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.
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References
Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108
Castanotto D, Rossi JJ (2009) The promises and pitfalls of RNA interference-based therapeutics. Nature 457:426–433
Marguerat S, Bähler J (2010) RNA-seq: from technology to biology. Cell Mol Life Sci 67:569–579
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
Zaratiegui M, Irvine DV, Robert A, Martienssen RA (2007) Noncoding RNAs and gene silencing. Cell 128:763–776
Lorkovic ZJ (2009) Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci 14(4):229–236
Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23:1494–1504
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
Romano N, Macino G (1992) Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 22:3343–3353
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
Hannon GJ (2002) RNA interference. Nature 418(244–251):2002
Kawaji H, Hayashizaki Y (2008) Exploration of Small RNAs. PLoS Genet 4(1):e22
Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655
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
Galun E (2005) RNA silencing in plants. In vitro Cell Dev Biol 41:113–123
YingBo M, XueYi X, XiaoYa C (2009) Are small RNAs a big help to plants? Sci China Ser C 52:212–223
Ali A, Datta SK, Datta K (2010) RNA interference in designing transgenic crops. GM Crops 1–4:207–213
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
Jagtap UB, Gurav RG, Bapat VA (2011) Role of RNAi in plant improvement. Naturwissenschaften 98(6):473–492
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
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
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
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
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
Wanil SH, Sanghera GS, Singh NB (2010) Biotechnology and plant disease control-role of RNA interference. Am J Plant Sci 1:55–68
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
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
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
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
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
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
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
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
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
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
Singh A, Kumar B, Srivastava AK (2011) Metabolic engineering of crops using RNA interference. AsPac J Mol Biol Biotechnol 19:137–148
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
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
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
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
Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45:490–495
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
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
Hannon GJ, Rossi JJ (2004) Unlocking the potential of the human genome with RNA interference. Nature 431:372–378
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
Burnett JC, Rossi JJ (2012) RNA-based therapeutics: current progress and future prospects. Chem Biol 2719(1):60–71
Sullenger BA, Gilboa E (2002) Emerging clinical applications of RNA. Nature 418(11):252–258
Sah DWY (2006) Therapeutic potential of RNA interference for neurological disorders. Life Sci 79:1773–1780
James, W. (2002)Encyclopedia of Analytical Chemistry(2002), R.A. Meyers (Ed.) Copyright JohnWiley & Sons Ltd 2002
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
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
Kole R, Krainer AR, Altman S (2012) RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov 11(2):125–140
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
Tiemann K, Rossi JJ (2009) RNAi-based therapeutics—current status, challenges and prospects. EMBO Mol Med 1:142–151
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
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
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
Bora RS, Gupta D, Mukkur TK, Saini KS (2012) RNA interference therapeutics for cancer: challenges and opportunities. Mol Med Rep 6(1):9–15
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
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
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
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
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
Malonel CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 36:656–668
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
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
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
Win MN, Smolke CD (2008) Higher-order cellular information processing with synthetic RNA devices. Science 322:456–460
Muranaka N, Yokobayashi Y (2010) Posttranscriptional signal integration of engineered riboswitches yields band-pass output. Angew Chem Int Ed Engl 49:4653–4655
Topp S, Gallivan JP (2007) Guiding bacteria with small molecules and RNA. J Am Chem Soc 129:6807–6811
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
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
Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ (2009) Synthetic gene networks that count. Science 324:1199–1202
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
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63
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
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
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
Guo P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol 5(12):833–842
Katz E, Willner I (2004) Integrated nanoparticle–biomolecule hybrid systems: synthesis, properties, and applications. Angew Chem Int Ed 43:6042–6108
Jin S, Ye K (2007) Nanoparticle mediated drug delivery and gene therapy. Biotech Prog 23:32–41
Sato F (2005) RNAi and functional genomics. Plant Biotechnol 22:431–442
Toub N, Malvy C, Fattal E, Couvreur P (2006) Innovative nanotechnologies for the delivery of oligonucleotides and siRNA. Biomed Pharm 60(9):607–620
Belhke MA (2006) Progress towards in vivo use of siRNAs. Mol Ther Apr 13(4):644–670
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
Shen H, Sun T, Ferrari M (2012) Nano vector delivery of siRNA for cancer therapy. Cancer Gene Ther 19:367–373
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
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
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
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Author wishes to thank Indian National Science Academy (INSA), New Delhi, for Senior Scientist position.
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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
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DOI: https://doi.org/10.1007/s40009-012-0102-2