Ortiz-Quintero B

Language: Spanish
References: 93
Page: 412-427
PDF size: 190.88 Kb.

ABSTRACT

RNA interference (RNAi) is a conserved biological mechanism triggered by double-stranded RNA from exogenous (small interfering RNA, siRNA) or endogenous origin (microRNAs, miRNA) that inhibits gene expression at transcriptional level. First discovered as an ancient anti-viral response, RNAi is now recognized as a natural regulatory mechanism for silencing gene expression in eukaryotes and as a powerful tool for investigating gene function. Over the last seven years, RNAi has become a valuable and standardized tool to silence gene expression in almost every scientific research field. This review describes the RNAi as a biological response and as a research tool for silencing gene expression, focusing on primary information required when the RNAi is applying for first time at a laboratory. It provides a basic guide to promote RNAi advantages and a list of available web tools for RNAi application in research field at a laboratory. Information about RNAi-based therapeutics development is included.

REFERENCES

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998; 391: 806-11.

2. Ratcliff F, Harrison BD, Baulcombe DC. A similarity between viral defense and gene silencing in plants. Science 1997; 276: 1558-60.

3. Ruiz MT, Voinnet O, Baulcombe DC. Initiation and maintenance of virus-induced gene silencing. Plant Cell 1998; 10: 937-46.

4. Angell SM, Baulcombe DC. Consistent gene silencing in transgenic plants expressing a replicating potato virus X RNA. EMBO J 1997; 16: 3675-84.

5. Romano N, Macino G. Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 1992; 22: 3343-53.

6. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001; 409: 363-6.

7. Zamore PD, Tuschl T, Sharp PA, Bartel DP. RNAi: doublestranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000; 101: 25-33.

8. Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 2001; 15: 188-200.

9. Hammond SM, Bernstein E, Beach D, Hannon GJ An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000; 404: 293-6.

10. Nykanen A, Haley B, Zamore PD. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 2001; 107: 309-21.

11. Schwarz DS, Hutvagner G, Haley B, Zamore PD. Evidence that RNAs function as guides, not primers, in the Drosophila and human RNAi pathway. Mol Cell 2002; 10: 537-48.

12. Williams BR. Role of the double-stranded RNA-activated protein kinase (PKR) in cell regulation. Biochem Soc Trans 1997; 25: 509-13.

13. Gil J, Alcamí J, Esteban M. Induction of apoptosis by doublestranded- RNA-dependent protein kinase (PKR) involves the alpha subunit of eukaryotic translation initiation factor 2 and NF-kappaB. Mol Cell Biol 1999; 19: 4653-63.

14. Gil J, Esteban M. Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): mechanism of action. Apoptosis 2000; 5: 107-14.

15. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001; 411: 494-8.

16. Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 2001; 98: 9742-7.

17. Provost P, Dishart D, Doucet J, Frendewey D, Samuelsson B, Rådmark O. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J 2002; 21: 5864-74.

18. Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ, Joshua- Tor L. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol 2005; 12: 340-9.

19. Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001; 294: 858-62.

20. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001; 294: 853-8.

21. Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001; 294: 862-4.

22. Saxena S, Jónsson ZO, Dutta A. 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 2003; 278: 44312-9.

23. Zeng Y, Yi R, Cullen BR. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc Natl Acad Sci USA 2003; 100: 9779-84.

24. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000; 408: 86-9.

25. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000; 403: 901-06.

26. Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM. Bantamencodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hidin Drosophila. Cell 2003; 113: 25-36.

27. Xu P, Vernooy SY, Guo M, Hay BA. The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 2003; 13: 790-5.

28. Chen CZ, Li L, Lodish HF, Bartel DP. MicroRNAs modulate hematopoietic lineage differentiation. Science 2004; 303: 83-6.

29. Hutvágner G, McLachlan J, Pasquinelli AE, Bálint E, Tuschl T, Zamore PD. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 2000; 293: 834-8.

30. Doench JG, Petersen CP, Sharp PA. siRNAs can function as miRNAs. Genes Dev 2003; 17: 438-42.

31. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 2007; 12: 1850-64.

32. Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J. Computational and experimental identification of C. elegans microRNAs. Mol Cell 2003; 11: 1253-63.

33. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008; 36(Database issue): D154-D158.

34. Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 2005; 1: e13.

35. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006; 125: 887-901.

36. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003; 425: 415-9.

37. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, et al. Molecular basis for the recognition of primary microRNAs by the Drosha–DGCR8 complex. Cell 2006; 125: 887-901.

38. Olsen PH, Ambros V. The lin-4 regulatory RNA controls developmental timing in C. elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol 1999; 2: 671-80.

39. Bohnsack MT, Czaplinski K, Gorlich D. Exportin 5 is a RanGTP- dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 2004; 10: 185-91.

40. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003; 115: 787-98.

41. Doench JG, Sharp PA Specificity of microRNA target selection in translational repression. Genes Dev 2004; 18: 504-11.

42. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120: 15-20.

43. Wang B, Love TM, Call ME, Doench JG, Novina CD. Recapitulation on Short RNA-Directed Translation Gene Silencing In Vitro. Mol Cell 2006; 22: 553-60.

44. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, et al. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 2005; 309: 1573-6.

45. Humphreys DT, Westman BJ, Martin DI, Preiss T. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc Natl Acad Sci USA 2005; 102: 16961-6.

46. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 2005; 122: 553-63.

47. Petersen CP, Bordeleau ME, Pelletier J, Sharp PA. Short RNAs repress translation after initiation in mammalian cells. Mol Cell 2006; 21: 533-42.

48. Wang B, Yanez A, Novina CD. MicroRNA-repressed mRNAs contain 40S but not 60S components. Proc Natl Acad Sci 2008; 105: 5343-8.

49. Liu J, et al. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nature Cell Biol 2005; 7: 719-23.

50. Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell 2009; 136: 642-55.

51. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 2007; 130(1): 89-100.

52. Ruby JG, Jan CH, Bartel DP. Intronic microRNA precursors that bypass Drosha processing. Nature 2007; 448(7149): 83-6

53. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor- independent, Dicer-dependent small RNAs. Genes Dev 2008; 22: 2773-85.

54. Okamura K, Chung WJ, Ruby JG, Guo H, Bartel DP, Lai EC. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 2008; 453: 803-06.

55. Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 2008; 453: 539-43.

56. Ding Y, Chan CY, Lawrence CE. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 2004; 32. W135–W141.

57. Santoyo J, Vaquerizas JM, Dopazo J. Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics 2005; 21: 1376-82.

58. Reynolds A, et al. Rational siRNA design for RNA interference. Nat Biotechnol 2004; 22: 326-30.

59. Huesken D, et al. Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol 2005; 23: 995-1001.

60. Shabalina SA, Spiridonov AN, Ogurtsov AY. Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics 2006; 7: 65-81.

61. Takasaki S, Kotani S, Konagaya A. An effective method for selecting siRNA target sequences in mammalian cells. Cell Cycle 2004; 3: 790-5.

62. Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 2004; 316: 1050-8.

63. Judge AD, et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol 2005; 23: 457-62.

64. Hornung V, et al. Sequence-specific potent induction of interferon- alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med 2005; 11: 263-70.

65. Czauderna F, et al. Structural variations and stabilizing modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res 2003; 31: 2705-16.

66. Morrissey DV, et al. Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs. Nature Biotechnol 2005; 23: 1002-7.

67. Barton GM, Medzhitov R. Retroviral delivery of small interfering RNA into primary cells. Proc Natl Acad Sci USA 2002; 99: 14943-5.

68. Devroe E, Silver PA. Retrovirus-delivered siRNA. BMC Biotechnol 2002; 2: 15.

69. Naldini L, Blömer U, Gallay P, Ory D, Mulligan R, Gage FH, et al. In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science 1996; 272: 263-7.

70. Miller DG, Adam MA, Miller AD. Gene transfer by retrovirus vectors occurs only in cells that are actively replicating at the time of infection. Mol Cell Biol 1990; 10: 4239-42.

71. Kappel S, Mattess Y, Kaufman M, Strebhardt K. Silencing of mammalian genes by tetracycline-inducible shRNA expression. Nature Protocols 2007; 2: 3257-60.

72. Wiznerowicz M, Szulc J, Trono D. Tuning silence: conditional systems for RNA interference. Nat Methods 2006; 3: 682-8.

73. Bitko V, Musiyenko A, Shulyayeva O, Barik S. Inhibition of respiratory viruses by nasally administered siRNA. Nat Med 2005; 11: 50-5.

74. Palliser D, Chowdhury D, Wang QY, Lee SJ, Bronson RT, Knipe DM, Lieberman J. An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection. Nature 2006; 439: 89-94.

75. Shen J, et al. Suppression of ocular neovascularization with siRNA targeting VEGF receptor. Gene Ther 2006; 13: 225-34.

76. Tolentino MJ, et al. Intravitreal injection of VEGF small interfering RNA inhibits growth and leakage in a nonhuman primate laser-induced model of chroidal neovascularization. Retina 2004; 24: 132-8.

77. Raoul C, Abbas-Terki T, Bensadoun JC, Guillot S, Haase G, Szulc J, et al. Lentiviral-mediated silencing of SOD1 through RNA interference retards disease onset and progression in a mouse model of ALS. Nat Med 2005; 11: 423-8.

78. Xia H, Mao Q, Eliason SL, Harper SQ, Martins IH, Orr HT, et al. RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia. Nat Med 2004; 10: 816-20.

79. Landen CN Jr, Chavez-Reyes A, Bucana C, Schmandt R, Deavers MT, Lopez-Berestein G, Sood AK. Therapeutic EphA2 gene targeting in vivo using neutral liposomal small interfering RNA delivery. Cancer Res 2005; 65: 6910-8.

80. Hu-Lieskovan S, Heidel JD, Bartlett DW, Davis ME, Triche TJ. Sequence-specific knockdown of EWS-FLI1 by targeted, nonviral delivery of small interfering RNA inhibits tumor growth in a murine model of metastatic Ewing's sarcoma. Cancer Res 2005; 65: 8984-92.

81. Kumar P, et al. T Cell-Specific siRNA Delivery suppresses HIV-1 Infection in Humanized Mice. Cell 2009; 134: 577-86.

82. Robbins M, et al. 2’-O-Methyl-modified RNAs act as TLR7 anatgonist. Mol Ther 2007; 15: 1663-9.

83. Grim D, et al. Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 2006; 441: 537-41.

84. An DS, et al. Optimization and functional effects of stable short hairpin RNA expression in primary human lymphocytes via lentiviral vectors. Mol Ther 2006; 14: 494-505.

85. Bitko V, et al. Inhibition of respiratory viruses by nasally administered siRNA. Nature Med 2005; 11: 50-5.

86. Soutschek J, et al. Therapeutic silencing o fan endogenous gene by systemic administration of modified siRNAs. Nature 2004; 432: 173-8.

87. Zimmermann TS, et al. RNAi-mediated gene silencing in nonhuman primates. Nature 2006; 441: 111-14.

88. Hu-Lieskovan S, Heidel JD, Bartlett DW, Davis ME, Triche TJ. Sequence-specific knockdown of EWS-FLI1 by targeted, nonviral delivery of small interfering RNA inhibits tumor growth in a murine model of metastactic Ewing’s sarcoma. Cancer Res 2005; 65: 8984-92.

89. Song E, et al. Antibody mediated in vivo delivery of siRNA via cell-surface receptors. Nature Biotechnol 2005; 23: 709-17.

90. McNamara JO, et al. Cell type-specific delivery of siRNA with aptamer-siRNA chimeras. Nature Biotechnol 2006; 24: 1005-15.

91. Hu-Lieskovan S, Heidel JD, Bartlett DW, Davis ME, Triche TJ. Sequence-specific knockdown of EWS-FLI1 by targeted, nonviral delivery of small interfering RNA inhibits tumor growth in a murine model of metastatic Ewing's sarcoma. Cancer Res 2005; 65: 8984-92.

92. Brummelkamp TR, Bernards R, Agami R. Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2002; 2: 243-7.

93. Huang B, Schiefer J, Sass C, Landwehrmeyer GB, Kosinski CM, Kochanek S. High-capacity adenoviral vector-mediated reduction of Huntington aggregate load in vitro and in vivo. Hum Gene Ther 2007; 18: 303-11.