An endogene-resembling transgene is resistant to DNA methylation and systemic silencing

References

• Martínez de Alba AE, Elvira-Matelot E, Vaucheret H. Gene silencing in plants: a diversity of pathways. Biochim Biophys Acta 2013; 1829:1300 - 8; http://dx.doi.org/10.1016/j.bbagrm.2013.10.005; PMID: 24185199
   PubMed Web of Science ®Google Scholar
• Pumplin N, Voinnet O. RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 2013; 11:745 - 60; http://dx.doi.org/10.1038/nrmicro3120; PMID: 24129510
   PubMed Web of Science ®Google Scholar
• Voinnet O. Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci 2008; 13:317 - 28; http://dx.doi.org/10.1016/j.tplants.2008.05.004; PMID: 18565786
   PubMed Web of Science ®Google Scholar
• Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009; 136:669 - 87; http://dx.doi.org/10.1016/j.cell.2009.01.046; PMID: 19239888
   PubMed Web of Science ®Google Scholar
• Fusaro AF, Matthew L, Smith NA, Curtin SJ, Dedic-Hagan J, Ellacott GA, Watson JM, Wang MB, Brosnan C, Carroll BJ, et al. RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep 2006; 7:1168 - 75; http://dx.doi.org/10.1038/sj.embor.7400837; PMID: 17039251
   PubMed Web of Science ®Google Scholar
• Yang Z, Ebright YW, Yu B, Chen X. HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res 2006; 34:667 - 75; http://dx.doi.org/10.1093/nar/gkj474; PMID: 16449203
   PubMed Web of Science ®Google Scholar
• Mallory A, Vaucheret H. Form, function, and regulation of ARGONAUTE proteins. Plant Cell 2010; 22:3879 - 89; http://dx.doi.org/10.1105/tpc.110.080671; PMID: 21183704
   PubMed Web of Science ®Google Scholar
• Kim VN. Sorting out small RNAs. Cell 2008; 133:25 - 6; http://dx.doi.org/10.1016/j.cell.2008.03.015; PMID: 18394983
   PubMed Web of Science ®Google Scholar
• Baulcombe D. RNA silencing in plants. Nature 2004; 431:356 - 63; http://dx.doi.org/10.1038/nature02874; PMID: 15372043
   PubMed Web of Science ®Google Scholar
• Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008; 320:1185 - 90; http://dx.doi.org/10.1126/science.1159151; PMID: 18483398
   PubMed Web of Science ®Google Scholar
• Lanet E, Delannoy E, Sormani R, Floris M, Brodersen P, Crété P, Voinnet O, Robaglia C. Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 2009; 21:1762 - 8; http://dx.doi.org/10.1105/tpc.108.063412; PMID: 19531599
   PubMed Web of Science ®Google Scholar
• Wassenegger M, Heimes S, Riedel L, Sänger HL. RNA-directed de novo methylation of genomic sequences in plants. Cell 1994; 76:567 - 76; http://dx.doi.org/10.1016/0092-8674(94)90119-8; PMID: 8313476
   PubMed Web of Science ®Google Scholar
• Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev 2012; 26:1825 - 36; http://dx.doi.org/10.1101/gad.197772.112; PMID: 22855789
   PubMed Web of Science ®Google Scholar
• Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 2000; 101:543 - 53; http://dx.doi.org/10.1016/S0092-8674(00)80864-8; PMID: 10850496
   PubMed Web of Science ®Google Scholar
• Vaistij FE, Jones L, Baulcombe DC. Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell 2002; 14:857 - 67; http://dx.doi.org/10.1105/tpc.010480; PMID: 11971140
   PubMed Web of Science ®Google Scholar
• Wassenegger M, Krczal G. Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci 2006; 11:142 - 51; http://dx.doi.org/10.1016/j.tplants.2006.01.003; PMID: 16473542
   PubMed Web of Science ®Google Scholar
• Gazzani S, Lawrenson T, Woodward C, Headon D, Sablowski R. A link between mRNA turnover and RNA interference in Arabidopsis. Science 2004; 306:1046 - 8; http://dx.doi.org/10.1126/science.1101092; PMID: 15528448
   PubMed Web of Science ®Google Scholar
• Luo Z, Chen Z. Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-mediated RNA silencing in Arabidopsis. Plant Cell 2007; 19:943 - 58; http://dx.doi.org/10.1105/tpc.106.045724; PMID: 17384170
   PubMed Web of Science ®Google Scholar
• Rajeswaran R, Aregger M, Zvereva AS, Borah BK, Gubaeva EG, Pooggin MM. Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis. Nucleic Acids Res 2012; 40:6241 - 54; http://dx.doi.org/10.1093/nar/gks242; PMID: 22434877
   PubMed Web of Science ®Google Scholar
• Rajeswaran R, Pooggin MM. RDR6-mediated synthesis of complementary RNA is terminated by miRNA stably bound to template RNA. Nucleic Acids Res 2012; 40:594 - 9; http://dx.doi.org/10.1093/nar/gkr760; PMID: 21930511
   PubMed Web of Science ®Google Scholar
• Moissiard G, Parizotto EA, Himber C, Voinnet O. Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins. RNA 2007; 13:1268 - 78; http://dx.doi.org/10.1261/rna.541307; PMID: 17592042
   PubMed Web of Science ®Google Scholar
• Mlotshwa S, Pruss GJ, Peragine A, Endres MW, Li J, Chen X, Poethig RS, Bowman LH, Vance V. DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis. PLoS One 2008; 3:e1755; http://dx.doi.org/10.1371/journal.pone.0001755; PMID: 18335032
   PubMedGoogle Scholar
• Vermeersch L, De Winne N, Depicker A. Introns reduce transitivity proportionally to their length, suggesting that silencing spreads along the pre-mRNA. Plant J 2010; 64:392 - 401; http://dx.doi.org/10.1111/j.1365-313X.2010.04335.x; PMID: 21049564
   PubMed Web of Science ®Google Scholar
• Voinnet O, Baulcombe DC. Systemic signalling in gene silencing. Nature 1997; 389:553; http://dx.doi.org/10.1038/39215; PMID: 9335491
   PubMed Web of Science ®Google Scholar
• Voinnet O, Vain P, Angell S, Baulcombe DC. Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 1998; 95:177 - 87; http://dx.doi.org/10.1016/S0092-8674(00)81749-3; PMID: 9790525
   PubMed Web of Science ®Google Scholar
• Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, Alioua A, Himber C, Voinnet O. An endogenous, systemic RNAi pathway in plants. EMBO J 2010; 29:1699 - 712; http://dx.doi.org/10.1038/emboj.2010.65; PMID: 20414198
   PubMed Web of Science ®Google Scholar
• Dunoyer P, Himber C, Ruiz-Ferrer V, Alioua A, Voinnet O. Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways. Nat Genet 2007; 39:848 - 56; http://dx.doi.org/10.1038/ng2081; PMID: 17558406
   PubMed Web of Science ®Google Scholar
• Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC, Voinnet O. Small RNA duplexes function as mobile silencing signals between plant cells. Science 2010; 328:912 - 6; http://dx.doi.org/10.1126/science.1185880; PMID: 20413458
   PubMed Web of Science ®Google Scholar
• Dunoyer P, Voinnet O. Mixing and matching: the essence of plant systemic silencing?. Trends Genet 2008; 24:151 - 4; http://dx.doi.org/10.1016/j.tig.2008.01.005; PMID: 18325623
   PubMed Web of Science ®Google Scholar
• Melnyk CW, Molnar A, Bassett A, Baulcombe DC. Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr Biol 2011; 21:1678 - 83; http://dx.doi.org/10.1016/j.cub.2011.08.065; PMID: 21962713
   PubMed Web of Science ®Google Scholar
• Melnyk CW, Molnar A, Baulcombe DC. Intercellular and systemic movement of RNA silencing signals. EMBO J 2011; 30:3553 - 63; http://dx.doi.org/10.1038/emboj.2011.274; PMID: 21878996
   PubMed Web of Science ®Google Scholar
• Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010; 328:872 - 5; http://dx.doi.org/10.1126/science.1187959; PMID: 20413459
   PubMed Web of Science ®Google Scholar
• Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM, Carroll BJ. Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc Natl Acad Sci U S A 2007; 104:14741 - 6; http://dx.doi.org/10.1073/pnas.0706701104; PMID: 17785412
   PubMed Web of Science ®Google Scholar
• Axtell MJ, Jan C, Rajagopalan R, Bartel DP. A two-hit trigger for siRNA biogenesis in plants. Cell 2006; 127:565 - 77; http://dx.doi.org/10.1016/j.cell.2006.09.032; PMID: 17081978
   PubMed Web of Science ®Google Scholar
• Sanders M, Maddelein W, Depicker A, Van Montagu M, Cornelissen M, Jacobs J. An active role for endogenous beta-1,3-glucanase genes in transgene-mediated co-suppression in tobacco. EMBO J 2002; 21:5824 - 32; http://dx.doi.org/10.1093/emboj/cdf586; PMID: 12411500
   PubMed Web of Science ®Google Scholar
• Palauqui JC, Elmayan T, De Borne FD, Crete P, Charles C, Vaucheret H. Frequencies, Timing, and Spatial Patterns of Co-Suppression of Nitrate Reductase and Nitrite Reductase in Transgenic Tobacco Plants. Plant Physiol 1996; 112:1447 - 56; PMID: 12226457
   PubMed Web of Science ®Google Scholar
• Wassenegger M, Pélissier T. Signalling in gene silencing. Trends Plant Sci 1999; 4:207 - 9; http://dx.doi.org/10.1016/S1360-1385(99)01416-8; PMID: 10366874
   PubMed Web of Science ®Google Scholar
• Jones L, Ratcliff F, Baulcombe DC. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol 2001; 11:747 - 57; http://dx.doi.org/10.1016/S0960-9822(01)00226-3; PMID: 11378384
   PubMed Web of Science ®Google Scholar
• Dalakouras A, Moser M, Boonrod K, Krczal G, Wassenegger M. Diverse spontaneous silencing of a transgene among two Nicotiana species. Planta 2011; 234:699 - 707; http://dx.doi.org/10.1007/s00425-011-1433-9; PMID: 21617990
   PubMed Web of Science ®Google Scholar
• Kalantidis K, Tsagris M, Tabler M. Spontaneous short-range silencing of a GFP transgene in Nicotiana benthamiana is possibly mediated by small quantities of siRNA that do not trigger systemic silencing. Plant J 2006; 45:1006 - 16; http://dx.doi.org/10.1111/j.1365-313X.2006.02664.x; PMID: 16507090
   PubMed Web of Science ®Google Scholar
• Dadami E, Moser M, Zwiebel M, Krczal G, Wassenegger M, Dalakouras A. An endogene-resembling transgene delays the onset of silencing and limits siRNA accumulation. FEBS Lett 2013; 587:706 - 10; http://dx.doi.org/10.1016/j.febslet.2013.01.045; PMID: 23380068
   PubMed Web of Science ®Google Scholar
• Schwach F, Vaistij FE, Jones L, Baulcombe DC. An RNA-dependent RNA polymerase prevents meristem invasion by potato virus X and is required for the activity but not the production of a systemic silencing signal. Plant Physiol 2005; 138:1842 - 52; http://dx.doi.org/10.1104/pp.105.063537; PMID: 16040651
   PubMed Web of Science ®Google Scholar
• Vaistij FE, Jones L. Compromised virus-induced gene silencing in RDR6-deficient plants. Plant Physiol 2009; 149:1399 - 407; http://dx.doi.org/10.1104/pp.108.132688; PMID: 19129420
   PubMed Web of Science ®Google Scholar
• Ruiz MT, Voinnet O, Baulcombe DC. Initiation and maintenance of virus-induced gene silencing. Plant Cell 1998; 10:937 - 46; http://dx.doi.org/10.1105/tpc.10.6.937; PMID: 9634582
   PubMed Web of Science ®Google Scholar
• Gosselé V, Faché I, Meulewaeter F, Cornelissen M, Metzlaff M. SVISS - a novel transient gene silencing system for gene function discovery and validation in tobacco plants. Plant J 2002; 32:859 - 66; http://dx.doi.org/10.1046/j.1365-313X.2002.01471.x; PMID: 12472699
   PubMed Web of Science ®Google Scholar
• Jones L, Hamilton AJ, Voinnet O, Thomas CL, Maule AJ, Baulcombe DC. RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell 1999; 11:2291 - 301; http://dx.doi.org/10.1105/tpc.11.12.2291; PMID: 10590159
   PubMed Web of Science ®Google Scholar
• Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJ, Matzke M. A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J 2009; 28:48 - 57; http://dx.doi.org/10.1038/emboj.2008.260; PMID: 19078964
   PubMed Web of Science ®Google Scholar
• Palauqui JC, Elmayan T, Pollien JM, Vaucheret H. Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO J 1997; 16:4738 - 45; http://dx.doi.org/10.1093/emboj/16.15.4738; PMID: 9303318
   PubMed Web of Science ®Google Scholar
• McHale M, Eamens AL, Finnegan EJ, Waterhouse PM. A 22-nt artificial microRNA mediates widespread RNA silencing in Arabidopsis. Plant J 2013; 76:519 - 29; http://dx.doi.org/10.1111/tpj.12306; PMID: 23937661
   PubMed Web of Science ®Google Scholar
• Bai S, Kasai A, Yamada K, Li T, Harada T. A mobile signal transported over a long distance induces systemic transcriptional gene silencing in a grafted partner. J Exp Bot 2011; 62:4561 - 70; http://dx.doi.org/10.1093/jxb/err163; PMID: 21652532
   PubMed Web of Science ®Google Scholar
• Haque AK, Yamaoka N, Nishiguchi M. Cytosine methylation is associated with RNA silencing in silenced plants but not with systemic and transitive RNA silencing through grafting. Gene 2007; 396:321 - 31; http://dx.doi.org/10.1016/j.gene.2007.04.003; PMID: 17521830
   PubMed Web of Science ®Google Scholar
• Mallory AC, Mlotshwa S, Bowman LH, Vance VB. The capacity of transgenic tobacco to send a systemic RNA silencing signal depends on the nature of the inducing transgene locus. Plant J 2003; 35:82 - 92; http://dx.doi.org/10.1046/j.1365-313X.2003.01785.x; PMID: 12834404
   PubMed Web of Science ®Google Scholar
• Bender J. RNA-directed DNA methylation: getting a grip on mechanism. Curr Biol 2012; 22:R400 - 1; http://dx.doi.org/10.1016/j.cub.2012.04.010; PMID: 22625855
   PubMedGoogle Scholar
• Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 2011; 12:483 - 92; http://dx.doi.org/10.1038/nrm3152; PMID: 21779025
   PubMed Web of Science ®Google Scholar
• Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010; 11:204 - 20; http://dx.doi.org/10.1038/nrg2719; PMID: 20142834
   PubMed Web of Science ®Google Scholar
• Dalakouras A, Dadami E, Wassenegger M. Viroid-induced DNA methylation in plants. BioMol Concepts 2013; 4:557 - 65
   Google Scholar
• Dalakouras A, Wassenegger M. Revisiting RNA-directed DNA methylation. RNA Biol 2013; 10:453 - 5; http://dx.doi.org/10.4161/rna.23542; PMID: 23324611
   PubMed Web of Science ®Google Scholar
• Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008; 135:635 - 48; http://dx.doi.org/10.1016/j.cell.2008.09.035; PMID: 19013275
   PubMed Web of Science ®Google Scholar
• Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 2009; 41:630 - 4; http://dx.doi.org/10.1038/ng.365; PMID: 19377477
   PubMed Web of Science ®Google Scholar
• Christie M, Brosnan CA, Rothnagel JA, Carroll BJ. RNA decay and RNA silencing in plants: competition or collaboration?. Front Plant Sci 2011; 2:99; http://dx.doi.org/10.3389/fpls.2011.00099; PMID: 22639621
   PubMed Web of Science ®Google Scholar
• Gy I, Gasciolli V, Lauressergues D, Morel JB, Gombert J, Proux F, Proux C, Vaucheret H, Mallory AC. Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell 2007; 19:3451 - 61; http://dx.doi.org/10.1105/tpc.107.055319; PMID: 17993620
   PubMed Web of Science ®Google Scholar
• Christie M, Carroll BJ. SERRATE is required for intron suppression of RNA silencing in Arabidopsis. Plant Signal Behav 2011; 6:2035 - 7; http://dx.doi.org/10.4161/psb.6.12.18238; PMID: 22112452
   PubMedGoogle Scholar
• Christie M, Croft LJ, Carroll BJ. Intron splicing suppresses RNA silencing in Arabidopsis. Plant J 2011; 68:159 - 67; http://dx.doi.org/10.1111/j.1365-313X.2011.04676.x; PMID: 21689169
   PubMed Web of Science ®Google Scholar
• Kertész S, Kerényi Z, Mérai Z, Bartos I, Pálfy T, Barta E, Silhavy D. Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res 2006; 34:6147 - 57; http://dx.doi.org/10.1093/nar/gkl737; PMID: 17088291
   PubMed Web of Science ®Google Scholar
• Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 2007; 19:926 - 42; http://dx.doi.org/10.1105/tpc.107.050062; PMID: 17400893
   PubMed Web of Science ®Google Scholar
• Horsch R, Fry J, Hoffmann N, Eichholz D, Rogers S, Fraley R. A simple and general method for transferring genes into plants. Science 1985; 227:1229 - 31; http://dx.doi.org/10.1126/science.227.4691.1229; PMID: 17757866
   PubMed Web of Science ®Google Scholar
• Dalakouras A, Moser M, Zwiebel M, Krczal G, Hell R, Wassenegger M. A hairpin RNA construct residing in an intron efficiently triggered RNA-directed DNA methylation in tobacco. Plant J 2009; 60:840 - 51; http://dx.doi.org/10.1111/j.1365-313X.2009.04003.x; PMID: 19702668
   PubMed Web of Science ®Google Scholar
• Hetzl J, Foerster AM, Raidl G, Mittelsten Scheid O. CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. Plant J 2007; 51:526 - 36; http://dx.doi.org/10.1111/j.1365-313X.2007.03152.x; PMID: 17559516
   PubMed Web of Science ®Google Scholar
• Helm JM, Dadami E, Kalantidis K. Local RNA silencing mediated by agroinfiltration. Methods Mol Biol 2011; 744:97 - 108; http://dx.doi.org/10.1007/978-1-61779-123-9_7; PMID: 21533688
   PubMedGoogle Scholar
• Dalakouras A, Dadami E, Zwiebel M, Krczal G, Wassenegger M. Transgenerational maintenance of transgene body CG but not CHG and CHH methylation. Epigenetics 2012; 7:1071 - 8; http://dx.doi.org/10.4161/epi.21644; PMID: 22863736
   PubMed Web of Science ®Google Scholar