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A model for RNA-mediated gene silencing in higher plants

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Abstract

Homology-dependent gene silencing (HdGS) which is the generic term for transcriptional gene silencing (TGS), post-transcriptional gene silencing (PTGS) and RNA-mediated virus-resistance (RmVR) has been shown to frequently occur in transgenic plants. The role of RNA as a target and initiator of PTGS and RmVR is more and more manifested. Because TGS is assumed to be induced by a DNA-DNA interaction-mediated promoter methylation, a possible involvement of RNA in TGS was not really considered up to now. In this review we attempt to demonstrate that all three types of HdGS could be triggered by one RNA-based mechanism. A model proposing TGS as a consequence of RNA-directed DNA methylation (RdDM) and a refined mRNA threshold mechanism are presented. In contrast to the view that high amounts of mRNA are required we assume that the concentration of RNAs that can serve as efficient templates for a plant-encoded RNA-directed RNA polymerase (RdRP) plays a key role in HdGS and possibly also in natural gene regulation of non-transformed cells. According to this idea a particular information must be encoded to render mRNA turn-over products a suitable RdRP substrate. It will be discussed that such a mechanism could account for the silencing phenomena of poorly transcribed transgenes. Finally, an explanation for the coherency between PTGS and DNA methylation is documented.

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References

  1. Abler ML, Green PJ: Control of mRNA stability in higher plants. Plant Mol Biol 32: 63–78 (1996).

    Google Scholar 

  2. Assaad FF, Tucker KL, Signer ER: Epigenetic repeat-induced gene silencing (RIGS) in Arabidopsis. Plant Mol Biol 22: 1067–1085 (1993).

    Google Scholar 

  3. Astier-Manifacier S, Cornuet P: Purification et poids moléculaire d'une RNApolymérase RNA dépendante de Brassica oleracea var. Botrytis. CR Acad Sci Paris 287: 1043–1046 (1978).

    Google Scholar 

  4. Astier-Manifacier S, Cornuet P: RNA-dependent RNA polymerase in Chinese cabbage. Biochim Biophys Acta 232: 484–493 (1971).

    Google Scholar 

  5. Baulcombe DC: Mechanisms of pathogen-derived resistance to viruses in transgenic plants. Plant Cell 8: 1833–1844 (1996).

    Google Scholar 

  6. Baulcombe DC: RNA as a target and an initiator of post-transcriptional gene silencing in transgenic plants. Plant Mol Biol 32: 79–88 (1996).

    Google Scholar 

  7. Baulcombe DC, English JJ: Ectopic pairing of homologous DNA and posttranscriptional gene silencing in transgenic plants. Curr Opin Biotech 7: 173–180 (1996).

    Google Scholar 

  8. Boege F, Sänger HL: RNAdependent RNA polymerase from healthy tomato leaf tissue. FEBS lett 121: 91–96 (1980).

    Google Scholar 

  9. Bolle C, Herrmann RG, Oelmüller R: Different sequences for 5′ untranslated leaders of nuclear genes for plastid proteins affect the expression of the βglucuronidase gene. Plant Mol Biol 32: 861–868 (1996).

    Google Scholar 

  10. Cogoni C, Macino G: Conservation of transgeneinduced post-transcriptional gene silencing in plants and fungi. Trends Plant Science 2: 438–443 (1997).

    Google Scholar 

  11. Cogoni C, Irelan JT, Schumacher M, Schmidhauser TJ, Selker EU, Macino G: Transgene silencing of the al1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNADNA interactions or DNA methylation. EMBO J 15: 3153–3163 (1996).

    Google Scholar 

  12. Cohen A, Mayfield SP: Translational regulation of gene expression in plants. Curr Opin Biotech 8: 189–194 (1997).

    Google Scholar 

  13. Dawson WO: Gene silencing and virus resistance: a common mechanism. Trends Plant Science 1: 107–108 (1996).

    Google Scholar 

  14. Depicker A, Van Montagu M: Post-transcriptional gene silencing in plants. Curr Opin Cell Biol 9: 373–382 (1997).

    Google Scholar 

  15. Diéguez MJ, Bellotto M, Afsar K, Mittelsten Scheid O, Paszkowski J: Methylation of cytosines in nonconventional acceptor sites can contribute to reduced gene expression. Mol Gen Genet 253: 581–588 (1997).

    Google Scholar 

  16. Dorer DR, Henikoff S: Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77: 993–1002 (1994).

    Google Scholar 

  17. Dougherty WG, Parks TD: Transgenes and gene suppression: telling us something new? Curr Opin Cell Biol 7: 399–405 (1995).

    Google Scholar 

  18. Duda CT: Synthesis of double-stranded RNA. Virology 92: 180–189 (1979).

    Google Scholar 

  19. Duda CT, Zaitlin M, Siegel A: In vitro synthesis of double-stranded RNA by an enzyme system isolated from tobacco leaves. Biochim Biophys Acta 319: 62–71 (1973).

    Google Scholar 

  20. Elmayan T, Vaucheret H: Expression of single copies of a strongly expressed 35S transgene can be silenced post-transcriptionally. Plant J 9: 787–797 (1996).

    Google Scholar 

  21. English JJ, Mueller E, Baulcombe DC: Suppression of virus accumulation in transgenic plants exhibiting silencing of nuclear genes. Plant Cell 8: 179–188 (1996).

    Google Scholar 

  22. Faugeron G, Rhounim L, Rossignol JL: How does the cell count the number of ectopic copies of a gene in the premeiotic inactivation process acting in Ascobolus immersus? Genetics 124: 585–591 (1990).

    Google Scholar 

  23. Flavell RB: Inactivation of gene expression in plants as a consequence of specific sequence duplication. Proc Natl Acad Sci USA 91: 34903496 (1994).

    Google Scholar 

  24. Goodwin J, Chapman K, Swaney S, Parks TD, Wernsman EA, Dougherty WG: Genetic and biochemical dissection of transgenic RNA-mediated virus resistance. Plant Cell 8: 95–105 (1996).

    Google Scholar 

  25. Goyon C, Faugeron G: Targeted transformation of Ascobolus immersus and de novo methylation of the resulting duplicated DNA sequences. Mol Cell Biol 9: 2818–2827 (1989).

    Google Scholar 

  26. Gruenbaum Y, Naveh Many T, Cedar H, Razin A: Sequence specificity of methylation in higher plant DNA. Nature 292: 860–862 (1981).

    Google Scholar 

  27. Hobbs SLA, Warkentin TD, DeLong CMO: Transgene copy number can be positively or negatively associated with transgene expression. Plant Mol Biol 21: 17–26 (1993).

    Google Scholar 

  28. Hobbs SLA, Kpodar P, DeLong CMO: The effect of TDNA copy number, position and methylation on reporter gene expression in tobacco transformants. Plant Mol Biol 15: 851–864 (1990).

    Google Scholar 

  29. Hochstrasser M: Ubiquitin-dependent protein degradation. Annu Rev Genet 30: 405–439 (1996).

    Google Scholar 

  30. Hohn T, Corsten S, Rieke S, Müller M, Rothnie H: Methylation of coding region alone inhibits gene expression in plant protoplasts. Proc Natl Acad Sci USA 93: 8334–8339 (1996).

    Google Scholar 

  31. Holliday R, Pugh JE: DNA modification mechanisms and gene activity during development. Science 187: 226–232 (1975).

    Google Scholar 

  32. Inamdar NM, Ehrlich KC, Ehrlich M: CpG methylation inhibits binding of several sequencespecific DNA-binding proteins from pea, wheat, soybean and cauliflower. Plant Mol Biol 17: 111–123 (1991).

    Google Scholar 

  33. Ingelbrecht I, Van Houdt H, Van Montagu M, Depicker A: Posttranscriptional silencing of reporter transgenes in tobacco correlates with DNA methylation. Proc Natl Acad Sci USA 91: 10502–10506 (1994).

    Google Scholar 

  34. Ingelbrecht ILW, Herman LMF, Dekeyser RA, Van Montagu MC, Depicker AG: Different 3′ end regions strongly influence the level of gene expression in plant cells. Plant Cell 1: 671–680 (1989).

    Google Scholar 

  35. Jorgensen RA: Cosuppression, flower color patterns, andmetastable gene expression states. Science 268: 686–691 (1995).

    Google Scholar 

  36. Judelson HS, Whittaker SL: Inactivation of transgenes in Phytophthora infestans is not associated with their deletion, methylation, or mutation. Curr Genet 28: 571–579 (1995).

    Google Scholar 

  37. Khan ZA, Hiriyanna KT, Chavez F, Fraenkel-Conrat H: RNA-directed RNA polymerase from healthy and from virus-infected cucumber. Proc Natl Acad Sci USA 83: 2383–2386 (1986).

    Google Scholar 

  38. Kunz C, Schöb H, Stam M, Kooter JM, Meins, Jr F: Developmentally regulated silencing and reactivation of tobacco chitinase transgene expression. Plant J 10: 437–450 (1996).

    Google Scholar 

  39. Lindbo JA, Silva-Rosales L, Proebsting WM, Dougherty WG: Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell 5: 1749–1759 (1993).

    Google Scholar 

  40. Lindsay H, Adams RLP: Spreading of methylation along DNA. Biochem J 320: 473–478 (1996).

    Google Scholar 

  41. Matzke MA, Matzke AJM, Eggleston WB: Paramutation and transgene silencing: a common response to invasive DNA? Trends Plant Sci 1: 382–388 (1996).

    Google Scholar 

  42. Matzke MA, Matzke AJM: Homologydependent gene silencing in transgenic plants: what does it really tell us? Trends Genet 11: 1–3 (1995).

    Google Scholar 

  43. Matzke MA, Matzke AJM: How and why do plants inactivate homologous (trans)genes? Plant Physiol. 107: 679–685 (1995).

    Google Scholar 

  44. Matzke AJM, Neuhuber F, Park YD, Ambros PF, Matzke MA: Homologydependent gene silencing in transgenic plants: epistatic silencing loci contain multiple copies of methylated transgenes. Mol Gen Genet 244: 219–229 (1994).

    Google Scholar 

  45. Metzlaff M, O'Dell M, Cluster PD, Flavell RB: RNA-mediated degradation and chalcone synthase A silencing in petunia. Cell 88: 845–854 (1997).

    Google Scholar 

  46. Meyer P: Repeatinduced gene silencing: common mechanisms in plants and fungi. Biol Chem Hoppe–Seyler 377: 87–95 (1996).

    Google Scholar 

  47. Meyer P, Saedler H: Homologydependent gene silencing in plants. Annu Rev Plant Physiol Plant Mol Biol 47: 23–48 (1996).

    Google Scholar 

  48. Meyer P: Understanding and controlling transgene expression. Trends Biotech 13: 332–337 (1995).

    Google Scholar 

  49. Meyer P, Niedenhof I, ten Lohuis M: Evidence for cytosine methylation of nonsymmetrical sequenes in transgenic Petunia hybrida. EMBO J 13: 2084–2088 (1994).

    Google Scholar 

  50. Mueller E, Gilbert J, Davenport G, Brigneti G, Baulcombe DC: Homology dependent resistance: transgenic virus resistance in plants related to homologydependent gene silencing. Plant J 7: 1001–1013 (1995).

    Google Scholar 

  51. Oakeley EJ, Jost JP: Non-symmetrical cytosine methylation in tobacco pollen DNA. Plant Mol Biol 31: 927–930 (1996).

    Google Scholar 

  52. Palauqui JC, Elmayan T, Pollien JM, Vaucheret H: Systemic acquired silencing: transgenespecific post-transcriptional silencing is transmitted by grafting from silenced stocks to nonsilenced scions. EMBO J 16: 4738–4745 (1997).

    Google Scholar 

  53. Pang S-Z, Jan F-J, Gonsalves D: Nontarget DNA sequences reduce the transgene length necessary for RNA-mediated tospovirus resistance in transgenic plant. Proc Natl Acad Sci USA 94: 8261–8266 (1997).

    Google Scholar 

  54. Park Y-D, Moscone EA, Iglesias VA, Vaucheret H, Matzke AJM, Matzke MA: Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity. Plant J 9: 183–194 (1996).

    Google Scholar 

  55. Prins M, Goldbach R: RNAmediated virus resistance in transgenic plants. Arch Virol 141: 2259–2276 (1996).

    Google Scholar 

  56. Que Q, Wang HY, English JJ, Jorgensen RA: The frequency and degree of cosuppression by sense chalcone synthase transgenes are dependent on transgene promoter strength and are reduced by premature nonsense codons in the transgene coding sequence. Plant Cell 9: 1357–1368 (1997).

    Google Scholar 

  57. Reik W. and Constancia M. Making sense or antisense? Nature 389: 669–671 (1997).

    Google Scholar 

  58. Riggs AD: X inactivation, differentiation, and DNA methylation. Cytogenet 14: 9–25 (1975).

    Google Scholar 

  59. Ross J: Control of messenger RNA stability in higher eukaryotes. Trends Genet 12: 171–175 (1996).

    Google Scholar 

  60. Rothnie HM: Plant mRNA 3′ end formation. Plant Mol Biol 32: 43–61 (1996).

    Google Scholar 

  61. Schiebel W, Haas B, Marinkovic S, Klanner A, Sänger HL: RNA-directed RNApolymerase from tomato leaves: I. Purification and physical properties. J Biol Chem 263: 11851–11857 (1993).

    Google Scholar 

  62. Schiebel W, Haas B, Marinkovic S, Klanner A, Sänger HL: RNA-directed RNA polymerase from tomato leaves: II. Catalytic in vitro properties. J BiolChem 263: 11858–11867 (1993).

    Google Scholar 

  63. Selker EU: Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet 24: 579–613 (1990).

    Google Scholar 

  64. Selker EU, Cambereri EB, Jensen BC, Haack KR: Rearrangements of duplicated DNA in specialized cells of Neurospora. Cell 51: 741–752 (1987).

    Google Scholar 

  65. Seymour GB, Fray RG, Hill P, Tucker GA: Down-regulation of two nonhomologous endogenous tomato genes with a single chimaeric sense gene construct. Plant Mol Biol 23: 1–9 (1993).

    Google Scholar 

  66. Sijen T, Wellink J, Hiriart JB, Van Kammen A: RNA-mediated virus resistance: role of repeated transgenes and delineation of targeted regions. Plant Cell 8: 2277–2294 (1996).

    Google Scholar 

  67. Smith HA, Swaney SL, Parks TD, Wernsman EA, Dougherty WG: Transgenic plant virus resistance mediated by untranslatable sense RNAs: expression, regulation, and fate of nonessential RNAs. Plant Cell 6: 1441–1453 (1994).

    Google Scholar 

  68. Soukup GA, Ellington AD, Maher LJ: Selection of RNAs that bind to duplex DNA at neutral pH. J Mol Biol 259: 216–228 (1996).

    Google Scholar 

  69. Staiger D, Kaulen H, Schell J: A CACGTG motif of the Antirrhinum majus chalcone synthase promoter is recognized by an evolutionarily conserved nuclear protein. Proc Natl Acad Sci USA 86: 6930–6934 (1989).

    Google Scholar 

  70. Stam M, Mol JNM, Kooter JM: The silence of genes in transgenic plants. Ann Bot 79: 3–12 (1997).

    Google Scholar 

  71. Stam M, de Bruin R, Kenter S, van der Hoorn RAL, van Blokland R, Mol JNM, Kooter JM: Post-transcriptional silencing of chalcone synthase in petunia by inverted transgene repeats. Plant J 12: 63–82 (1997).

    Google Scholar 

  72. Takanami Y, Fraenkel-Conrat H: Comparative studies on RNA-dependent RNA polymerases in cucumber mosaic virus-infected cucumber, tobacco, and uninfected tobacco. Biochemistry 21: 3161–3167 (1982).

    Google Scholar 

  73. Tanzer MM, Thompson WF, Law MD, Wernsman EA, Uknes S: Characterization of post-transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco. Plant Cell 9: 1411–1423 (1997).

    Google Scholar 

  74. Tollefsbol TO, Hutchison CA III: Control of methylation spreading in synthetic DNA sequences by the murine DNA methyltransferase. J Mol Biol 269: 494–504 (1997).

    Google Scholar 

  75. Van Blokland R, Van der Geest N, Mol JNM, Kooter JM: Transgene-mediated suppression of chalcone synthase expression in Petunia hybrida results from an increase in RNA turnover. Plant J 6: 861–877 (1994).

    Google Scholar 

  76. VanHoudt H, Ingelbrecht I, Van Montagu M, Depicker A: Post-transcriptional silencing of a neomycin phosphotransferase II transgene correlates with the accumulation of unproductive RNAs and with increased cytosine methylation of 3′ flanking regions. Plant J. 12: 379–392 (1997).

    Google Scholar 

  77. Vaucheret H, Nussaume L, Palauqui JC, Quilléré I, Elmayan T: A transcriptionally active state is required for post-transcriptional silencing (cosuppression) of nitrate reductase host genes and transgenes. Plant Cell 9: 1495–1504 (1997).

    Google Scholar 

  78. Vaucheret H: Promoter-dependent trans-inactivation in transgenic tobacco plants: kinetic aspects of gene silencing and gene reactivation. CR Acad Sci Paris 317: 310–323 (1994).

    Google Scholar 

  79. Vaucheret H: Identification of a general silencer for 19S and 35S promoters in a transgenic tobacco plant: 90 bp of homology in the promoter sequence are sufficient for trans-inactivation. CR Acad Sci Paris 316: 1471–1483 (1993).

    Google Scholar 

  80. Virtanen A, Aström J: Function and characterization of poly(A)specific 3′ exoribonucleases. In: Jeanteur P (eds) Cytoplasmic fate of messenger RNAs, PMSB 18: 199–220 (1997).

  81. Wassenegger M, Heimes S, Riedel L, Sänger HL: RNA-directed de novo methylation of genomic sequences in plants. Cell 76: 567–576 (1994).

    Google Scholar 

  82. Wu TT, Su YH, Block TM, Taylor JM: Evidence that two latency associated transcripts of herpes simplex virus type 1 are nonlinear. J Virol 70: 5962–5967 (1996)

    Google Scholar 

  83. Wutz A, Smrzka OW, Schweifer N, Schellander K, Wagner EF, Barlow DP: Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389: 745–749 (1997).

    Google Scholar 

  84. Ye F, Signer ER: RIGS (repeat-induced gene silencing) in Arabidopsis is transcriptional and alters chromatin configuration. Proc Natl Acad Sci USA 93: 10881–10886 (1996).

    Google Scholar 

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  1. Abteilung Viroidforschung, Max-Planck-Institut für Biochemie, 82152, Martinsried, Germany

    Michael Wassenegger & Thiery Pélissier

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  1. Michael Wassenegger
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Wassenegger, M., Pélissier, T. A model for RNA-mediated gene silencing in higher plants. Plant Mol Biol 37, 349–362 (1998). https://doi.org/10.1023/A:1005946720438

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