Skip to main content
Log in

Recent Advances in Ribonucleic Acid Interference (RNAi)

  • Review
  • Published:
National Academy Science Letters Aims and scope Submit manuscript

Abstract

Ribonucleic acid (RNA) is a most versatile nucleic acid involves in several cellular metabolic events and plays a significant role in various molecular maneuvers. Recent advances in molecular biology, material sciences and nanotechnology have helped and contributed immensely to understand and decipher RNA’s mechanism as well as exploitations of its noteworthy applications in many biological disciplines. RNA interference (RNAi) is a novel natural phenomenon first reported in plants and later on in other organisms has changed the scenario of RNA research substantially. Considerable progress has been accomplished in plant improvement using RNAi technology. This technology has been judiciously employed in overcoming various deadly human diseases in which effective remedies have been formulated. Protection of genome by RNAi and RNA switches are another focused areas of research currently being pursued vigorously. Additionally, RNA sequencing and RNA technology are emerging as new avenues of investigations currently being studied extensively. Practical demonstrations of the products based on RNAi technology mainly in medicines are continuously increasing indicating its applied feasibility without any doubts. This review highlights these multifaceted activities of this wonderful nucleic acid present in the living organisms.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108

    Article  Google Scholar 

  2. Castanotto D, Rossi JJ (2009) The promises and pitfalls of RNA interference-based therapeutics. Nature 457:426–433

    Article  Google Scholar 

  3. Marguerat S, Bähler J (2010) RNA-seq: from technology to biology. Cell Mol Life Sci 67:569–579

    Article  Google Scholar 

  4. Bhindi R, Fahmy RG, Lowe HC, Chesterman CN, Dass CR, Cairns MJ, Saravolac EG, Sun LQ, Khachigian LM (2007) Am J Pathol 171(4):1079–1088

    Article  Google Scholar 

  5. Zaratiegui M, Irvine DV, Robert A, Martienssen RA (2007) Noncoding RNAs and gene silencing. Cell 128:763–776

    Article  Google Scholar 

  6. Lorkovic ZJ (2009) Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci 14(4):229–236

    Article  Google Scholar 

  7. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23:1494–1504

    Article  Google Scholar 

  8. 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

    Google Scholar 

  9. Romano N, Macino G (1992) Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 22:3343–3353

    Article  Google Scholar 

  10. 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 391:806–811

    Article  Google Scholar 

  11. Hannon GJ (2002) RNA interference. Nature 418(244–251):2002

    Google Scholar 

  12. Kawaji H, Hayashizaki Y (2008) Exploration of Small RNAs. PLoS Genet 4(1):e22

    Article  Google Scholar 

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

    Article  Google Scholar 

  14. Chen T, Heller E, Beronja S, Oshimori N, Stokes N, Fuchs S (2012) An RNA interference screen uncovers a new molecule in stem cell self-renewal term regeneration. Nature 485:104–108

    Article  Google Scholar 

  15. Galun E (2005) RNA silencing in plants. In vitro Cell Dev Biol 41:113–123

    Google Scholar 

  16. YingBo M, XueYi X, XiaoYa C (2009) Are small RNAs a big help to plants? Sci China Ser C 52:212–223

    Google Scholar 

  17. Ali A, Datta SK, Datta K (2010) RNA interference in designing transgenic crops. GM Crops 1–4:207–213

    Article  Google Scholar 

  18. Angaji SA, Hedayati SH, Hosein Poor R, Sanaz Samad Poor S, Shiravil S, Madani S (2010) Application of RNA interference in plants. Plant Omics J 3(3):77–84

    Google Scholar 

  19. Jagtap UB, Gurav RG, Bapat VA (2011) Role of RNAi in plant improvement. Naturwissenschaften 98(6):473–492

    Article  Google Scholar 

  20. Hu Y, Qin F, Huang L, Sun Q, Li C, Zhao Y, Zhou D (2009) Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun 388:266–271

    Article  Google Scholar 

  21. Zhou H, He SJ, Cao Y, Chen T, Du B, Chu C, Zhang J, Chen S (2006) OsGLU1, a putative membrane bound endo-1, 4-b-D-glucanase from rice, affects plant internode elongation. Plant Mol Biol 60:137–151

    Article  Google Scholar 

  22. Schwind N, Zwiebel M, Itaya A, Ding B, Wang M, Krczal G, Wassenegger M (2009) RNAi-mediated resistance to potato spindle tuber viroid in transgenic tomato expressing a viroid hairpin RNA construct. Mol Plant Pathol 10:459–469

    Article  Google Scholar 

  23. Hernández I, Chacón O, Rodriguez R, Portieles R, Pujol YLM, Borrás-Hidalgo O (2009) Black shank resistant tobacco by silencing of glutathione S-transferase. Biochem Biophys Res Commun 387:300–304

    Article  Google Scholar 

  24. Yoder JI, Gunathilake P, Wu B, Tomilova N, Tomilov AA (2009) Engineering host resistance against parasitic weeds with RNA interference. Pest Manag Sci 65:460–466

    Article  Google Scholar 

  25. Wanil SH, Sanghera GS, Singh NB (2010) Biotechnology and plant disease control-role of RNA interference. Am J Plant Sci 1:55–68

    Article  Google Scholar 

  26. Dodo HW, Konan KN, Chen FC, Egnin M, Viquez OM (2008) Alleviating peanut allergy using genetic engineering: the silencing of the immunodominant allergen Ara h 2 leads to its significant reduction and a decrease in peanut allergenicity. Plant Biotech J 6:135–145

    Article  Google Scholar 

  27. Le LQ, Lorenz Y, Scheurer S, Fotisch K, Enrique E, Bartra J, Biemelt S, Vieths S, Sonnewald U (2006) Design of tomato fruits with reduced allergenicity by dsRNAi-mediated inhibition of ns-LTP (Lyc e 3) expression. Plant Biotech J 4:231–242

    Article  Google Scholar 

  28. Regina A, Kosar-Hashemi B, Ling S, Li Z, Rahman S, Morell M (2010) Control of starch branching in barley defined through differential RNAi suppression of starch branching enzyme IIa and IIb. J Exp Bot 61:1469–1482

    Article  Google Scholar 

  29. Gil-Humanes J, Pisto’n F, Hernando A, Alvarez JB, Shewry PR, Barro F (2008) Silencing of g-gliadins by RNA interference (RNAi) in bread wheat. J Cereal Sci 48:565–568

    Article  Google Scholar 

  30. Bapat VA, Trivedi PK, Ghosh A, Sane VA, Ganapathi TR, Nath P (2010) Ripening of fleshy fruit: molecular insight and the role of ethylene. Biotech Adv 28:94–107

    Article  Google Scholar 

  31. Vrebalov J, Pan IL, Arroyo AJM, McQuinn R, Chung M, Poole M, Rose J, Seymour G, Grandillo S, Giovannoni J, Iris VF (2009) Fleshy fruit expansion and ripening are regulated by the tomato shatter proof gene TAGL1. Plant Cell 21:3041–3062

    Article  Google Scholar 

  32. Nakatsuka T, Mishiba KI, Kubota A, Abe Y, Yamamura S, Nakamura N, Tanaka Y, Nishihara M (2010) Genetic engineering of novel flower colour by suppression of anthocyanin modification genes in gentian. J Plant Physiol 167:231–237

    Article  Google Scholar 

  33. Dexter R, Qualley A, Kish CM (2007) Characterization of a petunia acetyltransferase involved in the biosynthesis of the floral volatile isoeugenol. Plant J 49:265–275

    Article  Google Scholar 

  34. Kempe K, Higashi Y, Frick S, Sabarna K, Kutchan TM (2009) RNAi suppression of the morphine biosynthetic gene salAT and evidence of association of pathway enzymes. Phytochemistry 70:579–589

    Article  Google Scholar 

  35. Zhang L, Jing F, Li F, Li M, Wang Y, Wang G, Sun X, Tang K (2009) Development of transgenic Artemisia annua (Chinese wormwood) plants with an enhanced content of artemisinin, an effective Antimalarial drug, by hairpin-RNA mediated gene silencing. Biotechnol Appl Biochem 52:199–207

    Article  Google Scholar 

  36. Singh A, Kumar B, Srivastava AK (2011) Metabolic engineering of crops using RNA interference. AsPac J Mol Biol Biotechnol 19:137–148

    Google Scholar 

  37. Molesini B, Rotino GL, Spena A, Pandolfini T (2009) Expression profile analysis of early fruit development in iaaM-parthenocarpic tomato plants. BMC Res Notes 2:1–7

    Article  Google Scholar 

  38. De Jong M, Wolters-Arts M, Feron R, Mariani C, Vriezen WH (2009) The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development. Plant J 5:160–170

    Article  Google Scholar 

  39. Fujii S, Toriyama K (2008) DCW11, down-regulated gene 11 inCW-type cytoplasmic male sterile rice, encoding mitochondrial protein phosphatase 2C is related to CMS. Plant Cell Physiol 49:633–640

    Article  Google Scholar 

  40. Upadhyay SK, Chandrashekar K, Thakur N, Verma PC, Borgio JF, Singh PK, Tuli R (2011) RNA interference for the control of whiteflies (Bemisia tabaci) by oral route. J Biosci 36:153–161

    Article  Google Scholar 

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

    Article  Google Scholar 

  42. Mansoor S, Amin I, Hussain M, Zafar Y, Briddon RW (2006) Engineering novel traits in plants through RNA interference. Trends Plant Sci 11(11):559–565

    Article  Google Scholar 

  43. Travella S, Klimm TE, Keller B (2006) RNA interference-based gene silencing as an efficient tool for functional genomics in hexaploid bread wheat. Plant Physiol 142:7–20

    Article  Google Scholar 

  44. Hannon GJ, Rossi JJ (2004) Unlocking the potential of the human genome with RNA interference. Nature 431:372–378

    Article  Google Scholar 

  45. Lares MR, Rossi JJ, Dominique L, Ouellet DL (2010) RNAi and small interfering RNAs in human disease therapeutic applications. Trends Biotechnol 28(11):570–579

    Article  Google Scholar 

  46. Burnett JC, Rossi JJ (2012) RNA-based therapeutics: current progress and future prospects. Chem Biol 2719(1):60–71

    Article  Google Scholar 

  47. Sullenger BA, Gilboa E (2002) Emerging clinical applications of RNA. Nature 418(11):252–258

    Article  Google Scholar 

  48. Sah DWY (2006) Therapeutic potential of RNA interference for neurological disorders. Life Sci 79:1773–1780

    Article  Google Scholar 

  49. James, W. (2002)Encyclopedia of Analytical Chemistry(2002), R.A. Meyers (Ed.) Copyright JohnWiley & Sons Ltd 2002

  50. Love RA, Brodsky O, Hickey MJ, Wells PA, Cronin C (2009) Crystal structure of a novel dimeric form of NS5A domain I from hepatitis C virus. J Virol 83:4395–4403

    Article  Google Scholar 

  51. Lee H, Lytton-Jean AKR, Chen Y, Love KT, Park AI, Karagiannis ED, Sehgal A, Querbes W, Zurenko CS, Jayaraman M, Peng CG, Charisse K, Borodovsky A, Manoharan M, Donahoe JS, Truelove J, Nahrendorf M, Langer R, Anderson DG (2012) Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery. Nat Nanotechnol 7(6):389–393. doi:10.1038/nnano.2012.73

    Article  Google Scholar 

  52. Kole R, Krainer AR, Altman S (2012) RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov 11(2):125–140

    Google Scholar 

  53. Guo P, Coban O, Snead NM, Trebley J, Hoeprich S, Guo S, Shu Y (2010) Engineering RNA for targeted siRNA delivery and medical application. Adv Drug Deliv Rev 62:650–666

    Article  Google Scholar 

  54. Tiemann K, Rossi JJ (2009) RNAi-based therapeutics—current status, challenges and prospects. EMBO Mol Med 1:142–151

    Article  Google Scholar 

  55. Strumberg D, Schultheis B, Traugott U, Vank C, Santel A, Keil O, Giese K, Kaufmann J, Drevs J (2012) Phase I clinical development of Atu027, a siRNA formulation targeting PKN3 I patients with advanced solid tumors. Int J Clin Pharm Ther 50:76–78

    Google Scholar 

  56. Meliopoulos VA, Andersen LE, Birrer KF, Simpson KJ, Lowenthal JW, Bean AG, Stambas J, Stewart CR, Tompkins SM, van Beusechem VW, Fraser I, Mhlanga M, Barichievy S, Smith Q, Leake D, Karpilow J, Buck A, Jona G, Tripp RA (2012) Host gene targets for novel influenza therapies elucidated by high throughput RNA interference screens. FASEB J 26(4):1372–1386

    Article  Google Scholar 

  57. Alhoot MA, Wang SM, Sekaran SD (2012) RNA interference mediated inhibition of dengue virus multiplication and entry in HepG2 cells. PLoS ONE 7(3):e34060. doi:10.1371/journal.pone.0034060

    Article  Google Scholar 

  58. Bora RS, Gupta D, Mukkur TK, Saini KS (2012) RNA interference therapeutics for cancer: challenges and opportunities. Mol Med Rep 6(1):9–15

    Google Scholar 

  59. Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P, d’Adda di Fagagna F (2012) Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 488(7410):231–235. doi:10.1038/nature11179

    Article  Google Scholar 

  60. Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ, Joshua-Tor L (2012) The structure of human Argonaute-2 in complex with miR-20a. Cell 150(1):100–110. doi:10.1016/j.cell.2012.05.017

    Article  Google Scholar 

  61. Gagnon KT, Corey DR (2012) Argonaute and the nuclear RNAs: new pathways for RNA-mediated control of gene expression. Nucleic Acid Ther 22(1):3–16. doi:10.1089/nat.2011.0330

    Google Scholar 

  62. Nakanishi K, Weinberg DE, Bartel DP, Patel DJ (2012) Structure of yeast Argonaute with guide RNA. Nature 486(7403):368–374. doi:10.1038/nature11211

    Article  Google Scholar 

  63. Shirayama M, Seth M, Lee H-C, Gu W, Ishidate T, Conte D, Mello CC (2012) piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150(1):65–77. doi:10.1016/j.cell.2012.06.015

    Article  Google Scholar 

  64. Malonel CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 36:656–668

    Article  Google Scholar 

  65. Slotkin KR, Vaugn M, Borges F, Tanurd-zic M, Becker JD, Feijo JA, Martienssen RA (2009) Epigenetic reprogramming and small rna silencing of transposable elements in pollen. Cell 136:461–472

    Article  Google Scholar 

  66. Brennecke JB, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ (2007) Discrete Small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128(6):1089–1103

    Article  Google Scholar 

  67. Chang A, Wolf JJ, Smolke CD (2012) Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 23:1–10

    Article  Google Scholar 

  68. Win MN, Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322:456–460

    Article  Google Scholar 

  69. Muranaka N, Yokobayashi Y (2010) Posttranscriptional signal integration of engineered riboswitches yields band-pass output. Angew Chem Int Ed Engl 49:4653–4655

    Article  Google Scholar 

  70. Topp S, Gallivan JP (2007) Guiding bacteria with small molecules and RNA. J Am Chem Soc 129:6807–6811

    Article  Google Scholar 

  71. Chen YY, Jensen MC, Smolke CD (2010) Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory system. Proc Natl Acad Sci USA 107:8531–8536

    Article  Google Scholar 

  72. Stapleton JA, Endo K, Fujita Y, Hayashi K, Takinoue M, Saito H, Inoue T (2012) Feedback control of protein expression in mammalian cells by tunable synthetic translational inhibition. ACS Synth Biol 1:83–88

    Article  Google Scholar 

  73. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ (2009) Synthetic gene networks that count. Science 324:1199–1202

    Article  Google Scholar 

  74. Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson Bowers JF, Jarosz M, Milos PM (2009) Direct RNA sequencing. Nature 461:814–818

    Article  Google Scholar 

  75. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63

    Article  Google Scholar 

  76. Lipson D, Raz T, Kieu A, Jones DR, Giladi E, Thayer E, Thompson JF, Letovsky S, Milos P, Causey M (2009) Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol 27:652–658

    Article  Google Scholar 

  77. Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulm JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA (2011) A boost for the emerging field of RNA nanotechnology. ACS Nano 5:3405–3418

    Article  Google Scholar 

  78. Chaudhry Q, Castle L (2011) Food applications of nanotechnologies: an overview of opportunities and challenges for developing countries. Trends Food Sci Tech 22:595–603

    Article  Google Scholar 

  79. Guo P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol 5(12):833–842

    Article  Google Scholar 

  80. Katz E, Willner I (2004) Integrated nanoparticle–biomolecule hybrid systems: synthesis, properties, and applications. Angew Chem Int Ed 43:6042–6108

    Article  Google Scholar 

  81. Jin S, Ye K (2007) Nanoparticle mediated drug delivery and gene therapy. Biotech Prog 23:32–41

    Article  Google Scholar 

  82. Sato F (2005) RNAi and functional genomics. Plant Biotechnol 22:431–442

    Article  Google Scholar 

  83. Toub N, Malvy C, Fattal E, Couvreur P (2006) Innovative nanotechnologies for the delivery of oligonucleotides and siRNA. Biomed Pharm 60(9):607–620

    Article  Google Scholar 

  84. Belhke MA (2006) Progress towards in vivo use of siRNAs. Mol Ther Apr 13(4):644–670

    Article  Google Scholar 

  85. Bonoiu AC, Bergey EJ, Ding H, Hu R, Kumar R, Yong KT, Prasad PN, Mahajan S, Picchione KE, Bhattacharjee A, Ignatowski TA (2011) Gold nanorod-siRNA induces efficient in vivo gene silencing in the rat hippocampus. Nanomedicine (Lond) 6(4):617–630

    Article  Google Scholar 

  86. Shen H, Sun T, Ferrari M (2012) Nano vector delivery of siRNA for cancer therapy. Cancer Gene Ther 19:367–373

    Article  Google Scholar 

  87. Kenski DM, Butora G, Willingham A, Cooper AJ, Fu W, Qi N, Soriano F, Davies IW, Flanagan WM (2012) siRNA-optimized modifications for enhanced in vivo activity. Mol Ther Nucleic Acids 1:e5. doi:10.1038/mtna.2011.4

    Article  Google Scholar 

  88. Davis ME, Zuckerman JE, Choi CH, Seligson D, Tolcher A, Alabi CA, Yen Y, Heidel J, Ribas A (2010) Evidence of RNAi in humans from systemically administered siRNA via targeted nanoparticles. Nature 464:1067–1070

    Article  Google Scholar 

  89. Vaishnaw AK, Gollob J, Gamba-Vitalo C, Hutabarat R, Sah D, Meyers R, Fougerolles T, Maraganore J (2010) A status report on RNA therapeutics. Silence 1(14):2–13

    Google Scholar 

Download references

Acknowledgments

Author wishes to thank Indian National Science Academy (INSA), New Delhi, for Senior Scientist position.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to V. A. Bapat.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bapat, V.A. Recent Advances in Ribonucleic Acid Interference (RNAi). Natl. Acad. Sci. Lett. 36, 1–8 (2013). https://doi.org/10.1007/s40009-012-0102-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40009-012-0102-2

Keywords

Navigation