Small non-coding RNAs as magic bullets

Trends in Biochemical Sciences

Volumn 30, Issue 8, 2005, Pages 445-452

  Eckstein, Fritz ^a  

^a MAX PLANCK INSTITUTE OF EXPERIMENTAL MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRUS VECTOR; ANTIVIRUS AGENT; APOLIPOPROTEIN B; INTERCELLULAR ADHESION MOLECULE 1; INTERFERON; MENIN 1; MICRORNA; NUCLEASE; OLIGONUCLEOTIDE; PROTEIN; PROTEIN P21; PROTEIN P53; RECOMBINANT RNA; RNA POLYMERASE II; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; VIRUS RNA;

3' UNTRANSLATED REGION; CAENORHABDITIS ELEGANS; CELL DIVISION; CHEMICAL MODIFICATION; CHROMOSOME; CYTOTOXICITY; EPIGENETICS; GENE EXPRESSION REGULATION; GENE MUTATION; GENE SILENCING; GENE TARGETING; GENE VECTOR; HELA CELL; HEPATITIS B VIRUS; HETEROCHROMATIN; INFLUENZA; LIVER; NONHUMAN; NONVIRAL GENE DELIVERY SYSTEM; NUCLEAR LOCALIZATION SIGNAL; PARAINFLUENZA VIRUS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; RESPIRATORY SYNCYTIAL PNEUMOVIRUS; RETROVIRUS; REVIEW; RNA INTERFERENCE; RNA SEQUENCE; RNA TRANSCRIPTION; STRUCTURE ACTIVITY RELATION; TRANSGENIC MOUSE; VIRAL GENE DELIVERY SYSTEM;

ANIMALS; GENETIC VECTORS; HETEROCHROMATIN; HUMANS; MICRORNAS; MODELS, GENETIC; RNA INTERFERENCE; RNA, SMALL INTERFERING;

ANIMALIA;

EID: 22744453672     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2005.06.008     Document Type: Review

References (84)

1. C.C. Mello, and D. Conte Jr Revealing the world of RNA interference Nature 431 2004 338 342
2. C.D. Novina, and P.A. Sharp The RNAi revolution Nature 430 2004 161 164
3. G. Meister, and T. Tuschl Mechanism of gene silencing by double-standed RNA Nature 431 2004 343 349
4. Y. Dorsett, and T. Tuschl siRNAs: applications in functional genomis and potential as therapeutics Nat. Rev. Drug Discov. 3 2004 318 329
5. E.J. Sontheimer Assembly and function of RNA silencing complexes Nat. Rev. Mol. Cell Biol. 6 2005 127 138
6. Y. Tomari, and P.D. Zamore Perspective: machines for RNAi Genes Dev. 19 2005 517 529
7. G. Tang siRNA and miRNA: an insight into RISCs Trends Biochem. Sci. 30 2005 106 114
8. J. Liu Argonaute2 is the catalytic engine of mammalian RNAi Science 305 2004 1437 1441
9. G. Meister human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs Mol. Cell 15 2004 185 197
10. T.A. Rand Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity Proc. Natl. Acad. Sci. U. S. A. 101 2004 14385 14389
11. J. Martinez, and T. Tuschl RISC is a 5′phosphomonoester-ptroducing RNA endonuclease Genes Dev. 18 2004 975 980
12. 2+-dependent endonuclease Curr. Biol. 14 2004 787 791
13. J.J. Song Crystal structure of Argonaute and its implications for RISC slicer activity Science 305 2004 1434 1437
14. J.S. Parker Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex Nature 434 2005 663 666
15. J-B. Ma Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein Nature 434 2005 666 670
16. J-B. Ma Structural basis for overhang-specific small interfering RNA recogntion by the PAZ domain Nature 429 2004 318 322
17. F.V. Rivas Purified Argonaute2 and an siRNA form recombinant human RISC Nat. Struct. Mol. Biol. 12 2005 340 349
18. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
19. V. Ambros The functions of animal microRNAs Nature 431 2004 350 355
20. A.M. Denli Processing of microRNAs by the microprocessor complex Nature 432 2004 231 235
21. Y. Lee The nuclear RNase III Drosha initiates microRNA processing Nature 425 2003 415 419
22. B.R. Cullen Transcription and processing of human microRNA precursors Mol. Cell 16 2004 861 865
23. J.G. Doench, and P.A. Sharp Specificity of microRNA target selection in translatinal repression Genes Dev. 18 2004 504 511
24. M.C. Vella Archtecture of a validated microRNA: target interaction Chem. Biol. 11 2004 1619 1623
25. K. Huppi Defining and assaying RNAi in mammalian cells Mol. Cell 17 2005 1 10
26. D.S. Schwarz Asymmetry in the assembly of the RNAi enzyme complex Cell 115 2003 199 208
27. A. Khvorova Functional siRNAs and miRNAs exhibit strand bias Cell 115 2003 209 216
28. A. Reynolds Rational design for RNA interference Nat. Biotechnol. 22 2004 326 330
29. V. Bitko Inhibition of respiratory viruses by nasally administered siRNA Nat. Med. 11 2005 50 55
30. B. Haley, and P.D. Zamore Kinetic analysis of the RNAi complex Nat. Struct. Mol. Biol. 11 2004 599 606
31. D.H. Kim Synthetic dsRNA Dicer substrate enhance RNAi potency and efficiency Nat. Biotechnol. 23 2005 222 226
32. D. Siolas Synthetic shRNAs as potent RNAi triggers Nat. Biotechnol. 23 2005 227 231
33. R. Kretschmer-Kazemi, and G. Sczakiel The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides Nucleic Acids Res. 31 2003 4417 4424
34. G.B. Robb Specific and potent RNAi in the nucleus of human cells Nat. Struct. Mol. Biol. 12 2005 1 5
35. T. Shinagawa, and S. Ishii Generation of Ski-knockdown mice by expressing a long dsRNA from an RNA polymerase II promoter Genes Dev. 17 2003 1340 1345
36. A. Ventura Cre-lox-regulated conditional interference from transgenic mice Proc. Natl. Acad. Sci. U. S. A. 101 2004 10380 10385
37. J. Seibler Single copy shRNA configuration for ubiquitous gene knockdown in mice Nucleic Acids Res. 33 2005 e67
38. J. Soutschek Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs Nature 432 2004 173 178
39. D. Massaro Noninvasive delivery of small inhibitory RNA and other reagents to pulmonary alveoli in mice Am. J. Physiol. Lung Cell. Mol. Physiol. 287 2004 L1066 L1070
40. Q. Ge Inhibition of influenza virus production in viru-infected mice by RNA interference Proc. Natl. Acad. Sci. U. S. A. 101 2004 8676 8681
41. W. Zhang Inhibition of respiratory syncytial virus infection with intranasal siRNA nanoparticles targeting the viral NS1 gene Nat. Med. 11 2005 56 62
42. S.L. Uprichard Clearance of hepatitis B virus from the liver of transgenic mice by short heirpin RNAs Proc. Natl. Acad. Sci. U. S. A. 102 2005 773 778
43. E.M. Westerhout HIV-1 can escape form RNA interference by evolving an alternative structure in its RNA genome Nucleic Acids Res. 33 2005 796 804
44. S. Schubert Maintaining inhibition: siRNA double expression vectors against coxsackieviral RNAs J. Mol. Biol. 346 2005 457 465
45. K. Ye Recognition of a small interfering RNA by a viral suppressor of RNA silencing Nature 426 2003 874 878
46. S. Kennedy A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans Nature 427 2004 645 649
47. C-H. Lecellier A cellular microRNA mediates antiviral defense in human cells Science 308 2005 557 560
48. M. Manoharan RNA interference and chemically modified small interfering RNAs Curr. Opin. Chem. Biol. 8 2004 570 579
49. J.M. Layzer In vivo activity of nuclease-resistant siRNAs RNA 10 2004 766 771
50. Y.L. Chiu, and T.M. Rana siRNA function in RNAi: a chemical modification analysis RNA 9 2003 1034 1048
51. J. Harborth Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing Antisense Nucleic Acid Drug Dev. 13 2003 83 105
52. Y. Ikeda Specific 3′-terminal modification of DNA with a novel nucleoside analogue that allows a covalent linkage of nuclear localisation signal and enhancement of DNA stability ChemBioChem 6 2005 297 303
53. J.J. Turner Synthesis, cellular uptake and HIV-1 Tat-dependent trans-activation, inhibition activity of oligonucleotide analogues disulphide-conjugated to cell-penetrating peptides Nucleic Acids Res. 33 2005 27 42
54. P. Jarver, and U. Lanel The use of cell-penetrating peptides as a tool for gene regulation Drug Discov. Today 9 2004 395 402
55. Z. Lippman, and R. Martiensen The role of RNA interference in heterochromatin silencing Nature 431 2004 364 370
56. M.A. Matzke, and J.A. Bircher RNAi-mediated pathways in the nucleus Nat. Rev. Genet. 6 2005 24 35
57. K.V. Morris Small interfering RNA-induced transcriptional gene silencing in human cells Science 305 2004 1289 1292
58. H. Kawasaki, and K. Taira Induction of DNA methylation and gene silencing by short interfering RNAs in human cells Nature 431 2004 211 217
59. T. Fukagawa Dicer is essential for formation of heterochromatin structure in vertebrate cells Nat. Cell Biol. 6 2004 784 791
60. M. Pal-Bhadra Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery Science 303 2004 669 672
61. M. Ronemus, and R. Martienssen Methylation mystery Nature 433 2005 472 473
62. V.J. Roberts Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences Genes Dev. 19 2005 782 787
63. A. Grishok Transcriptional silencing of a transgene by RNAi in the soma of C. elegans Genes Dev. 19 2005 683 696
64. S. Yekta MicroRNA-directed cleavage of HOXB8 mRNA Science 304 2004 594 596
65. L.P. Lim Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs Nature 433 2005 769 773
66. S. Saxena Small RNAs with imperfect match to endogenous mRNA repress translation J. Biol. Chem. 278 2003 44312 44319
67. J.G. Doensch siRNAs can function as miRNAs Genes Dev. 17 2003 438 442
68. M.N. Poy A pancreatic islet-specific microRNA regulates insulin secretion Nature 432 2004 226 230
69. J.H. Mansfield MicroRNA-responsive sensor transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression Nat. Genet. 36 2004 1079 1083
70. A.J. Giraldez MicroRNAs regulate brain morphogenesis in Zebrafish Science 308 2005 833 838
71. B. John Human microRNA targets PLoS Biol. 2 2004 e363
72. B.P. Lewis Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 2005 15 20
73. Xie, X. et al. Systemic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Genes Dev. (in press)
74. A. Stark Identification of Drosophila microRNA targets PLoS Biol. 1 2003 E60
75. J. Brennecke Principles of microRNA-target recognition PLoS Biol. 3 2005 e85
76. A.L. Jackson, and P.S. Linsley Noise amidst the silence: off-target effects of siRNAs? Trends Genet. 20 2004 521 524
77. A.L. Jackson Expresion profiling reveals off-target gene regulation by RNAi Nat. Biotechnol. 21 2003 635 637
78. S.P. Persengiev Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small RNAs (siRNAs) RNA 10 2004 12 18
79. V. Hornung Sequence-specific potent induction of IFN-α by short interfering RNA in plasmacytoid dendritic cells through TLR7 Nat. Med. 11 2005 263 270
80. K. Kariko Small interfering RNAs mediate sequence-independent gene suppression and induce immune activation by signalling through Toll-like receptor 3 J. Immunol. 172 2004 6545 6549
81. C.A. Sledz Activation of the interfron system by short-interfering RNAs Nat. Cell Biol. 5 2003 834 839
82. E.G. Moss, and J.M. Taylor Small-interfering RNAs in the radar of the interferon system Nat. Cell Biol. 5 2003 771 772
83. J.D. Heidel Lack of interferon response in animals to naked siRNAs Nat. Biotechnol. 22 2004 1579 1582
84. P.C. Scacheri Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells Proc. Natl. Acad. Sci. U. S. A. 101 2004 1892 1897