Abstract
Plant transformation is a versatile method to introduce or alter a trait-of-interest through expression of a transgene or through transgene-induced mutation and/or expression changes of endogenes. Transgenes in plants, however, are subject to gene-silencing effects that are an obstacle to stable and heritable expression of transgene-encoded traits. In an exciting twist, natural gene-silencing processes have been harnessed by researchers to achieve highly specific and targeted down-regulation of endogenous or pathogen-derived genes for functional studies, crop protection and crop improvement. Part 1 of this chapter attempts to give an overview of the mechanistic pillars of gene silencing in plants. Part 2 summarizes the factors that may cause unintended silencing of transgene expression, with practical advice on how to minimize the risk of transgene silencing. Part 3 addresses the intentional use of gene silencing for biotechnological applications in transgenic plants, with particular emphasis on RNA interference approaches.
Similar content being viewed by others
References
Allen GC, Spiker S, Thompson WF (2000) Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Mol Biol 43:361–376
Allen RS, Millgate AG, Chitty JA, Thisleton J, Miller JA, Fist AJ, Gerlach WL, Larkin PJ (2004) RNAi-mediated replacement of morphine with the nonnarcotic alkaloid reticuline in opium poppy. Nat Biotechnol 22:1559–1566
Assaad FF, Tucker KL, Signer ER (1993) Epigenetic repeat-induced gene silencing (RIGS) in Arabidopsis. Plant Mol Biol 22:1067–1085
Baum JA, Bogaert T, Clinton W, Heck GR, Feldmann P, Ilagan O, Johnson S, Plaetinck G, Munyikwa T, Pleau M, Vaughn T, Roberts J (2007) Control of coleopteran insect pests through RNA interference. Nat Biotechnol 25:1322–1326
Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291
Brodersen P, Voinnet O (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22:268–280
Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190
Brummell DA, Balint-Kurti PJ, Harpster MH, Palys JM, Oeller PW, Gutterson N (2003) Inverted repeat of a heterologous 3'-untranslated region for high-efficiency, high-throughput gene silencing. Plant J 33:793–800
Bucher E, Lohuis D, van Poppel PMJA, Geerts-Dimitriadou C, Goldbach R, Prins M (2006) Multiple virus resistance at a high frequency using a single transgene construct. J Gen Virol 87:3697–3701
Butaye KM, Goderis IJ, Wouters PF, Pues JM, Delaure SL, Broekaert WF, Depicker A, Cammue BP, De Bolle MF (2004) Stable high-level transgene expression in Arabidopsis thaliana using gene silencing mutants and matrix attachment regions. Plant J 39:440–449
Butaye KMJ, Cammue BPA, Delaure SL, De Bolle MFC (2005) Approaches to minimize variation of transgene expression in plants. Mol Breed 16:79–91
Campbell MA, Fitzgerald HA, Ronald PC (2002) Engineering pathogen resistance in crop plants. Transgenic Res 11:599–613.
Candela H, Hake S (2008) The art and design of genetic screens: maize. Nat Rev Genet 9:192–203
Chan SW (2008) Inputs and outputs for chromatin-targeted RNAi. Trends Plant Sci 13:383–389
Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351–360
Chapman EJ, Carrington JC (2007) Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8:884–896
Chellappan P, Vanitharani R, Ogbe F, Fauquet CM (2005) Effect of temperature on geminivirus-induced RNA silencing in plants. Plant Physiol 138:1828–1841
Comai L, Henikoff S (2006) TILLING: practical single-nucleotide mutation discovery. Plant J 45:684–694
Dafny-Yelin M, Chung SM, Frankman EL, Tzfira T (2007) pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants. Plant Physiol 145:1272–1281
Davuluri GR, Tuinen A, Mustilli AC, Manfredonia A, Newman R, Burgess D, Brummell DA, King SR, Palys J, Uhlig J, Pennings HMJ, Bowler C (2004) Manipulation of DET1 expression in tomato results in photomorphogenic phenotypes caused by post-transcriptional gene silencing. Plant J 40:344–354
Davuluri GR, van Tuinen A, Fraser PD, Manfredonia A, Newman R, Burgess D, Brummell DA, King SR, Palys J, Uhlig J, Bramley PM, Pennings HMJ, Bowler C (2005) Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat Biotechnol 23:890–895
Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJ, Matzke M (2008) A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J 28:48–57
Day CD, Lee E, Kobayashi J, Holappa LD, Albert H, Ow DW (2000) Transgene integration into the same chromosome location can produce alleles that express at a predictable level, or alleles that are differentially silenced. Genes Dev 14:2869–2880
De Bolle MFC, Butaye KMJ, Coucke WJW, Goderis IJWM, Wouters PFJ, van Boxel N, Broekaert WF, Cammue BPA (2003) Analysis of the influence of promoter elements and a matrix attachment region on the inter-individual variation of transgene expression in populations of Arabidopsis thaliana. Plant Sci 165:169–179
De Bolle MF, Butaye KM, Goderis IJ, Wouters PF, Jacobs A, Delaure SL, Depicker A, Cammue BP (2007) The influence of matrix attachment regions on transgene expression in Arabidopsis thaliana wild type and gene silencing mutants. Plant Mol Biol 63:533–543
De Buck S, Windels P, De LM, Depicker A (2004) Single-copy T-DNAs integrated at different positions in the Arabidopsis genome display uniform and comparable beta-glucuronidase accumulation levels. Cell Mol Life Sci 61:2632–2645
De Haan P, Gielen JJ, Prins M, Wijkamp IG, Van SA, Peters D, van Grinsven MQ, Goldbach R (1992) Characterization of RNA-mediated resistance to tomato spotted wilt virus in transgenic tobacco plants. Biotechnology 10:1133–1137
De Wilde C, Podevin N, Windels P, Depicker A (2001) Silencing of antibody genes in plants with single-copy transgene inserts as a result of gene dosage effects. Mol Genet Genomics 265:647–653
Dennis ES, Peacock WJ (2007) Epigenetic regulation of flowering. Curr Opin Plant Biol 10:520–527
Di Nicola-Negri E, Brunetti A, Tavazza M, Ilardi V (2005) Hairpin RNA-mediated silencing of plum pox virus P1 and HC-Pro genes for efficient and predictable resistance to the virus. Transgenic Res 14:989–994
Ding SW, Voinnet O (2007) Antiviral immunity directed by small RNAs. Cell 130:413–426
Eamens A, Wang MB, Smith NA, Waterhouse PM (2008a) RNA silencing in plants: yesterday, today, and tomorrow. Plant Physiol 147:456–468
Eamens A, Vaistij FE, Jones L (2008b) NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis. Plant J 55:596–606
Eike MC, Mercy IS, Aalen RB (2005) Transgene silencing may be mediated by aberrant sense promoter sequence transcripts generated from cryptic promoters. Cell Mol Life Sci 62:3080–3091
Elmayan T, Vaucheret H (1996) Expression of single copies of a strongly expressed 35S transgene can be silenced post-transcriptionally. Plant J 9:787–797
Elmayan T, Balzergue S, Beon F, Bourdon V, Daubremet J, Guenet Y, Mourrain P, Palauqui JC, Vernhettes S, Vialle T, Wostrikoff K, Vaucheret H (1998) Arabidopsis mutants impaired in cosuppression. Plant Cell 10:1747–1758
Escobar MA, Civerolo EL, Summerfelt KR, Dandekar AM (2001) RNAi-mediated oncogene silencing confers resistance to crown gall tumorigenesis. Proc Natl Acad Sci USA 98:13437–13442
Fairbairn DJ, Cavallaro AS, Bernard M, Mahalinga-Iyer J, Graham MW, Botella JR (2007) Host-delivered RNAi: an effective strategy to silence genes in plant parasitic nematodes. Planta 226:1525–1533
Finnegan EJ, Sheldon CC, Jardinaud F, Peacock WJ, Dennis ES (2004) A cluster of Arabidopsis genes with a coordinate response to an environmental stimulus. Curr Biol 14:911–916
Fire A, Xu SQ, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811
Fischer U, Kuhlmann M, Pecinka A, Schmidt R, Mette MF (2008) Local DNA features affect RNA-directed transcriptional gene silencing and DNA methylation. Plant J 53:1–10
Fojtova M, Bleys A, Bedrichova J, Van HH, Krizova K, Depicker A, Kovarik A (2006) The trans-silencing capacity of invertedly repeated transgenes depends on their epigenetic state in tobacco. Nucleic Acids Res 34:2280–2293
Francis KE, Spiker S (2005) Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T-DNA integrations. Plant J 41:464–477
Fusaro AF, Matthew L, Smith NA, Curtin SJ, Dic-Hagan J, Ellacott GA, Watson JM, Wang MB, Brosnan C, Carroll BJ, Waterhouse PM (2006) RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep 7:1168–1175
Gendler K, Paulsen T, Napoli C (2008) ChromDB: the chromatin database. Nucleic Acids Res 36:D298–D302
Girard A, Hannon GJ (2008) Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol 18:136–148
Grant-Downton RT, Dickinson HG (2005) Epigenetics and its implications for plant biology. 1. The epigenetic network in plants. Ann Bot 96:1143–1164
Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286:950–952
Hebert CG, Valdes JJ, Bentley WE (2008) Beyond silencing -- engineering applications of RNA interference and antisense technology for altering cellular phenotype. Curr Opin Biotechnol 19:500–505
Helliwell CA, Waterhouse PM (2005) Constructs and methods for hairpin RNA-mediated gene silencing in plants. RNA Interfer 392:24–35
Henderson IR, Jacobsen SE (2007) Epigenetic inheritance in plants. Nature 447:418–424
Hobbs SL, Kpodar P, DeLong CM (1990) The effect of T-DNA copy number, position and methylation on reporter gene expression in tobacco transformants. Plant Mol Biol 15:851–864
Hollick JB (2008) Sensing the epigenome. Trends Plant Sci 13:398–404
Houmard NM, Mainville JL, Bonin CP, Huang S, Luethy MH, Malvar TM (2007) High-lysine corn generated by endosperm-specific suppression of lysine catabolism using RNAi. Plant Biotechnol J 5:605–614
Huang X, Han Y, Wiig A, McMillan J, Jones T, Talton W, Dong J, Offenheiser M, Ren P, Ascenzi R, Hill S, Zhen R, Chaudhuri S (2006) Engineering resistance against plant-parasitic nematodes. J Nematol 38:275
Huettel B, Kanno T, Daxinger L, Bucher E, van der Winden J, Matzke AJM, Matzke M (2007) RNA-directed DNA methylation mediated by DRD1 and Pol IVb: A versatile pathway for transcriptional gene silencing in plants. Biochim Biophys Acta -- Gene Struct Express 1769:358–374
Jakowitsch J, Papp I, Moscone EA, van der Winden J, Matzke M, Matzke AJM (1999) Molecular and cytogenetic characterization of a transgene locus that induces silencing and methylation of homologous promoters in trans. Plant J 17:131–140
Jan FJ, Fagoaga C, Pang SZ, Gonsalves D (2000) A single chimeric transgene derived from two distinct viruses confers multi-virus resistance in transgenic plants through homology-dependent gene silencing. J Gen Virol 81:2103–2109
Jiang D, Yang W, He Y, Amasino RM (2007) Arabidopsis relatives of the human lysine-specific demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell 19:2975–2987
Jin H, Vacic V, Girke T, Lonardi S, Zhu JK (2008) Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 9:6
Jones JDG, Gilbert DE, Grady KL, Jorgensen RA (1987) T-DNA structure and gene expression in petunia plants transformed by Agrobacterium tumefaciens C58 derivatives. Mol Gen Genet 207:478–485
Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53
Jorgensen RA (2003) Sense cosuppression in plants: past, present, and future. In: Hannon GJ (ed) RNAi: a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp 5–21
Jorgensen RA, Cluster PD, English J, Que Q, Napoli CA (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
Jorgensen RA, Doetsch N, Muller A, Que Q, Gendler K, Napoli CA (2007) A paragenetic perspective on integration of RNA silencing into the epigenome and its role in the biology of higher plants. Cold Spring Harbor Symp Quant Biol 71:481–485
Jung KH, An G, Ronald PC (2008) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat Rev Genet 9:91–101
Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJM (2005) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 37:761–765
Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A Jr, Zhu JK, Staskawicz BJ, Jin H (2006) A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci USA 103:18002–18007
Kato M, Takashima K, Kakutani T (2004) Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana. Genetics 168:961–969
Kim SI, Veena V, Gelvin SB (2007) Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions. Plant J 51:779–791
Kinoshita T, Miura A, Choi YH, Kinoshita Y, Cao XF, Jacobsen SE, Fischer RL, Kakutani T (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303:521–523
Levin JS, Thompson WF, Csinos AS, Stephenson MG, Weissinger AK (2005) Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to tomato spotted wilt virus in transgenic tobacco. Transgenic Res 14:193–206
Lindbo JA, Dougherty WG (2005) Plant pathology and RNAi: a brief history. Annu Rev Phytopathol 43:191–204
Lippman Z, May B, Yordan C, Singer T, Martienssen R (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 1:E67
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476
Lunerova-Bedrichova J, Bleys A, Fojtova M, Khaitova L, Depicker A, Kovarik A (2008) Trans-generation inheritance of methylation patterns in a tobacco transgene following a post-transcriptional silencing event. Plant J 54:1049–1062
Luo KM, Harding SA, Tsai CJ (2008) A modified T-vector for simplified assembly of hairpin RNAi constructs. Biotechnol Lett 30:1271–1274
Ma C, Mitra A (2002) Intrinsic direct repeats generate consistent post-transcriptional gene silencing in tobacco. Plant J 31:37–49
Mallory AC, Elmayan T, Vaucheret H (2008) MicroRNA maturation and action -- the expanding roles of ARGONAUTEs. Curr Opin Plant Biol 11:560–566
Mao YB, Cai WJ, Wang JW, Hong GJ, Tao XY, Wang LJ, Huang YP, Chen XY (2007) Silencing a cotton bollworm P450 monooxygenase gene by plant-mediated RNAi impairs larval tolerance of gossypol. Nat Biotechnol 25:1307–1313
Matzke AJ, Matzke MA (1998) Position effects and epigenetic silencing of plant transgenes. Curr Opin Plant Biol 1:142–148
Matzke MA, Primig M, Trnovsky J, Matzke AJ (1989) Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants. EMBO J 8:643–649
Matzke MA, Aufsatz W, Kanno T, Mette MF, Matzke AJ (2002) Homology-dependent gene silencing and host defense in plants. Adv Genet 46:235–275
Matzke MA, Kanno T, Huettel B, Daxinger L, Matzke AJM (2007) Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 10:512–519
McGinnis K, Chandler V, Cone K, Kaeppler H, Kaeppler S, Kerschen A, Pikaard C, Richards E, Sidorenko L, Smith T, Springer N, Wulan T (2005) Transgene-induced RNA interference as a tool for plant functional genomics. RNA Interfer 392:1–24
Mette MF, van der Winden J, Matzke MA, Matzke AJ (1999) Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J 18:241–248
Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJ (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J 19: 5194–5201
Meyer S, Nowak K, Sharma VK, Schulze J, Mendel RR, Hansch R (2004) Vectors for RNAi technology in poplar. Plant Biol 6:100–103
Meza TJ, Stangeland B, Mercy IS, Skarn M, Nymoen DA, Berg A, Butenko MA, Hakelien AM, Haslekas C, Meza-Zepeda LA, Aalen RB (2002) Analyses of single-copy Arabidopsis T-DNA-transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing. Nucleic Acids Res 30:4556–4566
Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45:490–495
Mlotshwa S, Pruss GJ, Vance V (2008) Small RNAs in viral infection and host defense. Trends Plant Sci 13:375–382
Mlynarova L, Loonen A, Heldens J, Jansen RC, Keizer P, Stiekema WJ, Nap JP (1994) Reduced position effect in mature transgenic plants conferred by the chicken lysozyme matrix-associated region. Plant Cell 6:417–426
Mlynarova L, Jansen RC, Conner AJ, Stiekema WJ, Nap JP (1995) The MAR-mediated reduction in position effect can be uncoupled from copy number-dependent expression in transgenic plants. Plant Cell 7:599–609
Mourrain P, van Blokland R, Kooter JM, Vaucheret H (2007) A single transgene locus triggers both transcriptional and post-transcriptional silencing through double-stranded RNA production. Planta 225:365–379
Muller AE (2006) Applications of RNA interference in transgenic plants. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour 1:1–13
Muller AE, Wassenegger M (2004) Control and silencing of transgene expression. In: Christou PKH (ed) Handbook of plant biotechnology. Wiley, Chichester, pp 291–330
Muskens MW, Vissers AP, Mol JN, Kooter JM (2000) Role of inverted DNA repeats in transcriptional and post-transcriptional gene silencing. Plant Mol Biol 43:243–260
Nagaya S, Kato K, Ninomiya Y, Horie R, Sekine M, Yoshida K, Shinmyo A (2005) Expression of randomly integrated single complete copy transgenes does not vary in Arabidopsis thaliana. Plant Cell Physiol 46:438–444
Obbard DJ, Gordon KH, Buck AH, Jiggins FM (2009) The evolution of RNAi as a defence against viruses and transposable elements. Philos Trans R Soc Lond B Biol Sci 364:99–115
Ogita S, Yamaguchi Y, Koizumi N, Sano H (2003) Supression of theobromine synthase gene by RNAi in coffee plants. Plant Cell Physiol 44:S88
Ogita S, Uefuji H, Morimoto M, Sano H (2004) Application of RNAi to confirm theobromine as the major intermediate for caffeine biosynthesis in coffee plants with potential for construction of decaffeinated varieties. Plant Mol Biol 54:931–941
Ossowski S, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53:674–690
Ostergaard L, Yanofsky MF (2004) Establishing gene function by mutagenesis in Arabidopsis thaliana. Plant J 39:682–696
Ow DW (2002) Recombinase-directed plant transformation for the post-genomic era. Plant Mol Biol 48:183–200
Petersen K, Leah R, Knudsen S, Cameron-Mills V (2002) Matrix attachment regions (MARs) enhance transformation frequencies and reduce variance of transgene expression in barley. Plant Mol Biol 49:45–58
Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 10:645–652
Pikaard CS, Haag JR, Ream T, Wierzbicki AT (2008) Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 13:390–397
Price DRG, Gatehouse JA (2008) RNAi-mediated crop protection against insects. Trends Biotechnol 26:393–400
Prins M, Laimer M, Noris E, Schubert J, Wassenegger M, Tepfer M (2008) Strategies for antiviral resistance in transgenic plants. Mol Plant Pathol 9:73–83
Que Q, Wang HY, English JJ, Jorgensen RA (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
Ramachandran V, Chen X (2008) Small RNA metabolism in Arabidopsis. Trends Plant Sci 13:368–374
Rommens CM, Haring MA, Swords K, Davies HV, Belknap WR (2007) The intragenic approach as a new extension to traditional plant breeding. Trends Plant Sci 12:397–403
Rommens CM, Yan H, Swords K, Richael C, Ye JS (2008) Low-acrylamide French fries and potato chips. Plant Biotechnol J 6:843–853
Schubert D, Lechtenberg B, Forsbach A, Gils M, Bahadur S, Schmidt R (2004) Silencing in Arabidopsis T-DNA transformants: the predominant role of a gene-specific RNA sensing mechanism versus position effects. Plant Cell 16:2561–2572
Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121–1133
Segal G, Song RT, Messing J (2003) A new opaque variant of maize by a single dominant RNA-interference-inducing transgene. Genetics 165:387–397
Sels J, Delaure SL, Aerts AM, Proost P, Cammue BPA, De Bolle MFC (2007) Use of a PTGS-MAR expression system for efficient in planta production of bioactive Arabidopsis thaliana plant defensins. Transgenic Res 16:531–538
Sindhu AS, Maier TR, Mitchum MG, Hussey RS, Davis EL, Baum TJ (2009) Effective and specific in planta RNAi in cyst nematodes: expression interference of four parasitism genes reduces parasitic success. J Exp Bot 60:315–324
Slade AJ, Knauf VC (2005) TILLING moves beyond functional genomics into crop improvement. Transgenic Res 14:109–115
Smith NA, Singh SP, Wang MB, Stoutjesdijk PA, Green AG, Waterhouse PM (2000) Gene expression -- total silencing by intron-spliced hairpin RNAs. Nature 407:319–320
Soppe WJ, Jacobsen SE, Onso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6:791–802
Srivastava V, Riza-Nieto M, Wilson AJ (2004) Cre-mediated site-specific gene integration for consistent transgene expression in rice. Plant Biotechnol J 2:169–179
Sung S, Amasino RM (2005) Remembering winter: toward a molecular understanding of vernalization. Annu Rev Plant Biol 56:491–508
Sunilkumar G, Campbell LM, Puckhaber L, Stipanovic RD, Rathore KS (2006) Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol. Proc Natl Acad Sci USA 103:18054–18059
Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C (2007) Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC. Proc Natl Acad Sci USA 104:3633–3638
Taliansky M, Kim SH, Mayo MA, Kalinina NO, Fraser G, McGeachy KD, Barker H (2004) Escape of a plant virus from amplicon-mediated RNA silencing is associated with biotic or abiotic stress. Plant J 39:194–205
Tang GL, Galili G, Zhuang X (2007) RNAi and microRNA: breakthrough technologies for the improvement of plant nutritional value and metabolic engineering. Metabolomics 3:357–369
Townsend BJ, Llewellyn DJ (2007) Reduced terpene levels in cottonseed add food to fiber. Trends Biotechnol 25:239–241
Tzfira T, White C (2005) Towards targeted mutagenesis and gene replacement in plants. Trends Biotechnol 23:567–569
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 -- Life Sci 316:1471–1483
Vaucheret H, Elmayan T, Mourrain P, Palauqui JC (1996) Analysis of a tobacco transgene locus that triggers both transcriptional and post-transcriptional silencing. V.E. Russo, R.A. Martienssen, and A.D. Riggs (eds) Cold Spring Harbor Laboratory, pp. 403–414
Voinnet O (2008) Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci 13:317–328
Wang H, Chua NH, Wang XJ (2006) Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biol 7:R92
Wang MB, Waterhouse PM (2000) High-efficiency silencing of a beta-glucuronidase gene in rice is correlated with repetitive transgene structure but is independent of DNA methylation. Plant Mol Biol 43:67–82
Wang XJ, Gaasterland T, Chua NH (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol 6:R30
Warthmann N, Chen H, Ossowski S, Weigel D, Herve P (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS ONE 3:e1829
Wassenegger M, Krczal G (2006) Nomenclature and functions of RNA-directed RNA polymerases. Trends Plant Sci 11:142–151
Waterhouse PM, Graham HW, Wang MB (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
Wesley SV, Helliwell CA, Smith NA, Wang MB, Rouse DT, Liu Q, Gooding PS, Singh SP, Abbott D, Stoutjesdijk PA, Robinson SP, Gleave AP, Green AG, Waterhouse PM (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J 27:581–590
Wielopolska A, Townley H, Moore I, Waterhouse P, Helliwell C (2005) A high-throughput inducible RNAi vector for plants. Plant Biotechnol J 3:583–590
Wierzbicki AT, Haag JR, Pikaard CS (2008) Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135:635–648
Wu XL, Hou WC, Wang MM, Zhu XP, Li F, Zhang JD, Li XZ, Guo XQ (2008) RNA silencing-mediated resistance is related to biotic/abiotic stresses and cellular RdRp expression in transgenic tobacco plants. BMB Rep 41:376–381
Xu X, Zhu D, Zhao Q, Ao G, Ma C, Yu J (2009) RNA silencing mediated by direct repeats in maize: a potential tool for functional genomics. Mol Biotechnol 41:213–223
Yadav BC, Veluthambi K, Subramaniam K (2006) Host-generated double stranded RNA induces RNAi in plant-parasitic nematodes and protects the host from infection. Mol Biochem Parasitol 148:219–222
Yan H, Chretien R, Ye J, Rommens CM (2006) New construct approaches for efficient gene silencing in plants. Plant Physiol 141:1508–1518
Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X, Cao X (2008) Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet 4:e1000056
Zhang J, Lu L, Ji L, Yang G, Zheng C (2009) Functional characterization of a tobacco matrix attachment region-mediated enhancement of transgene expression. Transgenic Res 18:377–385
Zilberman D (2008) The evolving functions of DNA methylation. Curr Opin Plant Biol 11:554–559
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Müller, A.E. (2010). Gene Silencing in Plants: Transgenes as Targets and Effectors. In: Kempken, F., Jung, C. (eds) Genetic Modification of Plants. Biotechnology in Agriculture and Forestry, vol 64. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02391-0_5
Download citation
DOI: https://doi.org/10.1007/978-3-642-02391-0_5
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02390-3
Online ISBN: 978-3-642-02391-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)