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Advances in Plant Gene Silencing Methods

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Plant Gene Silencing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1287))

Abstract

Understanding molecular mechanisms of transcriptional and posttranscriptional gene silencing pathways in plants over the past decades has led to development of tools and methods for silencing a target gene in various plant species. In this review chapter, both the recent understanding of molecular basis of gene silencing pathways and advances in various widely used gene silencing methods are compiled. We also discuss the salient features of the different methods like RNA interference (RNAi) and virus-induced gene silencing (VIGS) and highlight their advantages and disadvantages. Gene silencing technology is constantly progressing as reflected by rapidly emerging new methods. A succinct discussion on the recently developed methods like microRNA-mediated virus-induced gene silencing (MIR-VIGS) and microRNA-induced gene silencing (MIGS) is also provided. One major bottleneck in gene silencing approaches has been the associated off-target silencing. The other hurdle has been the lack of a universal approach that can be applied to all plants. For example, we face hurdles like incompatibility of VIGS vectors with the host and inability to use MIGS for plant species which are not easily transformable. However, the overwhelming research in this direction reflects the scope for overcoming the short comings of gene silencing technology.

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References

  1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811

    CAS  PubMed  Google Scholar 

  2. Vaucheret H, Fagard M (2001) Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet 17:29–35

    CAS  PubMed  Google Scholar 

  3. Baulcombe DC (2004) RNA silencing in plants. Nature 431:356–363

    CAS  PubMed  Google Scholar 

  4. Mello CC, Conte D Jr (2004) Revealing the world of RNA interference. Nature 2431(7006):338–342

    Google Scholar 

  5. Vaucheret H, Mallory AC, Bartel DP (2006) AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Mol Cell 22:129–136

    CAS  PubMed Central  PubMed  Google Scholar 

  6. Barry C, Faugeron G, Rossignol J-L (1993) Methylation induced premeiotically in Ascobolus: coextension with DNA repeat lengths and effect on transcript elongation. Proc Natl Acad Sci U S A 90:4557–4561

    CAS  PubMed Central  PubMed  Google Scholar 

  7. Selker EU (2002) Repeat-induced gene silencing in fungi. Adv Genet 46:439–450

    CAS  PubMed  Google Scholar 

  8. Selker EU (1997) Epigenetic phenomena in filamentous fungi: useful paradigms or repeat induced confusion? Trends Genet 13:296–301

    CAS  PubMed  Google Scholar 

  9. Waterhouse PM, Wang MB, Lough T (2001) Gene silencing as an adaptive defence against viruses. Nature 411(6839):834–842

    CAS  PubMed  Google Scholar 

  10. Chan SWL, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE (2004) RNA silencing genes control de novo DNA methylation. Science 303:1336

    CAS  PubMed  Google Scholar 

  11. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:E104

    PubMed Central  PubMed  Google Scholar 

  12. Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64:137–159

    CAS  PubMed  Google Scholar 

  13. Napoli C, Lemieux C, Jorgensen R (1990) Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2:279–289

    CAS  PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  15. Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in post-transcriptional gene silencing in plants. Science 286:950–952

    CAS  PubMed  Google Scholar 

  16. Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    CAS  PubMed Central  PubMed  Google Scholar 

  17. Borsani O, Zhu JH, 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

    CAS  PubMed Central  PubMed  Google Scholar 

  18. Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A, Zhu JK, Staskawicz BJ, Jin HL (2006) A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A 103:18002–18007

    CAS  PubMed Central  PubMed  Google Scholar 

  19. Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H (2007) A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev 21(23):3123–3134

    CAS  PubMed Central  PubMed  Google Scholar 

  20. Zubko E, Meyer P (2007) A natural antisense transcript of the Petunia hybrida Sho gene suggests a role for an antisense mechanism in cytokinin regulation. Plant J 52:1131–1139

    CAS  PubMed Central  PubMed  Google Scholar 

  21. Ron M, Saez MA, Williams LE, Fletcher JC, McCormick S (2010) Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. Genes Dev 24:1010–1021

    CAS  PubMed Central  PubMed  Google Scholar 

  22. 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

    PubMed Central  PubMed  Google Scholar 

  23. Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, Alioua A, Himber C, Voinnet O (2010) An endogenous, systemic RNAi pathway in plants. EMBO J 29:1699–1712

    CAS  PubMed Central  PubMed  Google Scholar 

  24. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221

    CAS  PubMed  Google Scholar 

  25. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crete P (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16:69–79

    CAS  PubMed  Google Scholar 

  26. Yoshikawa M, Peragine A, Park MY, Poethig RS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19:2164–2175

    CAS  PubMed Central  PubMed  Google Scholar 

  27. Yelina NE, Smith LM, Jones AM, Patel K, Kelly KA, Baulcombe DC (2010) Putative Arabidopsis THO/TREX mRNA export complex is involved in transgene and endogenous siRNA biosynthesis. Proc Natl Acad Sci U S A 107:13948–13953

    CAS  PubMed Central  PubMed  Google Scholar 

  28. Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, Sullivan CM, Alexander A, Nguyen G, Allen E, Ahn JH, Carrington JC (2008) AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci U S A 105:20055–20062

    CAS  PubMed Central  PubMed  Google Scholar 

  29. Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128–141

    CAS  PubMed  Google Scholar 

  30. Elmayan T, Adenot X, Gissot L, Lauressergues D, Gy I, Vaucheret H (2009) A neomorphic sgs3 allele stabilizing miRNA cleavage products reveals that SGS3 acts as a homodimer. FEBS J 276:835–844

    CAS  PubMed  Google Scholar 

  31. Hernandez-Pinzon N, Schwach F, Studholme DJ, Baulcombe D, Dalmay T (2007) SDE5 the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans-acting endogenous siRNA. Plant J 50:140–148

    CAS  PubMed  Google Scholar 

  32. Gasciolli V, Mallory AC, Bartel DP, Vaucheret H (2005) Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol 15:1494–1500

    CAS  PubMed  Google Scholar 

  33. Xie Z, Allen E, Wilken A, Carrington JC (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci U S A 102:12984–12989

    CAS  PubMed Central  PubMed  Google Scholar 

  34. Nakazawa Y, Hiraguri A, Moriyama H, Fukuhara T (2007) The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway. Plant Mol Biol 63:777–785

    CAS  PubMed  Google Scholar 

  35. de Alba AEM, Elvira-Matelot E, Vaucheret H (2013) Gene silencing in plants: a diversity of pathways. Biochim Biophys Acta 1829:1300–1308

    Google Scholar 

  36. de Felippes FF, Wang JW, Weigel D (2012) MIGS: miRNA induced gene silencing. Plant J 70:541–547

    PubMed  Google Scholar 

  37. Robertson D (2004) VIGS vectors for gene silencing, many targets, many tools. Annu Rev Plant Biol 55:495–519

    CAS  PubMed  Google Scholar 

  38. Senthil-Kumar M, Mysore KS (2010) RNAi in plants: recent developments and applications in agriculture. In: Catalano AJ (ed) Gene silencing: theory, techniques and applications. Nova Science Publishers, Inc., New York, NY

    Google Scholar 

  39. Senthil-Kumar M, Mysore KS (2011) New dimensions for VIGS in plant functional genomics. Trends Plant Sci 16:656–665

    CAS  PubMed  Google Scholar 

  40. Senthil-Kumar M, Mysore KS (2014) Tobacco rattle virus-based virus-induced gene silencing in Nicotiana benthamiana. Nat Protoc 9(7):1549–1562

    CAS  PubMed  Google Scholar 

  41. Filipowicz W, Jaskiewicz L, Kolb FA, Pillai RS (2005) Post-transcriptional gene silencing by siRNAs and miRNAs. Curr Opin Struct Biol 5(3):331–341

    Google Scholar 

  42. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    CAS  PubMed  Google Scholar 

  43. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004) The Drosha DGCR8 complex in primary microRNA processing. Genes Dev 18:3016–3027

    CAS  PubMed Central  PubMed  Google Scholar 

  44. Kim VN (2004) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6(5):376–385

    Google Scholar 

  45. Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136(4):642–655

    CAS  PubMed Central  PubMed  Google Scholar 

  46. 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

    CAS  PubMed Central  PubMed  Google Scholar 

  47. Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ (2007) Targets of RNA-directed DNA methylation. Curr Opin Plant Biol 10:512–519

    CAS  PubMed  Google Scholar 

  48. Pikaard CS, Haag JR, Ream T, Wierzbicki AT (2008) Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 13:390–397

    CAS  PubMed Central  PubMed  Google Scholar 

  49. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 1:204–220

    Google Scholar 

  50. Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE (2007) Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A 104:4536–4541

    CAS  PubMed Central  PubMed  Google Scholar 

  51. Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21:4671–4679

    CAS  PubMed Central  PubMed  Google Scholar 

  52. Yang Z, Ebright YW, Yu B, Chen X (2006) 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 34:667–675

    CAS  PubMed Central  PubMed  Google Scholar 

  53. Zhang H, Zhu J-K (2011) RNA directed DNA methylation. Curr Opin Plant Biol 14(2):142–147

    CAS  PubMed Central  PubMed  Google Scholar 

  54. Kooter JM, Matzke MA, Meyer P (1999) Listening to silent gene: transgene silencing, gene regulation and pathogen control. Trends Plant Sci 4:340–347

    PubMed  Google Scholar 

  55. Wassenegger M, Pelissier T (1998) A model for RNA-mediated gene silencing in higher plants. Plant Mol Biol 37:349–362

    CAS  PubMed  Google Scholar 

  56. Wassenegger M (2000) RNA-directed DNA methylation. Plant Mol Biol 43:203–220

    CAS  PubMed  Google Scholar 

  57. Cao X, Jacobsen SE (2002) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12:1138–1144

    CAS  PubMed  Google Scholar 

  58. Wesley SV, Helliwell CA, Smith NA, Wang M, Rouse DT, Liu Q, Gooding PS, Singh SP (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J 27:581–590

    CAS  PubMed  Google Scholar 

  59. Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45(4):490–495

    CAS  PubMed  Google Scholar 

  60. Himmelbach A, Zierold U, Hensel G, Riechen J, Douchkov D, Schweizer P, Kumlehn J (2007) A set of modular binary vectors for transformation of cereals. Plant Physiol 145:1192–1200

    CAS  PubMed Central  PubMed  Google Scholar 

  61. Xu G, Sui N, Tang Y, Xie K, Lai Y, Liu Y (2010) One-step, zero-background ligation-independent cloning intron-containing hairpin RNA constructs for RNAi in plants. New Phytol 187:240–250

    CAS  PubMed  Google Scholar 

  62. Yan P, Shen W, Gao X, Li X, Zhou P, Duan J (2012) High-Throughput Construction of Intron-Containing Hairpin RNA Vectors for RNAi in Plants. PLoS One 7(5):e38186

    CAS  PubMed Central  PubMed  Google Scholar 

  63. Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2:109–113

    CAS  PubMed  Google Scholar 

  64. Ruiz MT, Voinnet O, Baulcombe DC (1998) Initiation and maintenance of virus-induced gene silencing. Plant Cell 10:937–946

    CAS  PubMed Central  PubMed  Google Scholar 

  65. Liu Y, Schiff M, Marathe R, Dinesh-Kumar SP (2002) Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus. Plant J 30(4):415–429

    CAS  PubMed  Google Scholar 

  66. Lacomme C, Hrubikova K, Hein I (2003) Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats. Plant J 34(4):543–553

    CAS  PubMed  Google Scholar 

  67. Burch-Smith TM, Anderson JC, Martin GB, Dinesh-Kumar SP (2004) Applications and advantages of virus-induced gene silencing for gene function studies in plants. Plant J 39:734–746

    CAS  PubMed  Google Scholar 

  68. Carrillo-Tripp J, Shimada-Beltrán H, Rivera-Bustamante R (2006) Use of geminiviral vectors for functional genomics. Curr Opin Plant Biol 9(2):209–215

    CAS  PubMed  Google Scholar 

  69. de Felippes FF (2013) Downregulation of plant genes with miRNA-induced gene silencing. Methods Mol Biol 942:379–387

    PubMed  Google Scholar 

  70. Benstein RM, Ludewig K, Wulfert S, Wittek S, Gigolashvili T, Frerigmann H, Gierth M, Flügge UI, Krueger S (2013) Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis. Plant Cell 25(12):5011–5029

    CAS  PubMed Central  PubMed  Google Scholar 

  71. Imin N, Mohd-Radzman NA, Ogilvie HA, Djordjevic MA (2013) The peptide-encoding CEP1 gene modulates lateral root and nodule numbers in Medicago truncatula. J Exp Bot 64(17):5395–5409

    CAS  PubMed  Google Scholar 

  72. de Felippes FF, Weigel D (2009) Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173. EMBO Rep 10:264–270

    CAS  PubMed Central  PubMed  Google Scholar 

  73. Dai X, Zhao PX (2008) pssRNAMiner: a plant short small RNA regulatory cascade analysis server. Nucleic Acids Res 1:36

    Google Scholar 

  74. Zhang C, Li G, Zhu S, Zhang S, Fang J (2014) tasiRNAdb: a database of ta-siRNA regulatory pathways. Bioinformatics 30(7):1045–1046

    CAS  PubMed  Google Scholar 

  75. Li F, Orban R, Baker B (2012) SoMART: a web server for plant miRNA, tasiRNA and target gene analysis. Plant J 70(5):891–901

    CAS  PubMed  Google Scholar 

  76. Liang G, He H, Li Y, Yu D (2012) A new strategy for construction of artificial miRNA vectors in Arabidopsis. Planta 235(6):1421–1429

    CAS  PubMed  Google Scholar 

  77. Ossowski S, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53(4):674–690

    CAS  PubMed  Google Scholar 

  78. Warthmann N, Chen H, Ossowski S, Weige D, Hervé P (2008) Highly Specific Gene Silencing by Artificial miRNAs in Rice. PLoS One 3(3):e1829

    PubMed Central  PubMed  Google Scholar 

  79. Khraiwesh B, Ossowski S, Weigel D, Reski R, Frank W (2008) Specific gene silencing by artificial MicroRNAs in Physcomitrella patens: an alternative to targeted gene knockouts. Plant Physiol 148(2):684–693

    CAS  PubMed Central  PubMed  Google Scholar 

  80. Laganà A, Acunzo M, Romano G, Pulvirenti A, Veneziano D, Cascione L, Giugno R, Gasparini P, Shasha D, Ferro AC, Croce M (2014) miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs. Nucleic Acids Res 42:5416. doi:10.1093/nar/gku202

    PubMed Central  PubMed  Google Scholar 

  81. Alvarez JP, Pekker I, Goldshmidt A, Blum E, Amsellem Z, Eshed Y (2006) Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 18:1134–1151

    CAS  PubMed Central  PubMed  Google Scholar 

  82. Molnar A, Bassett A, Thuenemann E, Schwach F, Karkare S, Ossowski S, Weigel D, Baulcombe D (2008) Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. Plant J 58(1):165–174

    Google Scholar 

  83. Niu QW, Lin SS, Reyes JL, Chen KC, Wu HW, Yeh SD, Chua NH (2006) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 24:1420–1428

    CAS  PubMed  Google Scholar 

  84. Qu J, Ye J, Fang R (2007) Artificial microRNA-mediated virus resistance in plants. J Virol 81:6690–6699

    CAS  PubMed Central  PubMed  Google Scholar 

  85. Molesini B, Pii Y, Pandolfini T (2011) Fruit improvement using intra-genesis and artificial microRNA. Trends Biotech 30:80–88

    Google Scholar 

  86. Tang Y, Wang F, Zhao J, Xie K, Hong Y, Liu Y (2010) Virus-based microRNA expression for gene functional analysis in plants. Plant Physiol 153(2):632–641

    CAS  PubMed Central  PubMed  Google Scholar 

  87. Tang Y, Lai Y, Liu Y (2013) Virus-induced gene silencing using artificial miRNAs in Nicotiana benthamiana. Methods Mol Biol 975:99–107

    CAS  PubMed  Google Scholar 

  88. Nowara D, Gay A, Lacomme C, Shaw J, Ridout C, Douchkov D, Hensel G, Kumlehn J, Schweizer P (2010) HIGS: host-induced gene silencing in the obligate biotrophic fungal pathogen Blumeria graminis. Plant Cell 22:3130–3141

    CAS  PubMed Central  PubMed  Google Scholar 

  89. Nunes CC, Gowda M, Sailsbery J, Xue M, Chen F, Brown D, Oh Y, Mitchell TM, Dean RA (2011) Diverse and tissue-enriched small RNAs in the plant pathogenic fungus Magnaporthe oryzae. BMC Genomics 12:1–20

    Google Scholar 

  90. Tinoco ML, Dias BB, Dall’Astta RC, Pamphile JA, Aragao FJ (2010) In vivo trans-specific gene silencing in fungal cells by in planta expression of a double-stranded RNA. BMC Biol 8:1–11

    Google Scholar 

  91. Ghag SB, Shekhawat UK, Ganapathi TR (2014) Host-induced post-transcriptional hairpin RNA-mediated gene silencing of vital fungal genes confers efficient resistance against Fusarium wilt in banana. Plant Biotechnol J 12(5):541–553

    CAS  PubMed  Google Scholar 

  92. Huang G, Allen R, Davis EL, Baum TJ, Hussey RS (2006) Engineering broad root-knot resistance in transgenic plants by RNAi silencing of a conserved and essential root-knot nematode parasitism gene. Proc Natl Acad Sci U S A 103:14,302–14,306

    CAS  Google Scholar 

  93. Katiyar-Agarwal S, Jin H (2010) Role of small RNAs in host–microbe interactions. Annu Rev Phytopathol 48:225–246

    CAS  PubMed Central  PubMed  Google Scholar 

  94. 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

    CAS  PubMed  Google Scholar 

  95. Tomilov AA, Tomilova NB, Wroblewski T, Michelmore R, Yoder JI (2008) Trans-specific gene silencing between host and parasitic plants. Plant J 56:389–397

    CAS  PubMed  Google Scholar 

  96. Westwood JH, Roney JK, Khatibi PA, Stromberg VK (2009) RNA translocation between parasitic plants and their hosts. Pest Manag Sci 65:533–539

    CAS  PubMed  Google Scholar 

  97. Urwin PE, Lilley CJ, Atkinson HJ (2002) Ingestion of double-stranded RNA by preparasitic juvenile cyst nematodes leads to RNA interference. Mol Plant Microbe Interact 15:747–752

    CAS  PubMed  Google Scholar 

  98. 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

    CAS  PubMed  Google Scholar 

  99. Yin C, Jurgenson J, Hulbert S (2010) Development of a host-induced RNAi system in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. Mol Plant Microbe Interact 24:554–561

    Google Scholar 

  100. Khatri M, Rajam MV (2007) Targeting polyamines of Aspergillus nidulans by siRNA specific to fungal ornithine decarboxylase gene. Med Mycol 45:211–220

    CAS  PubMed  Google Scholar 

  101. Klahre U, Crete P, Leuenberger SA, Iglesias VA, Meins F Jr (2002) High molecular weight RNAs and small interfering RNAs induce systemic posttranscriptional gene silencing in plants. Proc Natl Acad Sci U S A 99:11981–11986

    CAS  PubMed Central  PubMed  Google Scholar 

  102. Numata K, Ohtani M, Yoshizumi T, Demura T, Kodama Y (2014) Local gene silencing in plants via synthetic dsRNA and carrier peptide. Plant Biotechnol J 12:1027. doi:10.1111/pbi.12208

    CAS  PubMed  Google Scholar 

  103. Fields GB, Noble RL (1990) Solid phase peptide synthesis utilizing 9-fluorenylmeth-oxycarbonyl amino acids. Int J Pept Protein Res 35:161–214

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  106. Rutherford G, Tanurdzic M, Hasebe M, Banks JA (2004) A systemic gene silencing method suitable for high throughput, reverse genetic analyses of gene function in fern gametophytes. BMC Plant Biol 4:6

    PubMed Central  PubMed  Google Scholar 

  107. Kawai-Toyooka H, Kuramoto C, Orui K, Motoyama K, Kikuchi K, Kanegae T, Wada M (2004) DNA interference: a simple and efficient gene-silencing system for high-throughput functional analysis in the fern Adiantum. Plant Cell Physiol 45:1648–1657

    CAS  PubMed  Google Scholar 

  108. Tsuboi H, Sutoh K, Wada M (2012) Epigenetic memory of DNAi associated with cytosine methylation and histone modification in fern. Plant Signal Behav 7(11):1477–1483

    CAS  PubMed Central  PubMed  Google Scholar 

  109. Jones L, Hamilton AJ, Voinnet O, Thomas CL, Maule AJ, Baulcombe DC (1999) RNA–DNA interactions and DNA methylation in posttranscriptional gene silencing. Plant Cell 11:2291–2301

    CAS  PubMed Central  PubMed  Google Scholar 

  110. Jones L, Ratcliff F, Baulcombe DC (2001) RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol 11:747–757

    CAS  PubMed  Google Scholar 

  111. Otagaki S, Arai M, Takahashi A, Goto K, Hong JS, Masuta C, Kazazawa A (2006) Rapid induction of transcriptional and post-transcriptional gene silencing using a novel Cucumber mosaic virus vector. Plant Biotechnol J 23:259–265

    CAS  Google Scholar 

  112. Kanazawa A, Inaba J, Shimura H, Otagaki S, Tsukahara S, Matsuzawa A, Kim BM, Goto K, Masuta C (2011) Virus-mediated efficient induction of epigenetic modifications of endogenous genes with phenotypic changes in plants. Plant J 65:156–168

    CAS  PubMed  Google Scholar 

  113. Sijen T, Kooter JM (2000) Post-transcriptional gene-silencing: RNAs on the attack or on the defense? Bioessays 22:520–531

    CAS  PubMed  Google Scholar 

  114. 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

    CAS  PubMed Central  PubMed  Google Scholar 

  115. Heilersig BH, Loonen AE, Janssen EM, Wolters AM, Visser RG (2006) Efficiency of transcriptional gene silencing of GBSSI in potato depends on the promoter region that is used in an inverted repeat. Mol Genet Genomics 275:437–449

    CAS  PubMed  Google Scholar 

  116. Cigan AM, Unger-Wallace E, Haug-Collet K (2005) Transcriptional gene silencing as a tool for uncovering gene function in maize. Plant J 43:929–940

    CAS  PubMed  Google Scholar 

  117. Okano Y, Miki D, Shimamoto K (2008) siRNA targeting of endogenous promoters induces DNA methylation but not necessarily gene silencing in rice. Plant J 53:65–77

    CAS  PubMed  Google Scholar 

  118. Eamens A, Wang MB, Smith NA, Waterhouse PM (2008) RNA silencing in plants: yesterday, today, and tomorrow. Plant Physiol 147(2):456–468

    CAS  PubMed Central  PubMed  Google Scholar 

  119. Deng S, Dai H, Arenas C, Wang H, Niu QW, Chua NH (2014) Transcriptional silencing of Arabidopsis endogenes by single-stranded RNAs targeting the promoter region. Plant Cell Physiol 55(4):823–833

    CAS  PubMed  Google Scholar 

  120. Qiu S, Adema CM, Lane T (2005) A computational study of off-target effects of RNA interference. Nucleic Acids Res 33:1834–1847

    CAS  PubMed Central  PubMed  Google Scholar 

  121. Jackson AL, Linsley PS (2004) Noise amidst the silence: off-target effects of siRNAs? Trends Genet 20:521–524

    CAS  PubMed  Google Scholar 

  122. Senthil-Kumar M, Mysore KS (2011) Caveat of RNAi in plants: the off-target effect. Methods Mol Biol 744:13–25

    CAS  PubMed  Google Scholar 

  123. Urano K, Kurihara Y, Seki M, Shinozaki K (2010) ‘Omics’ analyses of regulatory networks in plant abiotic stress responses. Curr Opin Plant Biol 13(2):132–138

    CAS  PubMed  Google Scholar 

  124. Wang Y, Beaith M, Chalifoux M, Ying J, Uchacz T, Sarvas C, Griffiths R, Kuzma M, Wan J, Huang Y (2009) Shoot-specific down-regulation of protein farnesyltransferase (a-subunit) for yield protection against drought in canola. Mol Plant 2:191–200

    CAS  PubMed Central  PubMed  Google Scholar 

  125. Senthil-Kumar M, Udayakumar M (2010) Posttranscriptional gene silencing methods for functional characterization of abiotic stress responsive genes in plants. In: Catalano AJ (ed) Gene silencing: theory, techniques and applications. Nova Science Publishers, Inc., New York, NY

    Google Scholar 

  126. Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21:367–376

    CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. National Institute of Plant Genome Research, Aruna Asaf Ali Marg, #10531, New Delhi, 110067, India

    Prachi Pandey & Muthappa Senthil-Kumar

  2. Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401, USA

    Kirankumar S. Mysore

Authors
  1. Prachi Pandey
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  2. Muthappa Senthil-Kumar
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  3. Kirankumar S. Mysore
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Corresponding author

Correspondence to Muthappa Senthil-Kumar .

Editor information

Editors and Affiliations

  1. Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA

    Kirankumar S. Mysore

  2. National Institute of Plant Genome Research, New Delhi, Delhi, India

    Muthappa Senthil-Kumar

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Pandey, P., Senthil-Kumar, M., Mysore, K.S. (2015). Advances in Plant Gene Silencing Methods. In: Mysore, K., Senthil-Kumar, M. (eds) Plant Gene Silencing. Methods in Molecular Biology, vol 1287. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2453-0_1

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  • DOI: https://doi.org/10.1007/978-1-4939-2453-0_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2452-3

  • Online ISBN: 978-1-4939-2453-0

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