About the nature of RNA interference

Applied Microbiology and Biotechnology

Volumn 67, Issue 4, 2005, Pages 429-435

  Schmidt, F R ^a  

^a SANOFI AVENTIS DEUTSCHLAND GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL ENGINEERING; BIOTECHNOLOGY; CHEMICAL MODIFICATION; GENES; MICROBIOLOGY; MICROORGANISMS; VIRUSES;

GENETIC TRAITS; HISTONE MODIFICATION; REPLICATION; RNA INTERFERENCE (RNAI); TRANSCRIPTION;

RNA;

COMPLEMENTARY RNA; DOUBLE STRANDED RNA; HISTONE; RNA DIRECTED RNA POLYMERASE;

RNA;

DNA MODIFICATION; ENZYME ACTIVITY; GENE EXPRESSION REGULATION; GENE INACTIVATION; GENETIC RECOMBINATION; GENETIC TRAIT; MOLECULAR EVOLUTION; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; RNA INTERFERENCE; RNA VIRUS; SHORT SURVEY; TRANSCRIPTION REGULATION; VIRUS REPLICATION; VIRUS SURVIVAL;

ANIMALS; GENE SILENCING; HUMANS; RNA INTERFERENCE; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, DOUBLE-STRANDED; RNA, SMALL INTERFERING; SIGNAL TRANSDUCTION;

RNA VIRUSES;

EID: 21344435745     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-004-1882-1     Document Type: Short Survey

References (82)

1. Agrawal N, Dasaradhi PVN, Mohmmed A, Malhotra P, Bhatnagar RK, Mukherjee SK (2003) RNA interference: biology, mechanism and applications. Microbiol Mol Biol Rev 67:657-685
2. Ait-Si-Ali S, Guasconi V, Harel-Bellan A (2004) RNA interference and its possible use in cancer therapy. Bull Cancer 91:15-18
3. Allshire R (2002) RNAi and heterochromatin - a hushed-up affair. Science 297:1818-1837
4. Ambros V (2004) The functions of animal microRNAs. Nature 431:350-355
5. Baril M, Dulude D, Steinberg SV, Brakier-Gingras L (2003) The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot. J Mol Biol 331:571-583
6. Bartel PB (2004) MicroRNAs: genomics, biogenesis, mechanism and function. Cell 116:281-297
7. Baulcombe D (2004) RNA silencing in plants. Nature 431:356-363
8. Berger G (2004) Hypotheses on a germline origin of antibody diversity. Possible applications: improvement of the efficiency of immune response and autoimmune disease treatment. Med Hypotheses 63:847-854
9. Bridge AJ, Pebernard S, Ducraux A, Nicoulaz AL, Iggo R (2003) Induction of an interferon response by RNAi vectors in mammalian cells. Nat Genet 34:263-264
10. Campbell MA, Fitzgerald HA, Ronald PC (2002) Engineering pathogen resistance in crop plants. Transgenic Res 11:599-613
11. Caplen NJ (2004) Gene therapy progress and prospects. Down-regulating gene expression: the impact of RNA interference. Gene Ther 11:1241-1248
12. Chen X, Chamarro M, Lee SI, Shen LX, Hines JV, Tinoco I, Varmus HE (1995) Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting. Nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting. EMBO J 14:842-852
13. Cheng JC, Sakamoto KM (2004) The emerging role of RNA interference in the design of novel therapies in oncology. Cell Cycle 3:1398-1401
14. Chiu YL, Cao H, Jacque JM, Stevenson M, Rana TM (2004) Inhibition of human immunodeficiency virus type 1 replication by RNA interference directed against human transcription elongation factor P-TEFb (CDK9/CyclinT1). J Virol 78:2517-2529
15. Clayton J (2004) The silent treatment. Nature 431:599-605
16. Cogoni C, Macino G (1999) Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399:166-169
17. Dave RS, Pomerantz RJ (2003) RNA interference: on the road to an alternate therapeutic strategy. Rev Med Virol 13:373-385
18. Djikeng A, Shi H, Tschudi C, Ullu E (2001) RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26 nucleotide RNAs. RNA 7:1522-1530
19. Duxberry MS, Matros E, Ito H, Zinner MJ, Ashley SW, Whang EE (2004) Systemic siRNA-mediated gene silencing - a new approach to targeted therapy of cancer. Ann Surg 240:667-676
20. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS (2003) MicroRNA targets in Drosophila. Gen Biol 5:R1
21. Ge Q, McManus MT, Nguyen T, Shen CH, Sharp PA, Eisen HN, Chen J (2003) RNA interference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription. Proc Natl Acad Sci USA 100:2718-2723
22. Gilbert N, Boyle S, Fiegler H, Woodfine K, Carter NP, Bickmore WA (2004) Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 116:555-566
23. Goldbach R, Bucher E, Prins M (2003) Resistance mechanisms to plant viruses: an overview. Virus Res 92:207-212
24. Grishok A, Tabara H, Mello CC (2000) Genetic requirements for inheritance of RNAi in C. elegans. Science 287:2494-2497
25. Guenther RH, Sit TL, Gracz HS, Dolan MA, Townsend HL, Liu G, Newman WH, Agris PF, Lommel SA (2004) Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus. Nucleic Acids Res 32:2819-2828
26. Hall IM, Shankaranarayana GD, Noma K, Ayoub N, Cohen A, Grewal SIS (2002) Establishment and maintenance of a heterochromatin domain. Science 297:2232-2237
27. Hall IM, Noma K, Grewal SS (2003) RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc Natl Acad Sci USA 100:193-198
28. Hamada M, Ohtsuka T, Kawaida R, Koizumi M, Morita K, Furukawa H, Imanishi T, Miyagishi M, Taira K (2002) Effects on RNA interference in gene expression (RNAi) in cultured mammalian cells of mismatches and the introduction of chemical modifications at the 3′-ends of siRNA. Antisense Nucleic Acid Drug Dev 12:301-309
29. Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21:4671-4679
30. Hannon GJ (2002) RNA interference. Nature 418:244-251
31. Hannon GJ, Conklin DS (2004) RNA interference by short hairpin RNAs expressed in vertebrate cells. Methods Mol Biol 257:255-266
32. Hannon GJ, Rossi JJ (2004) Unlocking the potential of the human genome with RNA interference. Nature 431:371-378
33. Hendrickson TL, Crécy-Lagard V, Schimmel P (2004) Incorporation of nonnatural amino acids into proteins. Annu Rev Biochem 73:147-176
34. Holen T, Amarzguioui M, Wiiger MT, Babaie E, Prydz H (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res 30:1757-1766
35. Hutvagner G, Zamore PD (2002) RNAi: nature abhors a double-strand. Curr Opin Genet Dev 12:225-232
36. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21:635-637
37. Jenuwein T (2002) An RNA-guided pathway for the epigenome. Science 297:2215-2218
38. Ji Y, Dezhong Y, Fox B, Holmes DJ, Payne D, Rosenberg M (2004) Validation of antibacterial mechanism of action using regulated antisense RNA expression in Staphylococcus aureus. FEMS Microbiol Lett 231:177-184
39. Kariko K, Bhuyan P, Capodici J, Ni H, Lubinski J, Friedman H, Weissman D (2004) Exogenous siRNA mediates sequence-independent gene suppression by signalling through toll-like receptor 3. Cells Tissues Organs 177:132-138
40. Klipcan L, Safro M (2004) Amino acid biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetases. J Theor Biol 228:389-396
41. Koonin EV (1991) Similarities in RNA helicases. Nature 325:290-292
42. Koonin EV (2003) Horizontal gene transfer: the path to maturity. Mol Microbiol 50:725-727
43. Koonin EV, Gorbalenya AE (1989) Evolution of RNA genomes: does the high mutation rate necessitate high rate of evolution of viral proteins? J Mol Evol 28:524-527
44. Koonin EV, Dolja VV (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28:375-430
45. Knight KL (1992) Restricted VH gene usage and generation of antibody diversity in rabbit. Annu Rev Immunol 10:593-616
46. Lawrence JG, Hendrickson H (2003) Lateral gene transfer: when will adolescence end? Mol Microbiol 50:739-749
47. Lipardi C, Wei Q, Paterson BM (2001) RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs. Cell 107:297-307
48. Lippman Z, Martienssen R (2004) The role of RNA interference in heterochromatic silencing. Nature 431:364-370
49. Lippman Z, May B, Yordan C, Singer T, Martienssen R (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PloS Biol 1:420-428
50. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 432:343-349
51. Mello CG, Conte D (2004) Revealing the world of RNA interference. Nature 431:338-342
52. Mitter N, Sulistyowati E, Dietzgen RG (2003) Cucumber mosaic virus infection transiently breaks ds-RNA induced transgenic immunity to potato virus Y in tobacco. Mol Plant-Microb Interact 16:936-944
53. Mochizuki K, Fine NA, Fujisawa T, Gorovski MA (2002) Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110:689-699
54. Murchison EP, Hannon GJ (2004) miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr Opin Cell Biol 16:223-229
55. Nixon PL, Rangan A, Kim YG, Rich A, Hoffman DW, Henning M, Giedroc DP (2002) Solution structure of a luteoviral P!-P2 frameshifting mRNA pseudoknot. J Mol Biol 322:621-633
56. Orgel LE (2004) Prepiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39:99-123
57. Pandit NN, Russo VE (1992) Reversible inactivation of a foreign gene, hph, during the asexual cycle in Neurospora crassa transformants. Mol Gen Genet 234:412-422
58. Pfeffer S, Zavolan M, Grässer FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T (2004) Identification of virus-encoded microRNAs. Science 304:734-736
59. Pickford AS, Catalanotto C, Cogoni C, Macino G (2002) Quelling in Neurospora crassa. Adv Genet 46:277-303
60. Reanny DC (1982) The evolution of RNA viruses. Annu Rev Microbiol 36:47-73
61. Reddy EP, Reynolds RX, Santos E, Barbacid M (1982) A point mutation is responsible for the acquisition of transforming properties by the 124 human bladder carcinoma oncogene. Nature 300:149-152
62. Romano N, Macino G (1992) Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6:3343-3353
63. Rose DR (1982) The generation of antibody diversity. Am J Hematol 13:91-99
64. Ryther RCC, Flynt AS, Phillips JA, Patton JG (2004) siRNA therapeutics: big potential from small RNAs. Gene Ther 12:5-11
65. Sakamoto KM (2004) Knocking down human disease: potential uses of RNA interference in research and gene therapy. Pediatr Res 55:912-913
66. Seeburg PH, Colby WW, Capon DJ, Goeddel DV, Levinson AD (1984) Biological properties of human c-Ha-ras 1 genes mutated at codon 12. Nature 312:71-75
67. Schmidt FR (2002) Beta-lactam antibiotics: aspects of manufacture and therapy. In: Osiewacz HD (ed) The Mycota vol X: industrial application. Springer, Berlin Heidelberg New York, pp 69-91
68. Schmidt FR (2004a) RNA interference detected 20 years ago? Nat Biotechnol 22:267-268
69. Schmidt FR (2004b) The challenge of multidrug resistance: actual strategies in the development of novel antibacterials. Appl Microbiol Biotechnol 63:335-343
70. Schramke V, Allshire R (2003) Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301:1069-1074
71. Seo MY, Abrignani S, Han JA (2003) Small interfering RNA-mediated inhibition of hepatitis C virus replication in the human hepatoma cell line Huh-7. J Virol 77:810-812
72. Sharp PA (2001) RNA interference - 2001. Genes Dev 15:485-490
73. Sledz CA, Williams BRG (2004) RNA interference and double-stranded-RNA- activated pathways. Biochem Soc Trans 32
74. Seitz H, Royo H, Bortolin ML, Lin SP, Ferguson-Smith AC, Cavaille J (2004) A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res 14:1741-1748
75. Tabin CJ, Bradley SM, Bargmann CI, Weinberg RA, Papageorge AG, Scolnick EM, Dhar R, Lowy DR, Chang EM (1982) Mechanism of activation of a human oncogene. Nature 300:143-149
76. Taparowski E, Suard E, Fasano D, Shimizu K, Goldfarb M, Wigler M (1982) Activation of the T24 bladder carcinoma transforming gene is linked to a single amino acid change. Nature 300:762-765
77. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed T (2004) RNAi mediated targeting of heterochromatin by the RITS complex. Science 303:672-676
78. Wang QC, Nie QH, Feng ZH (2003) RNA interference: antiviral weapon and beyond. World J Gastroenterol 9:1657-1661
79. Wassenegger M (2002) Gene silencing-based disease resistance. Transgenic Res 11:639-653
80. Weiner AM (2002) SINEs and LINEs: the art of biting the hand that feeds you. Curr Opin Cell Biol 14:343-350
81. Yin D, Fox B, Lonetto MI, Etherton MR, Payne DJ, Holmes DJ, Rosenberg M, Ji Y (2004) Identification of microbial targets using a comprehensive genomic approach. Pharmacogenomics 5:101-113
82. Zeng Y, Cullen BR (2003) Sequence requirements for micro RNA processing and function in human cells. RNA 9:112-123