNA probe, was We now understand that RNA silencing long. However, consistent with the past history suppressed if the sense transcription was blocked. influences many aspects of the interac- of RNA silencing research, a mystery remains Far left, hybridization probe without RNase tions between viruses and their plant hosts. because these 24-nucleotide siRNAs do not treatment. The two unmarked samples in the next It explains, for example, how viruses are have an obvious role. Mutant plants that do two lanes were from plants without a GUS reporter excluded from the meristem of infected not produce these 24-nucleotide siRNAs are gene; there is no evidence of any antisense RNA. plants, why some plants recover from viral able to grow and develop at a normal rate50. The other three samples (white symbols) were disease and why virus-infected plants may We can therefore rule out the possibility that from plants with a GUS transgene. The sample on the far right (blue symbol) had an untranscribed be protected from secondary infection. Many these RNAs have a major role in normal growth GUS transgene and there was also no antisense aspects of symptom production may also be and development. Many of these endogenous RNA. However, the two samples from a plant with due to suppression of endogenous genes by siRNAs correspond to transposons30. However, a transcribed GUS transgene (red symbols) that viral siRNA. Additionally, in a biomedical transposons are not mobilized in RNA silencing was silenced at the RNA level generated a smeared context and consistent with the model system mutants, and it seems unlikely that these RNAs signal centered on the 22-nucleotide length that justification for plant work, RNA silencing have the obvious role in protection against was the first evidence for siRNAs. can target viral RNA in animals. damage caused by mobile genetic elements. Invertebrates may use RNA silencing as part Resolution of this mystery may not have selection in certain environments. of natural antiviral defense, as in plants43. In immediate relevance to biomedicine because the If this RNA-directed epigenetic modification vertebrates, RNA silencing may not be part answer may involve mechanisms in . occurs in humans—and there are some indica- of the natural antiviral defense systems44. One possibility is that epigenetic RNA silenc- tions that it may52,53—the existence of separate However, artificial RNA silencing can be effec- ing by one parent may silence essential genes initiation and maintenance phases may allow tively targeted against viruses45. Given the diffi- in the opposite parental genome and thereby long-term silencing of some targets. Delivery culty of developing small molecule therapeutic influence formation. A second possible of promoter-targeted siRNA would initiate agents to target viruses, there is much interest role is prompted by Louise Jones’s finding that silencing of a selected disease-causing gene. The in the possibility of delivering double-stranded RNA-directed epigenetic changes may persist RNA-independent maintenance mechanism RNA or siRNAs to protect against viral disease. for several generations even in the absence of would then mediate long-term persistence of A major challenge in such a task is to find ways the initiator RNA51. This finding illustrates how the silencing effect. to chemically modify the RNA so that it is stable there are separate initiation and maintenance until it is taken up by cells and targeted to the phases to the RNA-directed epigenetic mecha- Postscript desired cell type. This challenge is therefore nism. It also illustrates how endogenous siRNAs The focus of this article should not be taken as essentially pharmacological and probably out- that are induced by environmental stimuli could special pleading for plants. It is more intended side the influence of plant biology. However, it induce heritable phenotypic changes. Such as an attempt to use a set of case histories to may be possible, on the basis of an understand- changes would not be associated with genetic justify model systems in general, with plants ing of the plant viral systems, to optimize the but nevertheless could be subject to given an equal footing alongside yeast, worms,

xxii volume 14 | number 10 | october 2008 nature medicine commentary fungi and the rest. I realize that it is not easy transferring genes into plants. Science 227, 1229– biogenesis. Proc. Natl. Acad. Sci. USA 105, 3145– 1231 (1985). 3150 (2008). for science policy makers and funding agen- 8. Fischhoff, D.A. et al. Insect tolerant transgenic tomato 31. Kasschau, K.D., et al. Genome-wide profiling and cies to prioritize funding and also that basic plants. Bio/Technology 5, 807–813 (1987). analysis of Arabidopsis siRNAs. PLoS Biol. 5, e57 —myself included—do not always 9. Shah, D.M. et al. Engineering herbicide tolerance in (2007). transgenic plants. Science 233, 478–481 (1986). 32. Lu, C. et al. Elucidation of the small RNA compo- make their task easy because we often prefer 10. Abel., P.P. et al. Delay of disease development in trans- nent of the transcriptome. Science 309, 1567–1569 to stay in the comfort zone of basic research. genic plants that express the tobacco mosaic virus (2005). It is easier there than in the uncompromising coat protein gene. Science 232, 738–743 (1986). 33. Vasudevan, S. & Steitz, J.A. AU-rich-element-mediated 11. Baulcombe, D.C., Saunders, G.R., Bevan, M.W., Mayo, upregulation of translation by FXR1 and Argonaute 2. world of technology, in which the only impor- M.A. & Harrison, B.D. Expression of biologically active Cell 128, 1105–1118 (2007). tant consideration is whether something works viral satellite RNA from the nuclear genome of trans- 34. Covey, S.N., Al-Kaff, N.S., Lángara, A. & Turner, D.S. formed plants. Nature 321, 446–449 (1986). Plants combat infection by gene silencing. Nature in the field or patient. Nevertheless, I hope that 12. van Dun, C.M.P., Bol, J.F. & Van Vloten-Doting, L. 385, 781–782 (1997). some of the decision makers in biomedical sci- Expression of alfalfa mosaic virus and tobacco rattle 35. Ratcliff, F., Harrison, B.D. & Baulcombe, D.C. A ence will bear in mind the small-RNA story virus coat protein genes in transgenic tobacco plants. similarity between viral defense and gene silencing 159, 299–305 (1987). in plants. Science 276, 1558–1560 (1997). when they decide how to allocate their funds. 13. Smith, C.J.S. et al. Antisense RNA inhibition of poly- 36. Anandalakshmi, R. et al. A viral suppressor of gene There will be other discoveries through work galacturonase in transgenic tomatoes. silencing in plants. Proc. Natl. Acad. Sci. USA 95, in model systems that will have application in Nature 334, 724–726 (1988). 13079–13084 (1998). 14. Jorgensen, R. Altered gene expression in plant due to 37. Brigneti, G. et al. Viral pathogenicity determinants diagnosis or treatment of disease. trans interactions between homologous genes. Trends are suppressors of transgene silencing in Nicotiana I hope that this short account may encour- Biotechnol. 8, 340–344 (1990). benthamiana. EMBO J. 17, 6739–6746 (1998). 15. Napoli, C., Lemieux, C. & Jorgensen, R.A. Introduction 38. Kasschau, K.D. & Carrington, J.C. A counterdefen- age young scientists setting out on their career of a chimeric chalcone synthase gene into petunia sive strategy of plant viruses: suppression of post- or deciding which systems to use as they set results in reversible co-suppression of homologous transcriptional gene silencing. Cell 95, 461–470 up their first research group. It may well be genes in trans. Plant Cell 2, 279–289 (1990). (1998). 16. Smith, C.J.S. et al. Expression of a truncated tomato 39. Voinnet, O., Pinto, Y.M. & Baulcombe, D.C. that plants will help you address whatever polygalacturonase gene inhibits expression of the Suppression of gene silencing: a general strategy used scientific questions you are attracted toward. endogenous gene in transgenic plants. Mol. Gen. by diverse DNA and RNA viruses. Proc. Natl. Acad. There is also the possibility, of course, that your Genet. 224, 477–481 (1990). Sci. USA 96, 14147–14152 (1999). 17. van der Krol, A.R., Mur, L.A., Beld, M., Mol, J.N.M. & 40. Llave, C., Kasschau, K.D. & Carrington, J.C. Virus- efforts with plant systems will help with the Stuitji, A.R. Flavonoid genes in petunia: addition of encoded suppressor of posttranscriptional gene small problem of harvesting the sun and feed- a limited number of gene copies may lead to a sup- silencing targets a maintenance step in the silenc- pression of gene expression. Plant Cell 2, 291–299 ing pathway. Proc. Natl. Acad. Sci. USA 97, 13401– ing the world. (1990). 13406 (2000). 18. Matzke, M.A., Primig, M., Trnovsky, J. & Matzke, 41. Palauqui, J.-C., Elmayan, T., Pollien, J.-M. & ACKNOWLEDGMENTS A.J.M. Reversible methylation and inactivation of Vaucheret, H. Systemic acquired silencing: transgene- My research has always been a group effort. Without marker genes in sequentially transformed tobacco specific post-transcriptional silencing is transmitted colleagues mentioned here and others, I would not plants. EMBO J. 8, 643–649 (1989). by grafting from silenced stocks to non-silenced sci- even be considered for this prestigious Lasker Award. 19. Longstaff, M., Brigneti, G., Boccard, F., Chapman, ons. EMBO J. 16, 4738–4745 (1997). I would feel much more comfortable if an award S.N. & Baulcombe, D.C. Extreme resistance to potato 42. Voinnet, O. & Baulcombe, D.C. Systemic signalling in could be made to a research group. Special mention virus X infection in plants expressing a modified com- gene silencing. Nature 389, 553 (1997). ponent of the putative viral replicase. EMBO J. 12, 43. Wang, X.-H. et al. RNA interference directs innate is to be made of A. Hamilton for his commitment 379–386 (1993). immunity against viruses in adult Drosophila. Science to the search for the elusive antisense RNAs. I have 20. English, J.J., Mueller, E. & Baulcombe, D.C. 312, 452–454(2006). been fortunate to receive generous long-term funding Suppression of virus accumulation in transgenic 44. Cullen, B.R. Is RNA interference involved in intrinsic from the Gatsby Charitable Foundation that allowed plants exhibiting silencing of nuclear genes. Plant antiviral immunity in mammals? Nat. Immunol. 7, me to respond to the unexpected developments in Cell 8, 179–188 (1996). 563–567 (2006). the early days of my interest in RNA silencing and 21. Lindbo, J.A., Silva-Rosales, L., Proebsting, W.M. & 45. Palliser, D. et al. An siRNA-based microbicide protects to follow them over a period of 20 years. I thank the Dougherty, W.G. Induction of a highly specific antiviral mice from lethal herpes simplex virus 2 infection. foundation trustees for their confidence and support. state in transgenic plants: implications for regulation Nature 439, 89–94 (2006). of gene expression and virus resistance. Plant Cell 5, 46. Mette, M.F., Aufsatz, W., van der Winden, J., Matzke, R. Freedman alerted Gatsby to my existence, and I 1749–1759 (1993). M.A. & Matzke, A.J.M. Transcriptional silencing and will always be grateful to him for that. Other support 22. Potrykus, I. Golden rice and beyond. Plant Physiol. promoter methylation triggered by double-stranded I have received has come from the UK 125, 1157–1161 (2001). RNA. EMBO J. 19, 5194–5201 (2000). and Biological Sciences Research Council and from 23. Hamilton, A.J., Lycett, G.W. & Grierson, D. Antisense 47. Volpe, T.A. et al. Regulation of heterochromatic silenc- a UK Royal Society Research Professorship. Finally, gene that inhibits synthesis of the hormone ethylene ing and histone H3 lysine-9 methylation by RNAi. I acknowledge that I am afflicted with a slightly in transgenic plants. Nature 346, 284–287 (1990). Science 297, 1833–1837 (2002). obsessive streak that must be difficult to live with. 24. Hamilton, A.J. & Baulcombe, D.C. A species of small 48. Pontes, O. et al. The Arabidopsis chromatin-modifying I am thankful beyond words to those who have antisense RNA in post-transcriptional gene silencing nuclear siRNA pathway involves a nucleolar RNA pro- in plants. Science 286, 950–952 (1999). cessing center. Cell 126, 79–92 (2006). tolerated its consequences. 25. Hamilton, A., Voinnet, O., Chappell, L. & Baulcombe, 49. Zhang, X., Henderson, I.R., Lu, C., Green, P.J. & D. Two classes of short interfering RNA in RNA silenc- Jacobsen, S.E. Role of RNA polymerase IV in plant 1. Comfort, N.C. From controlling elements to transpo- ing. EMBO J. 21, 4671–4679 (2002). small RNA metabolism. 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Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional ited independently of the RNA trigger and requires mouse homologue, polycystic kidney disease gene regulation of the heterochronic gene lin-14 by lin-4 Met1 for maintenance. Curr. Biol. 11, 747–757 Tg737, are required for assembly of cilia and flagella. mediates temporal pattern formation in C. elegans. (2001). J. Cell Biol. 151, 709–718 (2000). Cell 75, 855–862 (1993). 52. Morris, K.V., Chan, S.W.-L., Jacobsen, S.E. & Looney, 5. Matzke, M. & Matzke, A.J.M. Planting the seeds of a 29. Fire, A. et al. Potent and specific genetic interference D.J. Small interfering RNA-induced transcriptional new paradigm. PLoS Biol. 2, e133 (2004). by double-stranded RNA in Caenorhabditis elegans. gene silencing in human cells. Science 305, 1289– 6. Zamore, P.D. RNA interference: big applause for Nature 391, 806–811 (1998). 1292 (2004). silencing in Stockholm. Cell 127, 1083–1086 30. Mosher, R.A., Schwach, F., Studholme, D.J. & 53. 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