Gene discovery by ribozyme and siRNA libraries

Nature Reviews Molecular Cell Biology

Volumn 6, Issue 5, 2005, Pages 413-422

  Akashi, Hideo ^a   Matsumoto, Sahohime ^b   Taira, Kazunari ^a,c  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; POLYADENYLIC ACID BINDING PROTEIN; RETROVIRUS VECTOR; RIBOZYME; RNA HELICASE; SMALL INTERFERING RNA;

APOPTOSIS; BREAST CANCER; CARCINOGENESIS; CELL INVASION; CELL MIGRATION; CHEMOTAXIS; FIBROBLAST; FLUORESCENCE ACTIVATED CELL SORTING; GENE AMPLIFICATION; GENE DISRUPTION; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LIBRARY; GENE SILENCING; GENE VECTOR; GENETIC SCREENING; HUMAN; METASTASIS; MOLECULAR GENETICS; MUSCLE DEVELOPMENT; NERVE CELL DIFFERENTIATION; NUCLEOTIDE SEQUENCE; OVARY CANCER; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW;

ANIMALS; GENE EXPRESSION; GENE LIBRARY; GENE SILENCING; GENETIC TECHNIQUES; RNA, CATALYTIC; RNA, SMALL INTERFERING;

UNIDENTIFIED RETROVIRUS;

EID: 18344385842     PISSN: 14710072     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrm1646     Document Type: Review

References (88)

1. Austin, C. P. et al. The knockout mouse project. Nature Genet. 36, 921-924 (2004).
2. Auwerx, J. et al. The European dimension for the mouse genome mutagenesis program. Nature Genet. 36, 925-927 (2004).
3. Stein, C. A. Two problems in antisense biotechnology: in vitro delivery and the design of antisense experiments, Biochim. Biophys. Acta 1489, 45-52 (1999).
4. Scherer, L. J. & Rossi, J. J. Approaches for the sequencespecific knockdown of mRNA. Nature Biotechnol. 21, 1457-1465 (2003).
5. Beger, C. et al. Identification of ld4 as a regulator of BRCA 1 expression by using a ribozyme-library-based inverse genomics approach. Proc. Natl Acad. Sci. USA 98, 130-135 (2001).
6. Kawasaki, H., Onuki, R., Suyama, E. & Taira, K. Identification of genes that function in the TNF-α-mediated apoptotic pathway using randomized hybrid ribozyme libraries. Nature Biotechnol. 20, 376-380 (2002).
7. Kawasaki, H. & Taira, K. Identification of genes by hybrid ribozymes that couple cleavage activity with the unwinding activity of an endogenous RNA helicase. EMBO Rep. 3, 443-450 (2002).
8. Kawasaki, H. & Taira, K. A functional gene discovery in the Fas-mediated pathway to apoptosis by analysis of transiently expressed randomized hybrid-ribozyme libraries. Nucleic Acids Res. 30, 3609-3614 (2002). References 6-8 are the first reports of gene discovery using a randomized library of hammerhead ribozymes with a helicase-recruiting motif.
9. Kruger, M. et al. Identification of elF2Bγ and elF2γ as cofactors of hepatitis C virus internal nbosome entry site-mediated translation using a functional genomics approach. Proc. Natl Acad. Sci. USA 97, 8566-8571 (2000).
10. Kuwabara, T., Hsieh, J., Nakashima, K., Taira, K. & Gage, F. H. A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116, 779-793 (2004). Reports the discovery, using a randomized hammerhead ribozyme library, of a new type of small RNA, which regulates neuronal differentiation through a dsRNA-protein interaction in the nucleus rather than through siRNA or miRNA.
11. Li, Q. X., Robbins, J. M., Welch, P. J., Wong-Staal, F. & Barber, J. R. A novel functional genomics approach identifies mTERT as a suppressor of fibroblast transformation. Nucleic Acids Res. 28, 2605-2612 (2000).
12. Onuki, R. et al. An RNA-dependent protein kinase is involved in tunicamycin-induced apoptosis and Alzheimer's disease. EMBO J. 23, 959-968 (2004).
13. Suyama, E., Kawasaki, H., Kasaoka, T. & Taira, K. Identification of genes responsible for cell migration by a library of randomized ribozymes. Cancer Res. 63, 119-124 (2003).
14. Suyama, E., Kawasaki, H., Nakajima, M. & Taira, K. Identification of genes involved in cell invasion by using a library of randomized hybrid ribozymes. Proc. Natl Acad. Sci. USA 100, 5616-5621 (2003).
15. Suyama, E. et al. Identification of metasiasis-related genes in a mouse model using a library of randomized ribozymes. J. Biol. Chem. 279, 38083-38086 (2004).
16. Suyama, E. et al. LIM kinase-2 targeting as a possible antimetastasis therapy. J. Gene Med. 6, 357-363 (2004).
17. Wadhwa, R. et al. Use of a randomized hybrid ribozyme library for identification of genes involved in muscle differentiation. J. Biol. Chem. 279, 51622-51629 (2004).
18. Waninger, S. et al. Identification of cellular cofactors for human immunodeficiency virus replication via a ribozyme-based genomics approach. J. Virol. 78, 12829-12837 (2004).
19. Welch, P. J. et al. Identification and validation of a gene involved in anchorage-independent cell growth control using a library of randomized hairpin ribozymes. Genomics 66, 274-283 (2000). Reports the first gene that was discovered using a library of randomized hairpin ribozymes.
20. Haseloff, J. & Gerlach, W. L. Simple RNA enzymes with new and highly specific end oribonuclease activities. Nature 334, 585-591 (1988).
21. Uhlenbeck, O. C. A small catalytic oligoribonucleotide. Nature 328, 596-600 (1987).
22. Zhou, D. M. & Taira, K. The hydrolysis of RNA: from theoretical calculations to the hammerhead ribozyme-mediated cleavage of RNA. Chem. Rev. 98, 991-1026 (1998).
23. Suzumura, K., Takagi, Y., Orita, M. & Taira, K. NMR-based reappraisal of the coordination of a metal ion at the pro-Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme. J. Am. Chem. Soc. 126, 15504-15511 (2004).
24. Takagi, Y, Inoue, A. & Taira, K. Analysis of a cooperative pathway involving multiple cations in hammerhead reactions. J. Am. Chem. Soc. 126, 12856-12864 (2004).
25. Tanaka, Y. et al. Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes. J. Am. Chem. Soc. 126, 744-752 (2004).
26. Warashina, M. et al. Analysis of the conserved P9-G10.1 metal binding motif in hammerhead ribozymes with an extra nucleotide inserted between A9 and G10.1 residues. J. Am. Chem. Soc. 126, 12291-12297 (2004).
27. Shimayama, T., Nishikawa, S. & Taira, K. Generality of the NUX rule: kinetic analysis of the results of systematic mutations in the trinucleotide at the cleavage site of hammerhead ribozymes. Biochemistry 34, 3649-3654 (1995).
28. Sarver, N. et al. Ribozymes as potential anti-HIV-1 therapeutic agents. Science 247, 1222-1225 (1990).
29. Rossi, J. J. Controlled, targeted, intracellular expression of ribozymes: progress and problems. Trends Biotechnol. 13, 301-306 (1995).
30. Rossi, J. J. & Sarver, N. RNA enzymes (ribozymes) as antiviral therapeutic agents. Trends Biotechnol. 8, 179-183 (1990).
31. Sioud, M. (ed.) Methods in Molecular Biology: Ribozymes and siRNA Protocols (Humana, Totowa, New Jersey, 2004).
32. Geiduschek, E. P. & Tocchini-Valentini, G. P. Transcription by RNA polymerase III. Annu. Rev. Biochem. 57, 873-914 (1988).
33. Cotten, M. & Birnstiel, M. L. Ribozyme mediated destruction of RNA in vivo. EMBO J. 8, 3861-3866 (1989).
34. Shiota, M., Sano, M., Miyagishi, M. & Taira, K. Ribozymes: applications to functional analysis and gene discovery. J. Biochem. (Tokyo) 136, 133-147 (2004).
35. Good, P. D. et al. Expression of small, therapeutic RNAs in human cell nuclei. Gene Ther. 4, 45-54 (1997).
36. Bertrand, E, et al. The expression cassette determines the functional activity of ribozymes in mammalian cells by controlling their intracellular localization. RNA 3, 75-88 (1997).
37. Kato, Y., Kuwabara, T., Warashina, M., Toda, H. & Taira, K. Relationships between the activities in vitro and in vivo of various kinds of ribozyme and their intracellular localization in mammalian cells. J. Biol. Chem. 276, 15378-15385 (2001).
38. Koseki, S. et al. Factors governing the activity in vivo of ribozymes transcribed by RNA polymerase III. J. Virol. 73, 1868-1877 (1999). Demonstrates that the localization and the stability of the ribozyme, which depends on its promoter species and/or the linker sequence, are crucial for its cleavage activity.
39. Kuwabara, T, et al. Recognition of engineered tRNAs with an extended 3′ end by exportin-t (Xpo-t) and transport of tRNA-attached ribozymes to the cytoplasm in somatic cells. Biomacromol. 2, 1229-1242 (2001).
40. Luking, A., Stahl, U. & Schmidt, U. The protein family of RNA helicases. Crit. Rev. Biochem. Mol. Biol. 33, 259-296 (1998).
41. Agrawal, N. et al. RNA interference: biology, mechanism, and applications, Microbiol. Mol. Biol. Rev. 67, 657-685 (2003).
42. Warashina, M., Kuwabara, T., Kato, Y., Sano, M. & Taira, K. RNA-protein hybrid ribozymes that efficiently cleave any mRNA independently of the structure of the target RNA. Proc. Natl Acad. Sci. USA 98, 5572-5577 (2001).
43. Chatterton, J. E., Hu, X. & Wong-Staal, F. Ribozymes in gene identification, target validation, and drug discovery. Targets 3, 10-17 (2004).
44. Nelson, D. L., Suyama, E., Kawasaki, H. & Taira, K. Use of random ribozyme libraries for the rapid screening of apoptosis- and metastasis-related genes. Targets 2, 191-200 (2003).
45. Onuki, R. et al. Confirmation by FRET in individual living cells of the absence of significant amyloid β-mediated caspase 8 activation. Proc. Natl Acad. Sci. USA 99, 14716-14721 (2002).
46. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998). Provides the first evidence for a new gene silencing phenomenon that is mediated by dsRNA in a sequence-specific manner.
47. Zamore, P. D. RNA interference: listening to the sound of silence. Nature Struct. Biol. 8, 746-750 (2001).
48. Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498 (2001). Shows for the first time that RNAi can be applied in mammalian cells without nonspecific side effects by using 21-nucleotide siRNAs.
49. Novina, C. D. & Sharp, P. A. The RNAi revolution. Nature 430, 161-164 (2004).
50. Nykanen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309-321 (2001).
51. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146-1150 (2001).
52. Fraser, A. G. et al. Functional genomic analysis of C. elegans chromosome by systematic RNA interference. Nature 408, 325-330 (2000).
53. Gonczy, P. et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331-336 (2000).
54. Miyagishi, M. & Taira, K. Strategies for generation of an siRNA expression library directed against the human genome. Oligonucleotides 13, 325-333 (2003). Reports a strategy for the construction of a large, genome-wide library of siRNA expression vectors. The utility of the vector-based library compared with the siRNA library Is discussed.
55. Aza-Blanc, P. et al. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell 12. 627-637 (2003). Provides a good example of the utility of large-scale screening using a siRNA library, which resulted in the identification of several new factors that are involved in TRAIL-induced apoptosis.
56. Berns, K. et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431-137 (2004).
57. Paddison, P. J. et al. A resource for large-scale RNA-interference-based screens in mammals. Nature 428, 427-431 (2004).
58. Sen, G., Wehrman, T. S., Myere, J. W. & Blau, H. M. Restriction enzyme-generated siRNA (REGS) vectors and libraries. Nature Genet. 36, 183-189 (2004).
59. Shirane, D. et al. Enzymatic production of RNAi libraries from cDNAs. Nature Genet. 36, 190-196 (2004).
60. Hsieh, A. C. et al. A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res. 32, 893-901 (2004).
61. Kaykas, A. & Moon, R. T. A plasmid-based system for expressing small interfering RNA libraries in mammalian cells. BMC Cell Biol. 5, 16 (2004).
62. Colland, F. et al. Functional proteomics mapping of a human signaling pathway. Genome Res. 14, 1324-1332 (2004).
63. Luo, B., Heard, A. D, & Lodish, H. F. Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc. Natl Acad. Sci. USA 101, 5494-5499 (2004).
64. Zheng, L. et al. An approach to genomewide screens of expressed small interfering RNAs in mammalian cells. Proc. Natl Acad. Sci. USA 101, 135-140 (2004).
65. Futami, T., Miyagishi, M. & Taira, K. Identification of a network involved in thapsigargin-induced apoptosis using a library of small interfering RNA expression vectors. J. Biol. Chem. 280, 826-831 (2005).
66. Miyagishi, M., Matsumoto, S. & Taira, K. Generation of an shRNAi expression library against the whole human transcripts. Virus Res. 102, 117-124 (2004).
67. Yoshinari, K., Miyagishi, M. & Taira, K. Effects on RNAi of the tight structure, sequence and position of the targeted region. Nucleic Acids Res. 32, 691-699 (2004).
68. Katoh, T., Susa, M., Suzuki, T., Umeda, N. & Watanabe, K. Simple and rapid synthesis of siRNA derived from in vitro transcribed shRNA. Nucleic Acids Res. Suppl. 3, 249-250 (2003).
69. Jackson, A. L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotechnol. 21, 635-637 (2003).
70. Lewin, A. S. et al. Ribozyme rescue of photoreceptor cells in a transgenic rat model of autosomal dominant retinitis pigmentosa. Nature Med. 4, 967-971 (1998).
71. Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216 (2003).
72. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208 (2003).
73. Kim, D. H. et al. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nature Biotechnol. 23, 222-226 (2005).
74. Siolas, D. et al. Synthetic shRNAs as potent RNAi triggers. Nature Biotechnol. 23, 227-231 (2005).
75. Bridge, A. J., Pebernard, S., Ducraux, A., Nicoulaz, A, L. & Iggo, R. Induction of an interferon response by RNAi vectors in mammalian cells. Nature Genet. 34, 263-264 (2003).
76. Sledz, C. A., Holko, M., de Veer, M. J., Silverman, R. H. & Williams, B. R. Activation of the interferon system by short-interfering RNAs. Nature Cell Biol. 5, 834-839 (2003).
77. Kawasaki, H. & Taira, K. Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 431, 211-217 (2004).
78. Morris, K. V., Chan. S. W., Jacobsen, S. E. & Looney, D. J. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305, 1289-1292 (2004).
79. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and functjon. Cell 116, 281-297 (2004).
80. Khvorova, A., Lescoute, A., Westhof. E. & Jayasena, S. D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nature Struct. Bol. 10, 708-712 (2003).
81. Ambros, V. MicroRNA pathways in flies and worms: growth death, fat, stress, and timing. Cell 113, 673-676 (2003).
82. Stark, A., Brennecke, J., Russell, R. B. Cohen, S. M. Identification of Drosophila microRN A targets. PLoS Biol. 1 E60 (2003).
83. Enright, A. J. et al. MicroRNA targets in Drosophila. Genome Biol. 5, R1 (2003).
84. Hartig, J. S., Grune, I., Najafi-Shoushtari, S. H, & Famulok, M. Sequence-specific detection of microRNAs by signalamplifying ribozymes, J. Am. Chem. Soc. 126, 722-723 (2004).
85. Liang, R. Q. et al. An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 33, e17 (2005).
86. Valoczi, A. et al. Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res. 32, e175 (2004).
87. Allawi, H. T. et al. Quantitation of microRNAs using a modified Invader assay. RNA 10, 1153-1161 (2004).
88. Eis, P. S. et al. An invasive cleavage assay for direct quantitation of specific RNAs. Nature Biotechnol. 19, 673-676 (2001).