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Bioinformatics Tools for Achieving Better Gene Silencing in Plants

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Plant Gene Silencing

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

Abstract

RNA interference (RNAi) is one of the most popular and effective molecular technologies for knocking down the expression of an individual gene of interest in living organisms. Yet the technology still faces the major issue of nonspecific gene silencing, which can compromise gene functional characterization and the interpretation of phenotypes associated with individual gene knockdown. Designing an effective and target-specific small interfering RNA (siRNA) for induction of RNAi is therefore the major challenge in RNAi-based gene silencing. A ‘good’ siRNA molecule must possess three key features: (a) the ability to specifically silence an individual gene of interest, (b) little or no effect on the expressions of unintended siRNA gene targets (off-target genes), and (c) no cell toxicity. Although several siRNA design and analysis algorithms have been developed, only a few of them are specifically focused on gene silencing in plants. Furthermore, current algorithms lack a comprehensive consideration of siRNA specificity, efficacy, and nontoxicity in siRNA design, mainly due to lack of integration of all known rules that govern different steps in the RNAi pathway. In this review, we first describe popular RNAi methods that have been used for gene silencing in plants and their serious limitations regarding gene-silencing potency and specificity. We then present novel, rationale-based strategies in combination with computational and experimental approaches to induce potent, specific, and nontoxic gene silencing in plants.

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References

  1. Rana TM (2007) Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 8(1):23–36

    Article  CAS  PubMed  Google Scholar 

  2. Horn T, Sandmann T, Fischer B et al (2011) Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat Methods 8(4):341–346

    Article  CAS  PubMed  Google Scholar 

  3. Gunsalus KC, Rhrissorrakrai K (2011) Networks in Caenorhabditis elegans. Curr Opin Genet Dev 21(6):787–798

    Article  CAS  PubMed  Google Scholar 

  4. Duan CG, Wang CH, Guo HS (2012) Application of RNA silencing to plant disease resistance. Silence 3(1):5

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Senthil-Kumar M, Mysore KS (2011) Virus-induced gene silencing can persist for more than 2 years and also be transmitted to progeny seedlings in Nicotiana benthamiana and tomato. Plant Biotechnol J 9(7):797–806

    Article  CAS  PubMed  Google Scholar 

  6. Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25(7):2383–2399

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Ahmed F, Kaundal R, Raghava GP (2013) PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. BMC Bioinform 14(Suppl 14):S9

    Article  Google Scholar 

  8. Ahmed F, Ansari H, Raghava G (2009) Prediction of guide strand of microRNAs from its sequence and secondary structure. BMC Bioinform 10(1):105

    Article  Google Scholar 

  9. Wilson RC, Doudna JA (2013) Molecular mechanisms of RNA interference. Annu Rev Biophys 42:217–239

    Article  CAS  PubMed  Google Scholar 

  10. Hilson P, Allemeersch J, Altmann T et al (2004) Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res 14(10B):2176–2189

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Wielopolska A, Townley H, Moore I et al (2005) A high-throughput inducible RNAi vector for plants. Plant Biotechnol J 3(6):583–590

    Article  CAS  PubMed  Google Scholar 

  12. Schwab R, Ossowski S, Riester M et al (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18(5):1121–1133

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Ramegowda V, Senthil-kumar M, Udayakumar M et al (2013) A high-throughput virus-induced gene silencing protocol identifies genes involved in multi-stress tolerance. BMC Plant Biol 13:193

    Article  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  16. Lu R, Martin-Hernandez AM, Peart JR et al (2003) Virus-induced gene silencing in plants. Methods 30(4):296–303

    Article  CAS  PubMed  Google Scholar 

  17. Lange M, Yellina AL, Orashakova S et al (2013) Virus-induced gene silencing (VIGS) in plants: an overview of target species and the virus-derived vector systems. Methods Mol Biol 975:1–14

    Article  CAS  PubMed  Google Scholar 

  18. Senthil-Kumar M, Mysore KS (2011) New dimensions for VIGS in plant functional genomics. Trends Plant Sci 16(12):656–665

    Article  CAS  PubMed  Google Scholar 

  19. Thareau V, Dehais P, Serizet C et al (2003) Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics 19(17):2191–2198

    Article  CAS  PubMed  Google Scholar 

  20. Naito, Y., Yamada, T., Matsumiya, et al. (2005) dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. Nucleic Acids Res 33(Web Server issue), W589-91.

    Google Scholar 

  21. Xu P, Zhang Y, Kang L et al (2006) Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol 142(2):429–440

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115(2):209–216

    Article  CAS  PubMed  Google Scholar 

  23. Schwarz DS, Hutvagner G, Du T et al (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115(2):199–208

    Article  CAS  PubMed  Google Scholar 

  24. Reynolds A, Leake D, Boese Q et al (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22(3):326–330

    Article  CAS  PubMed  Google Scholar 

  25. Hsieh AC, Bo R, Manola J et al (2004) A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res 32(3):893–901

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Ui-Tei K, Naito Y, Takahashi F et al (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res 32(3):936–948

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Amarzguioui M, Prydz H (2004) An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 316(4):1050–1058

    Article  CAS  PubMed  Google Scholar 

  28. Takasaki S (2013) Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques. Methods Mol Biol 942:17–55

    Article  CAS  PubMed  Google Scholar 

  29. Kaundal R, Saini R, Zhao PX (2010) Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis. Plant Physiol 154(1):36–54

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Rashid M, Saha S, Raghava GP (2007) Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs. BMC Bioinform 8:337

    Article  Google Scholar 

  31. Ahmed F, Kumar M, Raghava GP (2009) Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies. Silico Biol 9(3):135–148

    CAS  Google Scholar 

  32. Rashid M, Ramasamy S, Raghava GP (2010) A simple approach for predicting protein-protein interactions. Curr Protein Pept Sci 11(7):589–600

    Article  CAS  PubMed  Google Scholar 

  33. Huesken D, Lange J, Mickanin C et al (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol 23(8):995–1001

    Article  CAS  PubMed  Google Scholar 

  34. Ahmed F, Raghava GPS (2011) Designing of highly effective complementary and mismatch siRNAs for silencing a gene. PLoS One 6(8):e23443

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Matveeva O, Nechipurenko Y, Rossi L et al (2007) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res 35(8):e63

    Article  PubMed Central  PubMed  Google Scholar 

  36. Ichihara M, Murakumo Y, Masuda A et al (2007) Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Res 35(18):e123

    Article  PubMed Central  PubMed  Google Scholar 

  37. Jackson AL, Bartz SR, Schelter J et al (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21(6):635–637

    Article  CAS  PubMed  Google Scholar 

  38. Tyagi A, Ahmed F, Thakur N et al (2011) HIVsirDB: a database of HIV inhibiting siRNAs. PLoS One 6(10):e25917

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  39. Ahmed F, Ansari JA, Ansari ZE et al (2014) A molecular bridge: connecting type 2 diabetes and Alzheimer’s disease. CNS Neurol Disord Drug Targets 13(2):312–321

    Article  CAS  PubMed  Google Scholar 

  40. Malefyt A, Angart P, Chan C et al (2012) siRNA therapeutic design: tools and challenges. In: Mallick B, Ghosh Z (eds) Regulatory RNAs. Springer, Berlin, pp 475–503

    Chapter  Google Scholar 

  41. Jackson AL, Burchard J, Schelter J et al (2006) Widespread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity. RNA 12(7):1179–1187

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Birmingham A, Anderson EM, Reynolds A et al (2006) 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3(3):199–204

    Article  CAS  PubMed  Google Scholar 

  43. Du Q, Thonberg H, Wang J et al (2005) A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites. Nucleic Acids Res 33(5):1671–1677

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Dahlgren C, Zhang HY, Du Q et al (2008) Analysis of siRNA specificity on targets with double-nucleotide mismatches. Nucleic Acids Res 36(9):e53

    Article  PubMed Central  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  46. Naito Y, Yamada T, Ui-Tei K et al (2004) siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. Nucleic Acids Res 32(Web Server issue):W124–W129

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Grimm D, Streetz KL, Jopling CL et al (2006) Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441(7092):537–541

    Article  CAS  PubMed  Google Scholar 

  48. Judge AD, Sood V, Shaw JR et al (2005) Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol 23(4):457–462

    Article  CAS  PubMed  Google Scholar 

  49. Hornung V, Guenthner-Biller M, Bourquin C et al (2005) Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med 11(3):263–270

    Article  CAS  PubMed  Google Scholar 

  50. Alder MN, Dames S, Gaudet J et al (2003) Gene silencing in Caenorhabditis elegans by transitive RNA interference. RNA 9(1):25–32

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  51. Moissiard G, Parizotto EA, Himber C et al (2007) 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 13(8):1268–1278

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Vazquez F, Hohn T (2013) Biogenesis and biological activity of secondary siRNAs in plants. Scientifica (Cairo) 2013:783253

    PubMed Central  Google Scholar 

  53. Saumet A, Lecellier C-H (2006) Anti-viral RNA silencing: do we look like plants? Retrovirology 3(1):3

    Article  PubMed Central  PubMed  Google Scholar 

  54. Fedorov Y, Anderson EM, Birmingham A et al (2006) Off-target effects by siRNA can induce toxic phenotype. RNA 12(7):1188–1196

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  55. Hausser J, Landthaler M, Jaskiewicz L et al (2009) Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res 19(11):2009–2020

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  56. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(Suppl 2):W155–W159

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  57. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31(13):3429–3431

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  58. Marco A, Macpherson JI, Ronshaugen M et al (2012) MicroRNAs from the same precursor have different targeting properties. Silence 3(1):8

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  59. Krol J, Sobczak K, Wilczynska U et al (2004) Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem 279(40):42230–42239

    Article  CAS  PubMed  Google Scholar 

  60. Vert JP, Foveau N, Lajaunie C et al (2006) An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinform 7:520

    Article  Google Scholar 

  61. Jackson AL, Linsley PS (2010) Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov 9(1):57–67

    Article  CAS  PubMed  Google Scholar 

  62. Caffrey DR, Zhao J, Song Z et al (2011) siRNA off-target effects can be reduced at concentrations that match their individual potency. PLoS One 6(7):e21503

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. Saxena S, Jonsson ZO, Dutta A (2003) Small RNAs with imperfect match to endogenous mRNA repress translation. Implications for off-target activity of small inhibitory RNA in mammalian cells. J Biol Chem 278(45):44312–44319

    Article  CAS  PubMed  Google Scholar 

  64. Tafer H, Ameres SL, Obernosterer G et al (2008) The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26(5):578–583

    Article  CAS  PubMed  Google Scholar 

  65. Mysara M, Garibaldi JM, Elhefnawi M (2011) MysiRNA-designer: a workflow for efficient siRNA design. PLoS One 6(10):e25642

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  66. Yamada T, Morishita S (2004) Computing highly specific and noise-tolerant oligomers efficiently. J Bioinform Comput Biol 2(1):21–46

    Article  CAS  PubMed  Google Scholar 

  67. Park YK, Park SM, Choi YC et al (2008) AsiDesigner: exon-based siRNA design server considering alternative splicing. Nucleic Acids Res 36(Web Server issue):W97–W103

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  68. Ui-Tei K, Naito Y, Nishi K et al (2008) Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect. Nucleic Acids Res 36(22):7100–7109

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  69. Yamada T, Morishita S (2005) Accelerated off-target search algorithm for siRNA. Bioinformatics 21(8):1316–1324

    Article  CAS  PubMed  Google Scholar 

  70. Naito Y, Yoshimura J, Morishita S et al (2009) siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinform 10:392

    Article  Google Scholar 

  71. Dai X, Zhuang Z, Zhao PX (2011) Computational analysis of miRNA targets in plants: current status and challenges. Brief Bioinform 12(2):115–121

    Article  CAS  PubMed  Google Scholar 

  72. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  73. Bartel B, Bartel DP (2003) MicroRNAs: at the root of plant development? Plant Physiol 132(2):709–717

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  74. Yu Z, Teng X, Bonini NM (2011) Triplet repeat-derived siRNAs enhance RNA-mediated toxicity in a Drosophila model for myotonic dystrophy. PLoS Genet 7(3):e1001340

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  75. Lawlor KT, O’Keefe LV, Samaraweera SE et al (2012) Ubiquitous expression of CUG or CAG trinucleotide repeat RNA causes common morphological defects in a Drosophila model of RNA-mediated pathology. PLoS One 7(6):e38516

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  76. Zhao Z, Guo C, Sutharzan S et al (2014) Genome-wide analysis of tandem repeats in plants and green algae. G3 (Bethesda) 4(1):67–78

    Article  Google Scholar 

  77. Sofola OA, Jin P, Botas J et al (2007) Argonaute-2-dependent rescue of a Drosophila model of FXTAS by FRAXE premutation repeat. Hum Mol Genet 16(19):2326–2332

    Article  CAS  PubMed  Google Scholar 

  78. Krzyzosiak WJ, Sobczak K, Wojciechowska M et al (2012) Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target. Nucleic Acids Res 40(1):11–26

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  79. Ahmed F, Benedito VA, Zhao PX (2011) Mining functional elements in messenger RNAs: overview, challenges, and perspectives. Front Plant Sci 2:84

    Article  PubMed Central  PubMed  Google Scholar 

  80. Silva AT, Nguyen A, Ye C et al (2010) Conjugated polymer nanoparticles for effective siRNA delivery to tobacco BY-2 protoplasts. BMC Plant Biol 10:291

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  81. Vanitharani R, Chellappan P, Fauquet CM (2003) Short interfering RNA-mediated interference of gene expression and viral DNA accumulation in cultured plant cells. Proc Natl Acad Sci U S A 100(16):9632–9636

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  82. Jung HI, Zhai Z, Vatamaniuk OK (2011) Direct transfer of synthetic double-stranded RNA into protoplasts of Arabidopsis thaliana. Methods Mol Biol 744:109–127

    Article  CAS  PubMed  Google Scholar 

  83. Parsons BD, Schindler A, Evans DH et al (2009) A direct phenotypic comparison of siRNA pools and multiple individual duplexes in a functional assay. PLoS One 4(12):e8471

    Article  PubMed Central  PubMed  Google Scholar 

  84. Allen E, Howell MD (2010) miRNAs in the biogenesis of trans-acting siRNAs in higher plants. Semin Cell Dev Biol 21(8):798–804

    Article  CAS  PubMed  Google Scholar 

  85. Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44

    Article  PubMed  Google Scholar 

  86. Allen E, Xie Z, Gustafson AM et al (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121(2):207–221

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  88. Felippes FF, Wang JW, Weigel D (2012) MIGS: miRNA-induced gene silencing. Plant J 70(3):541–547

    Article  PubMed  Google Scholar 

  89. Yi R, Doehle BP, Qin Y et al (2005) Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA 11(2):220–226

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  90. Persengiev SP, Zhu X, Green MR (2004) Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA 10(1):12–18

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  91. Sijen T, Steiner FA, Thijssen KL et al (2007) Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 315(5809):244–247

    Article  CAS  PubMed  Google Scholar 

  92. Chen HM, Chen LT, Patel K et al (2010) 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A 107(34):15269–15274

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  93. Manavella PA, Koenig D, Weigel D (2012) Plant secondary siRNA production determined by microRNA-duplex structure. Proc Natl Acad Sci U S A 109(7):2461–2466

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  94. Buhler M, Moazed D (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14(11):1041–1048

    Article  PubMed  Google Scholar 

  95. Matzke MA, Birchler JA (2005) RNAi-mediated pathways in the nucleus. Nat Rev Genet 6(1):24–35

    Article  CAS  PubMed  Google Scholar 

  96. Volpe TA, Kidner C, Hall IM et al (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297(5588):1833–1837

    Article  CAS  PubMed  Google Scholar 

  97. Weinberg MS, Villeneuve LM, Ehsani A et al (2006) The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12(2):256–262

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Acknowledgment

This work was supported by the National Science Foundation (Grant DBI: 0960897 to P.X.Z.) and The Samuel Roberts Noble Foundation.

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Authors and Affiliations

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

    Firoz Ahmed, Xinbin Dai & Patrick Xuechun Zhao

  2. Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA

    Firoz Ahmed

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  1. Firoz Ahmed
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  2. Xinbin Dai
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  3. Patrick Xuechun Zhao
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Correspondence to Patrick Xuechun Zhao .

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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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Ahmed, F., Dai, X., Zhao, P.X. (2015). Bioinformatics Tools for Achieving Better Gene Silencing in Plants. 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_3

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  • DOI: https://doi.org/10.1007/978-1-4939-2453-0_3

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