Ligand-dependent regulatory RNA parts for Synthetic Biology in eukaryotes

Current Opinion in Biotechnology

Volumn 21, Issue 6, 2010, Pages 760-765

  Wieland, Markus ^a   Fussenegger, Martin ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL CHANGE; DESIGNING COMPLEX; EUKARYOTIC GENES; LIGAND BINDING; RNA INTERFERENCE; SMALL SIZE; SYNTHETIC BIOLOGY;

GENES; LIGANDS; TRANSCRIPTION;

RNA;

4 [5 (4 METHYL 1 PIPERAZINYL)[2,5' BI 1H BENZIMIDAZOL] 2' YL]PHENOL; APTAMER; HAMMERHEAD RIBOZYME; MESSENGER RNA; MICRORNA; REGULATORY RNA; RNA; SHORT HAIRPIN RNA; TETRACYCLINE; TETRAMETHYLROSAMINE; THEOPHYLLINE; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; BIOSYNTHESIS; CONFORMATIONAL TRANSITION; EUKARYOTE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENE SWITCHING; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA INTERFERENCE; RNA STABILITY; TRANSCRIPTION REGULATION; TRANSLATION REGULATION;

EUKARYOTA; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RNA; RNA STABILITY; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 78349306846     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2010.06.010     Document Type: Review

References (37)

1. Mello C.C., Conte D. Revealing the world of RNA interference. Nature 2004, 431:338-342.
2. Dorsett Y., Tuschl T. siRNAs: applications in functional genomics and potential as therapeutics. Nat Rev Drug Discov 2004, 3:318-329.
3. Winkler W., Nahvi A., Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002, 419:952-956.
4. Tucker B.J., Breaker R.R. Riboswitches as versatile gene control elements. Curr Opin Struct Biol 2005, 15:342-348.
5. Stoltenburg R., Reinemann C., Strehlitz B. SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 2007, 24:381-403.
6. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
7. Patel D.J., Suri A.K., Jiang F., Jiang L., Fan P., Kumar R.A., Nonin S. Structure, recognition and adaptive binding in RNA aptamer complexes. J Mol Biol 1997, 272:645-664.
8. Martick M., Scott W.G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 2006, 126:309-320.
9. Soukup G.A., Breaker R.R. Engineering precision RNA molecular switches. Proc Natl Acad Sci U S A 1999, 96:3584-3589.
10. Link K.H., Guo L., Ames T.D., Yen L., Mulligan R.C., Breaker R.R. Engineering high-speed allosteric hammerhead ribozymes. Biol Chem 2007, 388:779-786.
11. Kettenberger H., Eisenführ A., Brueckner F., Theis M., Famulok M., Cramer P. Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs. Nat Struct Mol Biol 2006, 13:44-48.
12. Thomas M., Chedin S., Carles C., Riva M., Famulok M., Sentenac A. Selective targeting and inhibition of yeast RNA polymerase II by RNA aptamers. J Biol Chem 1997, 272:27980-27986.
13. Cassiday L.A., Maher L.J. In vivo recognition of an RNA aptamer by its transcription factor target. Biochemistry 2001, 40:2433-2438.
14. Wang S., Shepard J.R.E., Shi H. An RNA-based transcription activator derived from an inhibitory aptamer. Nucleic Acids Res 2010, 38:2378-2386.
15. Buskirk A.R., Landrigan A., Liu D.R. Engineering a ligand-dependent RNA transcriptional activator. Chem Biol 2004, 11:1157-1163.
16. Werstuck G., Green M. Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998, 282:296-298.
17. Grate D., Wilson C. Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg Med Chem 2001, 9:2565-2570.
18. Suess B., Hanson S., Berens C., Fink B., Schroeder R., Hillen W. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res 2003, 31:1853-1858.
19. Harvey I., Garneau P., Pelletier J. Inhibition of translation by RNA-small molecule interactions. RNA 2002, 8:452-463.
20. Bayer T., Smolke C. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 2005, 23:337-343.
21. Saito H., Kobayashi T., Hara T., Fujita Y., Hayashi K., Furushima R., Inoue T. Synthetic translational regulation by an L7Ae-kink-turn RNP switch. Nat Chem Biol 2010, 6:71-78.
22. Schlatter S., Fussenegger M. Novel CNBP- and La-based translation control systems for mammalian cells. Biotechnol Bioeng 2003, 81:1-12.
23. Yen L., Magnier M., Weissleder R., Stockwell B., Mulligan R. Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries. RNA 2006, 12:797-806.
24. Yen L., Svendsen J., Lee J., Gray J., Magnier M., Baba T., D'Amato R., Mulligan R. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 2004, 431:471-476.
25. Agop-Nersesian C., Pfahler J., Lanzer M., Meissner M. Functional expression of ribozymes in Apicomplexa: towards exogenous control of gene expression by inducible RNA-cleavage. Int J Parasitol 2008, 38:673-681.
26. Chen X., Ellington A.D. Design principles for ligand-sensing, conformation-switching ribozymes. PLoS Comput Biol 2009, 5:e1000620.
27. Win M., Smolke C. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A 2007, 104:14283-14288.
28. Chen Y.Y., Jensen M.C., Smolke C.D. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc Natl Acad Sci U S A 2010, 107:8531-8536.
29. Win M., Smolke C. Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322:456-460.
30. Win M, Smolke C: Raw Data and comment to relevance of the publication: " Higher-order cellular information processing with synthetic RNA devices" 2008. http://openwetware.org/images/4/49/Fulldata.pdf.
31. Wieland M., Hartig J.S. Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew Chem Int Ed Engl 2008, 47:2604-2607.
32. Auslaender S., Ketzer P., Hartig J. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol BioSyst 2010, 6:807-814.
33. Macrae I.J., Zhou K., Li F., Repic A., Brooks A.N., Cande W.Z., Adams P.D., Doudna J.A. Structural basis for double-stranded RNA processing by Dicer. Science 2006, 311:195-198.
34. An C., Trinh V., Yokobayashi Y. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 2006, 12:710-716.
35. Kumar D., An C., Yokobayashi Y. Conditional RNA interference mediated by allosteric ribozyme. J Am Chem Soc 2009, 131:13906-13907.
36. Zeng Y., Cullen B.R. Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J Biol Chem 2005, 280:27595-27603.
37. Rinaudo K., Bleris L., Maddamsetti R., Subramanian S., Weiss R., Benenson Y. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 2007, 25:795-801.