Skip to main content
SpringerLink
Log in

Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing

  • Chapter
Plant Gene Silencing

Abstract

Transgenes and endogenous genes are sensitive to silencing, in particular when the genes are tandemly repeated. Their expression can be transcriptionally or post-transcriptionally repressed, or both. It is remarkable that very often, two or more genes or parts of the genes are arranged as inverted repeats (IR). Many of such IRs are dominant silencing loci. They can repress the expression of homologous genes elsewhere in the genome in trans which is usually associated with an increase in the level of DNA methylation. Trans-silencing has been explained by DNA DNA pairing between a repetitive silencing locus and a homologous target locus. However, there is accumulating evidence that the trans effect might be mediated by dsRNA transcribed from the IR (trans)genes. Besides dsRNA-directed DNA methylation, dsRNA in plants as well as in other systems also induces the degradation of homologous RNAs and silence genes post-transcriptionally. These findings indicate that several features associated with gene silencing can be attributed to the activities of dsRNA, which would explain why inverted transgene repeats are such efficient silencing loci.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Akgün, E., Zahn, J., Baumes, S., Brown, G., Liang, F., Romanienko, P.J., Lewis, S. and Jasin, M. 1997. Palindrome resolution and recombination in the mammalian germ line. Mol. Cell. Biol. 17: 5559–5570.

    PubMed  Google Scholar 

  • Angell, S.M. and Baulcombe, D.C. 1997. Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA. EMBO J. 16: 3675–3684.

    Article  PubMed  CAS  Google Scholar 

  • Assaad, F.F., Tucker, K.L. and Signer, E.R. 1993. Epigenetic repeatinduced gene silencing (RIGS) in Arabidopsis. Plant Mol. Biol. 22: 1067–1085.

    Article  PubMed  CAS  Google Scholar 

  • Baulcombe, D.C. and English, J.J. 1996. Ectopic pairing of homologous DNA and post-transcriptional silencing in transgenic plants. Curr. Opin. Biotechnol. 7: 173–180.

    Article  CAS  Google Scholar 

  • Bender, J. 1998. Cytosine methylation of repeated sequences in eukaryotes: the role of DNA pairing. Trends Biochem. Sci. 23: 252–256.

    Article  PubMed  CAS  Google Scholar 

  • Bender. J. and Fink, G.R. 1995. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant oi Arabidopsis. Cell 83: 725–734.

    Article  PubMed  CAS  Google Scholar 

  • Bestor, T.H. 1987. Supercoiling-dependent sequence specificity of mammalian DNA methyltransferase. Nucl. Acids Res. 15: 3835–3843.

    Article  PubMed  CAS  Google Scholar 

  • Bester, T.H. and Coxon, A. 1993. Cytosine methylation: the pros and cons of DNA methylation. Curr. Biol. 3: 384–386.

    Article  Google Scholar 

  • Bi, X. and Liu, L.F. 1996. DNA rearrangement mediated by inverted repeats. Proc. Natl. Acad. Sci. USA 93: 819–823.

    Article  PubMed  CAS  Google Scholar 

  • Bird, A.P. and Wolffe, A.P. 1999. Methylation-induced repression: belts, braces and chromatin. Cell 99: 451–454.

    Article  PubMed  CAS  Google Scholar 

  • Blaho, A.J., Larson, J.E., McLean, M.J. and Wells, R.D. 1988. Multiple DNA secondary structures in perfect inverted repeat inserts in plasmids. J. Biol. Chem. 263: 14446–14455.

    PubMed  CAS  Google Scholar 

  • Bollmann, J., Carpenter, R. and Coen, E.S. 1991. Allelic interactions at the nivea locus of Antirrhinum. Plant Cell 3: 1327–1336.

    PubMed  CAS  Google Scholar 

  • Christou, P. 1992. Genetic transformation of crop plants using microprojectile bombardment. Plant J. 2: 275–281.

    Article  CAS  Google Scholar 

  • Cluster, P., O’Dell, M., Metzlaff, M. and Flavell, R.B. 1996. Details of T-DNA structural organization from a transgenic Petunia population exhibiting co-suppression. Plant Mol. Biol. 32: 1197–1203.

    Article  PubMed  CAS  Google Scholar 

  • Coen, E.S. and Carpenter, R. 1988. A semi-dominant allele, niv5 25, acts in trans to inhibit the expression of its wild-type homologue in Antirrhinum majus. EMBO J. 7: 877–883.

    PubMed  CAS  Google Scholar 

  • Cogoni, C. and Macino, G. 1999. Homology-dependent gene silencing in plants and fungi: a number of variations on the same theme. Curr. Opin. Microbiol. 2: 657–662.

    Article  PubMed  CAS  Google Scholar 

  • Collick, A., Drew, J., Penberth, J., Bois, P., Luckett, J., Scaerou, F., Jeffreys, A. and Reik, W. 1996. Instability of long inverted repeats within mouse transgenes. EMBO J. 15: 1163–1171.

    PubMed  CAS  Google Scholar 

  • Collins, J. 1980. Instability of palindromic DNA in Escherichia coli. Cold Spring Harbor Symp. Quant. Biol. 45: 409–416.

    Article  Google Scholar 

  • Collins, J., Volkaert, G. and Nevers, P. 1982. Precise and nearlyprecise excision of the symmetrical inverted repeats of Tn5; common features of recA-independent deletion events in Escherichia coli. Gene 19: 139–146.

    Article  PubMed  CAS  Google Scholar 

  • Colot, V., Maloisel, L. and Rossignol, J.L. 1996. Interchromosomal transfer of epigenetic states in Ascobolus: transfer of DNA methylation is mechanistically related to homologous recombination. Cell 86: 855–864.

    Article  PubMed  CAS  Google Scholar 

  • DasGupta, U., Weston-Hafer, K. and Berg, D.E. 1987. Local DNA sequence control of deletion formation in Escherichia coli Plasmid pBR322. Genetics 115: 41–49.

    PubMed  CAS  Google Scholar 

  • Dehio, C. and Schell, J. 1994. Identification of plant genetic loci involved in a posttranscriptional mechanism for meiotically reversible transgene silencing. Proc. Natl. Acad. Sci. USA 91: 5538–5542.

    Article  PubMed  CAS  Google Scholar 

  • De Neve, M., De Buck, S., Jacobs, A., Van Montagu, M. and Depicker, A. 1997. T-DNA integration patterns in cotransformed plant cells suggest that T-DNA repeats originate from co-integration of separate T-DNAs. Plant J. 11: 15–29.

    Article  PubMed  Google Scholar 

  • Depicker, A., Ingelbrecht, I., Van Houdt, H., De Loose, M. and Van Montagu, M. 1996. Post-transcriptional reporter transgene silencing in transgenic tobacco. In: D. Grierson, G.W. Lycett and G.A. Tucker GA (Eds.) Mechanisms and Applications of Gene Silencing, Nottingham University Press, Nottingham, UK, pp. 71–84.

    Google Scholar 

  • Dorer, D.R. 1997. Do transgene arrays form heterochromatin in vertebrates? Transgen. Res. 6: 3–10.

    Article  CAS  Google Scholar 

  • Dorer, D.R. and Henikoff, S. 1994. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77: 993–1002.

    Article  PubMed  CAS  Google Scholar 

  • Dorer, D.R. and Henikoff, S. 1997. Transgene repeat arrays interact with distant heterochromatin and cause silencing in cis and trans. Genetics 147: 1181–1190.

    PubMed  CAS  Google Scholar 

  • Ehrlich, S.D. 1989. Illegitimate recombination in bacteria. In: D.E. Berg and M.M. Howe (Eds.) Mobile DNA, American Society for Microbiology, Washington, D.C., pp. 799–832.

    Google Scholar 

  • Elmayan, T. and Vaucheret, H. 1996. A strongly-expressed 35S-driven transgene undergoes post-transcriptional silencing in all tobacco transformants irrespective of the copy number. Plant J. 9: 787–797.

    Article  CAS  Google Scholar 

  • English, J.J., Mueller, E. and Baulcombe, D.C. 1996. Suppression of virus accumulation in transgenic plants exhibiting silencing of nuclear genes. Plant Cell 8: 179–188.

    PubMed  CAS  Google Scholar 

  • English, J.J., Davenport, G.F., Elmayan, T., Vaucheret, H. and Baulcombe, D.C. 1997. Requirement of sense transcription for homology-dependent virus resistance and trans-inactivation. Plant J. 12: 597–603.

    Article  CAS  Google Scholar 

  • Faugeron. G., Rhounim, L. and Rossignol, J.-L. 1990. How does the cell count the number of ectopic copies of a gene in the premeiotic inactivation process acting in Ascobolus immersus. Genetics 135:357–366.

    Google Scholar 

  • Fire, A. 1999. RNA-triggered gene silencing. Trends Genet. 15: 358–363.

    Article  PubMed  CAS  Google Scholar 

  • Fire, A., Xu, S.Q., 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: 806–811.

    Article  PubMed  CAS  Google Scholar 

  • Garrick, D., Fiering, S., Martin, D.I.K. and Whitelaw, E. 1998. Repeat-induced gene silencing in mammals. Nature Genet. 18: 56–59.

    Article  PubMed  CAS  Google Scholar 

  • Goodwin, J., Chapman, K., Swaney, S., Parks, T.D., Wernsman, E.A. and Dougherty, W.G. 1996. Genetic and biochemical dissection of transgenic RNA-mediated virus resistance. Plant Cell 8: 95–105.

    PubMed  CAS  Google Scholar 

  • Gordenin, D.A., Lobachev, K.S., Degtyareva, N.P., Malkova, A.L., Perkins, E. and Resnick, M.A. 1993. Inverted DNA repeats: a source of eukaryotic genomic instability. Mol. Cell. Biol. 13: 5315–5322.

    PubMed  CAS  Google Scholar 

  • Goyon, C., Nogueira, T.I.V. and Faugeron, G. 1994. Perpetuation of cytosine methylation in Ascobolus immersus implies a novel type of maintenance methylase. J. Mol. Biol. 240: 42–51.

    Article  PubMed  CAS  Google Scholar 

  • Hamilton, A.J., Brown, S., Han, Y.H., Ishizuka, M., Lowe, A., Solis, A.G.A. and Grierson, D. 1998. A transgene with repeated DNA causes high-frequency, post-transcriptional suppression of ACC-oxidase gene expression in tomato. Plant J. 15: 737–746.

    Article  CAS  Google Scholar 

  • Hanke, J.H., Hambor, J.E. and Kavathas, P. 1995. Repetitive Alu elements form a cruciform structure that regulates the function of the human CD8a T cell-specific enhancer. J. Mol. Biol. 246: 63–73.

    Article  PubMed  CAS  Google Scholar 

  • Henikoff, S. and Comai, L. 1998. Trans-sensing effects: the ups and downs of being together. Cell 93: 329–332.

    Article  PubMed  CAS  Google Scholar 

  • Hobbs, S.L.A., Kpodar, P. and Delong, C.M.O. 1990. The effect of T-DNA copy number, position and methylation on reporter gene expression in tobacco transformants. Plant Mol. Biol. 15: 851–864.

    Article  PubMed  CAS  Google Scholar 

  • Hobbs, S.L.A., Warkentin, T.D. and Delong, C.M.O. 1993. Transgene copy number can be positively or negatively associated with transgene expression. Plant Mol. Biol. 21: 17–26.

    Article  PubMed  CAS  Google Scholar 

  • Hollick, J.B., Dorweiler, J.E. and Chandler, V.L. 1997. Paramutation and related allelic interactions. Trends Genet. 13: 302–308.

    Article  PubMed  CAS  Google Scholar 

  • Ingelbrecht, I. 1993. Analysis of 3′ processing signals and study of transgene silencing in Nicotiana tabacum. Ph.D. thesis, Universiteit Gent, Gent, Belgium.

    Google Scholar 

  • Jakowitsch, J., Papp, I., Moscone, E.A., van der Winden, J., Matzke, M. and Matzke, A.J.M. 1999. Molecular and cytogenetic characterization of a transgene locus that induces silencing and methylation of homologous promoters in trans. Plant J. 17: 131–140.

    Article  PubMed  CAS  Google Scholar 

  • Jeddeloh, J.A., Stokes, T.L. and Richards, E.J. 1999. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nature Genet. 22: 94–96.

    Article  PubMed  CAS  Google Scholar 

  • Jones, A.L., Thomas, C.L.and Maule, A.J. 1998. De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus. EMBO J. 17:6385–6393.

    Article  PubMed  CAS  Google Scholar 

  • Jorgensen, R., Snyder, C. and Jones, J.D.G. 1987. T-DNA is organized predominantly in inverted repeat structures in plants transformed with Agrobacterium tumefaeiens C58 derivates. Mol. Gen. Genet. 207: 471–477.

    Article  CAS  Google Scholar 

  • Jorgensen, R., Cluster, P., Que, Q., English, J. and Napoli, C. 1996. Chalcone synthase cosuppression phenotypes in petunia flowers: comparison of sense vs. antisense constructs and single copy vs. complex T-DNA sequences. Plant Mol. Biol. 31: 957–973.

    Article  PubMed  CAS  Google Scholar 

  • 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: 1017–1026.

    Article  PubMed  CAS  Google Scholar 

  • Ketting, R.F., Haverkamp, T.H.A., van Luenen, H.G.A.M. and Plasterk, R.H.A. 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.

    Article  PubMed  CAS  Google Scholar 

  • Konokov, M., Bassuner, B. and Gelvin, S. 1997. Integration of T-DNA binary vector backbone sequences into the tobacco genome: evidence for multiple complex patterns of integration. Plant J. 11:945–957.

    Article  Google Scholar 

  • Kooter, J.M., Matzke, M.A. and Meyer, P. 1999. Listening to the silent genes: transgene silencing research identifies new mechanisms of gene regulation and pathogen control. Trends Plant Sci. 4: 340–347.

    Article  PubMed  Google Scholar 

  • Kumagai, M.H., Donson, J., Dellacioppa, G., Harvey, D., Hanley, K. and Grill, L.K. 1995. Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc. Natl. Acad. Sci. USA 92: 1679–1683.

    Article  PubMed  CAS  Google Scholar 

  • Leach, D.R.F. 1994. Long palindromes, cruciform structures, genetic instability and secondary structure repair. BioEssays 16: 893–900.

    Article  PubMed  CAS  Google Scholar 

  • Leach, D.R.F. and Stahl, F.W. 1983. Viability of lambda phages carrying a perfect palindrome in the absence of recombination nucleases. Nature 305: 448–451.

    Article  PubMed  CAS  Google Scholar 

  • Lilley, D.M.J. 1981. In vivo consequences of plasmid topology. Nature 292: 380–382.

    Article  PubMed  CAS  Google Scholar 

  • Lindbo, J.A., Silva-Rosales, L., Proebsting, W.M. and Dougherty, W.G. 1993. Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell 5: 1749–1759.

    PubMed  CAS  Google Scholar 

  • Lobachev, K.S., Shor, B.M., Tran, H.T., Taylor, W., Keen, J.D., Resnick, M.A. and Gordenin, D.A. 1998. Factors affecting inverted repeat stimulation of recombination and deletion in Saccharomyces cerevisiae. Genetics 148: 1507–1524.

    PubMed  CAS  Google Scholar 

  • Lloyd, R.G. and Buckman, C. 1985. Identification and genetic analysis of sbcC mutations in commonly used recBC sbcB strains of Escherichia coli K-12. J. Bact. 164: 836–844.

    PubMed  CAS  Google Scholar 

  • Luff, B., Pawlowski, L. and Bender, J. 1999. An inverted repeat triggers cytosine methylation of identical sequences in Arabidopsis. Mol. Cell 3: 505–511.

    Article  PubMed  CAS  Google Scholar 

  • Martienssen, R. 1996. Epigenetic phenomena: paramutation and gene silencing in plants. Curr. Biol. 6: 810–813.

    Article  PubMed  CAS  Google Scholar 

  • Matzke, M.A. and Matzke, A.J.M. 1998. Epigenetic silencing of plant transgenes as a consequence of diverse cellular defence responses. Cell. Mol. Life Sci. 54: 94–103.

    Article  PubMed  CAS  Google Scholar 

  • Matzke, A.J.M., Neuhuber, F., Park, Y.D., Ambros, P.F. and Matzke, M.A. 1994. Homology-dependent gene silencing in transgenic plants: epistatic silencing loci contain multiple copies of methylated transgenes. Mol. Gen. Genet. 244: 219–229.

    Article  PubMed  CAS  Google Scholar 

  • Matzke, M.A., Matzke, A.J.M. and Eggeiston, W.B. 1996. Paramutation and transgene silencing: a common response to invasive DNA? Trends Plant Sci. 1: 382–388.

    Google Scholar 

  • Mette, M.F., van der Winden, J., Matzke, M.A.and Matzke, A.J.M. 1999. Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J. 18:241–248.

    Article  PubMed  CAS  Google Scholar 

  • Meyer, P., Heidmann, I. and Niedenhof, I. 1993. Differences in DNA-methylation are associated with a paramutation phenomenon in transgenic petunia. Plant J. 4: 89–100.

    Article  PubMed  CAS  Google Scholar 

  • Meyer, P., Niedenhof, I. and ten Lohuis, M. 1994. Evidence for cytosine methylation of non-symmetrical sequences in transgenic Petunia hybrida. EMBO J. 13: 2084–2088.

    PubMed  CAS  Google Scholar 

  • Meyer, P. and Saedler, H. 1996. Homology-dependent gene silencing in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47: 23–48.

    Article  PubMed  CAS  Google Scholar 

  • 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. USA 95: 15502–15507.

    Article  PubMed  CAS  Google Scholar 

  • Nan, X.S., Ng, H.H., Johnson, CA., Laherty, CD., Turner, B.M., Eisenman, R.N. and Bird, A. 1998. Transcriptional repression by the methy1-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386–389.

    Article  PubMed  CAS  Google Scholar 

  • Ngô, H., Tschudi, C., Gull, K. and Ullu, E. 1998. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 95: 14687–14692.

    Article  PubMed  Google Scholar 

  • Palauqui, J.C. and Balzergue, S. 1999. Activation of systemic acquired silencing by localised introduction of DNA. Curr. Biol. 9: 59–66.

    Article  PubMed  CAS  Google Scholar 

  • Park, Y-D., Papp, I., Moscone, E.A., Iglesias, V.A., Vaucheret, H., Matzke, A.J.M. and Matzke, M.A. 1996. 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.

    Article  PubMed  CAS  Google Scholar 

  • Pawlowski, W.P. and Somers, D.A. 1998. Transgenic DNA integrated into the oat genome is frequently interspersed by host DNA. Proc. Natl. Acad. Sci. USA 95: 12106–12110.

    Article  PubMed  CAS  Google Scholar 

  • Pélissier, T., Thalmeir, S., Kempe, D., Sanger, H.L. and Wassenegger, M. 1999. Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucl. Acids Res. 27: 1625–1634.

    Article  PubMed  Google Scholar 

  • Que, Q.D., Wang, H.Y., English, J.J. and Jorgensen, R.A. 1997. 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.

    PubMed  CAS  Google Scholar 

  • Rossignol, J.L. and Faugeron, G. 1995. MIP: an epigenetic gene silencing process in Ascobolus immersus. In: P. Meyer (Ed.) Gene Silencing in Higher Plants and Related Phenomena in Other Eukaryotes, Springer-Verlag, Berlin, pp. 179–191.

    Chapter  Google Scholar 

  • Ruiz, M.T., Voinnet, O. and Baulcombe, D.C. 1998. Initiation and maintenance of virus-induced gene silencing. Plant Cell 10: 937–946.

    PubMed  CAS  Google Scholar 

  • Saedler, H. and Nevers, P. 1985. Transposition in plants: a molecular model. EMBO J. 4: 585–590.

    PubMed  CAS  Google Scholar 

  • Sanchez Alvardo, A. and Newmark, P.A. 1999. Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proc. Natl. Acad. Sci. USA 96: 5049–5054.

    Article  Google Scholar 

  • Selker, E.U. 1993. Control of DNA methylation in fungi. In: J.P. Jost and H.P. Saluz (Eds.) DNA Methylation: Molecular Biology and Biological Significance, Birkhäuser Verlag, Basel, pp. 212–217.

    Google Scholar 

  • Selker, E.U. 1998. Trichostatin A causes selective loss of DNA methylation in Neurospom. Proc. Natl. Acad. Sci. USA 95: 9430–9535.

    Article  PubMed  CAS  Google Scholar 

  • Selker, E.U. 1999. Gene silencing: repeats that count. Cell 97: 157–160.

    Article  PubMed  CAS  Google Scholar 

  • Singer, M.J. and Selker, E.U. 1995. Genetic and epigenetic inactivation of repetitive sequences in Neurospora crassa: RIP, DNA methylation, and quelling. In: P. Meyer (Ed.) Gene Silencing in Higher Plants and Other Phenomena in Other Eukaryotes, Springer-Verlag, Berlin, pp. 165–178.

    Chapter  Google Scholar 

  • Sijen, T. and Kooter, J.M. 2000. Post-transcriptional silencing: RNAs on the attack or on the defensive? BioEssays, in press.

    Google Scholar 

  • Sijen, T., Wellink, J., Hiriart, J.B. and van Kammen, A. 1996. RNA-mediated virus resistance: role of repeated transgenes and delineation of targeted regions. Plant Cell 8: 2277–2294.

    PubMed  CAS  Google Scholar 

  • Stam, M., de Bruin, R., Renter, S., van der Hoorn, R.A.L., van Blok-land, R., Mol, J.N.M. and Kooter, J.M. 1997. Post-transcriptional silencing of chalcone synthase in Petunia by inverted transgene repeats. Plant J. 12: 63–82.

    Article  CAS  Google Scholar 

  • Stam, M., Viterbo, A., Mol, J.N.M. and Kooter, J.M. 1998. Position-dependent methylation and transcriptional silencing of transgenes in inverted T-DNA repeats: Implications for posttran-scriptional silencing of homologous host genes in plants. Mol. Cell. Biol. 18: 6165–6177.

    PubMed  CAS  Google Scholar 

  • Stam, M., de Bruin, R., van Blokland, R., ten Hoorn, R.A.L., Mol, J.N.M. and Kooter, J.M. 2000. Distinct features of posttranscriptional gene silencing by antisense transgenes in single copy and inverted T-DNA repeat loci. Plant J. 21: 27–42.

    Article  PubMed  CAS  Google Scholar 

  • Stinard, P.S., Robertson, D.S. and Schnable, P.S. 1993. Genetic isolation, cloning, and analysis of a mutator-induced, dominant antimorph of the maize amylose extender1 locus. Plant Cell 5: 1555–1566.

    PubMed  CAS  Google Scholar 

  • 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: 123–132.

    Article  PubMed  CAS  Google Scholar 

  • Tinland, B. 1996. The integration of T-DNA into plant genomes. Trends Plant Sci. 1: 178–184.

    Article  Google Scholar 

  • Todd, J.J. and Vodkin, L.O. 1996. Duplications that suppress and deletions that restore expression from a chalcone synthase multigene family. Plant Cell 8: 687–699.

    PubMed  CAS  Google Scholar 

  • Tran, H., Degtyareva, N., Gordenin, D. and Resnick, M.A. 1997. Altered replication and inverted repeats induce mismatch repair-independent recombination between highly divergent DNAs in yeast. Mol. Cell. Biol. 17: 1027–1036.

    PubMed  CAS  Google Scholar 

  • Trinh, T.Q. and Sinden, R.R. 1991. Preferential DNA secondary structure mutagenesis in the lagging strand of DNA replication in E. coli. Nature 352: 544–547.

    Article  PubMed  CAS  Google Scholar 

  • van Blokland, R., van der Geest, N., Mol, J.N.M. and Kooter, J.M. 1994. Transgene-mediated suppression of chalcone synthase expression in Petunia hybrida results from an increase in RNA turnover. Plant J. 6: 861–877.

    Article  CAS  Google Scholar 

  • Van Houdt, H., Ingelbrecht, I., Van Montagu, M. and Depicker, A. 1997. Post-transcriptional silencing of a neomycin phosphotransferase II transgene correlates with the accumulation of unproductive RNAs and with increased cytosine methylation. Plant J. 12: 379–392.

    Article  Google Scholar 

  • Vaucheret, H. 1993. 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. C. R. Acad. Sci. [III] 316: 1471–1483.

    CAS  Google Scholar 

  • Vaucheret, H., Elmayan, T., Mourrain, P. and Palauqui, J-C. 1996. Analysis of a tobacco transgene locus that triggers both transcriptional and post-transcriptional silencing. In: Russo, V.E., Martienssen, R.A. and Riggs, A.D (Eds.) Epigenetic Mechanisms of Gene Regulation, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 403–414.

    Google Scholar 

  • Vaucheret, H., Béclin, 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 J. 16: 651–659.

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Voinnet, O., Vain, P., Angell, S. and Baulcombe, D.C. 1998. Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 95: 177–187.

    Article  PubMed  CAS  Google Scholar 

  • Wade, P.A., Gegonne, A., Jones, P.L., Ballestar, E., Aubry, F. and Wolffe, A.P. 1999. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nature Genet. 23: 1–5.

    Article  CAS  Google Scholar 

  • Wassenegger, M. and Pélissier, T. 1998. A model for RNA-mediated gene silencing in higher plants. Plant Mol. Biol. 37: 349–362.

    Article  PubMed  CAS  Google Scholar 

  • Wassenegger, M., Heimes, S., Riedel, L. and Sänger, H.L. 1994. RNA-directed de novo methylation of genomic sequences in plants. Cell 76: 567–576.

    Article  PubMed  CAS  Google Scholar 

  • 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. USA 95: 13959–13964.

    Article  PubMed  CAS  Google Scholar 

  • Waterhouse, P.M., Smith, N.A. and Wang, M.B. 1999. Virus resistance and gene silencing: killing the messenger. Trends Plant Sci. 4: 452–457.

    Article  PubMed  Google Scholar 

  • Wenck, A., Czako, M., Kanevski, I. and Marton, L. 1997. Frequent collinear long transfer of DNA inclusive of the whole binary vector during Agrobacterium-mediaied transformation. Plant Mol. Biol. 34:913–922.

    Article  PubMed  CAS  Google Scholar 

  • Wolffe, A.P. and Matzke, M.A. 1999. Epigenetics: regulation through repression. Science 286: 481–486.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Zupan, J.R. and Zambryski, P. 1995. Transfer of T-DNA from Agrobacterium to the plant cell. Plant Physiol. 107: 1041–1047.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Developmental Genetics, Institute for Molecular Biological Sciences, BioCentrum Amsterdam, Vrije Universiteit, De Boelelaan 1087, 1081 HV, Amsterdam, Netherlands

    Mariëlle W. M. Muskens, Adriënne P. A. Vissers, Joseph N. M. Mol & Jan M. Kooter

Authors
  1. Mariëlle W. M. Muskens
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adriënne P. A. Vissers
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joseph N. M. Mol
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jan M. Kooter
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute of Molecular Biology, Austrian Academy of Sciences, Salzburg, Austria

    M. A. Matzke  & A. J. M. Matzke  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2000 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Muskens, M.W.M., Vissers, A.P.A., Mol, J.N.M., Kooter, J.M. (2000). Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing. In: Matzke, M.A., Matzke, A.J.M. (eds) Plant Gene Silencing. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4183-3_9

Download citation

  • DOI: https://doi.org/10.1007/978-94-011-4183-3_9

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-5821-6

  • Online ISBN: 978-94-011-4183-3

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation