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Synthetic RNA circuits

Nature Chemical Biology volume 3, pages 23–28 (2007)Cite this article

Abstract

Natural and engineered RNA 'parts' can perform a variety of functions, including hybridizing to targets, binding ligands and undergoing programmed conformational changes, and catalyzing reactions. These RNA parts can in turn be assembled into synthetic genetic circuits that regulate gene expression by acting either in cis or in trans on mRNAs. As more parts are discovered and engineered, it should be increasingly possible to create synthetic RNA circuits that are able to carry out complex logical operations in cells, either superimposed on or autonomous to extant gene regulation.

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Figure 1: Conformation-switching aptamers.
Figure 2: Designed riboregulators that control translation initiation in prokaryotic mRNAs.
Figure 3: Designed antiswitches that control translation initiation in eukaryotic mRNAs.
Figure 4: Selection scheme for RNA activators of transcription.

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References

  1. Blencowe, B.J. Alternative splicing: new insights from global analyses. Cell 126, 37–47 (2006).

    Article  CAS  PubMed  Google Scholar 

  2. Henkin, T.M. & Yanofsky, C. Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. Bioessays 24, 700–707 (2002).

    Article  CAS  PubMed  Google Scholar 

  3. Keene, J.D. Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc. Natl. Acad. Sci. USA 98, 7018–7024 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Lewis, B.P., Burge, C.B. & Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).

    Article  CAS  PubMed  Google Scholar 

  5. Gilbert, W. Origin of life: the RNA world. Nature 319, 618 (1986).

    Article  Google Scholar 

  6. Clop, A. et al. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat. Genet. 38, 813–818 (2006).

    Article  CAS  PubMed  Google Scholar 

  7. Bartel, D.P. & Chen, C.Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5, 396–400 (2004).

    Article  CAS  PubMed  Google Scholar 

  8. Hornstein, E. & Shomron, N. Canalization of development by microRNAs. Nat. Genet. 38 (suppl.), 20–24 (2006).

    Article  CAS  Google Scholar 

  9. Inouye, M. Antisense RNA: its functions and applications in gene regulation–a review. Gene 72, 25–34 (1988).

    Article  CAS  PubMed  Google Scholar 

  10. Fichou, Y. & Ferec, C. The potential of oligonucleotides for therapeutic applications. Trends Biotechnol. 24, 563–570 (2006).

    Article  CAS  PubMed  Google Scholar 

  11. Dykxhoorn, D.M., Palliser, D. & Lieberman, J. The silent treatment: siRNAs as small molecule drugs. Gene Ther. 13, 541–552 (2006).

    Article  CAS  PubMed  Google Scholar 

  12. Cullen, B.R. Transcription and processing of human microRNA precursors. Mol. Cell 16, 861–865 (2004).

    Article  CAS  PubMed  Google Scholar 

  13. Wassarman, K.M. & Storz, G. 6S RNA regulates E. coli RNA polymerase activity. Cell 101, 613–623 (2000).

    Article  CAS  PubMed  Google Scholar 

  14. Allen, T.A., Von Kaenel, S., Goodrich, J.A. & Kugel, J.F. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11, 816–821 (2004).

    Article  CAS  PubMed  Google Scholar 

  15. Espinoza, C.A., Allen, T.A., Hieb, A.R., Kugel, J.F. & Goodrich, J.A. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat. Struct. Mol. Biol. 11, 822–829 (2004).

    Article  CAS  PubMed  Google Scholar 

  16. Thomas, M. et al. Selective targeting and inhibition of yeast RNA polymerase II by RNA aptamers. J. Biol. Chem. 272, 27980–27986 (1997).

    Article  CAS  PubMed  Google Scholar 

  17. Kettenberger, H. et al. Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs. Nat. Struct. Mol. Biol. 13, 44–48 (2006).

    Article  CAS  PubMed  Google Scholar 

  18. Held, D.M., Kissel, J.D., Patterson, J.T., Nickens, D.G. & Burke, D.H. HIV-1 inactivation by nucleic acid aptamers. Front. Biosci. 11, 89–112 (2006).

    Article  CAS  PubMed  Google Scholar 

  19. Yan, A.C., Bell, K.M., Breeden, M.M. & Ellington, A.D. Aptamers: prospects in therapeutics and biomedicine. Front. Biosci. 10, 1802–1827 (2005).

    Article  CAS  PubMed  Google Scholar 

  20. Joshi, P.J., Fisher, T.S. & Prasad, V.R. Anti-HIV inhibitors based on nucleic acids: emergence of aptamers as potent antivirals. Curr. Drug Targets Infect. Disord. 3, 383–400 (2003).

    Article  CAS  PubMed  Google Scholar 

  21. Cho, E.J., Rajendran, M. & Ellington, A.D. in Advanced Concepts in Fluorescence Spectroscopy; Macromolecular Sensing (eds. Geddes, C.D. & Lakowicz, J.R.) 127–155 (Springer, Baltimore, 2005).

    Book  Google Scholar 

  22. Knudsen, S.M. & Ellington, A.D. Ribozyme deja vu. Nat. Struct. Mol. Biol. 11, 301–303 (2004).

    Article  CAS  PubMed  Google Scholar 

  23. Winkler, W., Nahvi, A. & Breaker, R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002).

    Article  CAS  PubMed  Google Scholar 

  24. Mironov, A.S. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111, 747–756 (2002).

    Article  CAS  PubMed  Google Scholar 

  25. Thore, S., Leibundgut, M. & Ban, N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312, 1208–1211 (2006).

    Article  CAS  PubMed  Google Scholar 

  26. Serganov, A., Polonskaia, A., Phan, A.T., Breaker, R.R. & Patel, D.J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441, 1167–1171 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Sudarsan, N. et al. Tandem riboswitch architectures exhibit complex gene control functions. Science 314, 300–304 (2006).

    Article  CAS  PubMed  Google Scholar 

  28. Mandal, M. et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306, 275–279 (2004).

    Article  CAS  PubMed  Google Scholar 

  29. Winkler, W.C. & Breaker, R.R. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59, 487–517 (2005).

    Article  CAS  PubMed  Google Scholar 

  30. Sudarsan, N., Barrick, J.E. & Breaker, R.R. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9, 644–647 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Kubodera, T. et al. Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR. FEBS Lett. 555, 516–520 (2003).

    Article  CAS  PubMed  Google Scholar 

  32. Doudna, J.A. & Lorsch, J.R. Ribozyme catalysis: not different, just worse. Nat. Struct. Mol. Biol. 12, 395–402 (2005).

    Article  CAS  PubMed  Google Scholar 

  33. Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A. & Breaker, R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281–286 (2004).

    Article  CAS  PubMed  Google Scholar 

  34. Teixeira, A. et al. Autocatalytic RNA cleavage in the human beta-globin pre-mRNA promotes transcription termination. Nature 432, 526–530 (2004).

    Article  CAS  PubMed  Google Scholar 

  35. Salehi-Ashtiani, K., Luptak, A., Litovchick, A. & Szostak, J.W. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 313, 1788–1792 (2006).

    Article  CAS  PubMed  Google Scholar 

  36. Przybilski, R. et al. Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana. Plant Cell 17, 1877–1885 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Fiammengo, R. & Jaschke, A. Nucleic acid enzymes. Curr. Opin. Biotechnol. 16, 614–621 (2005).

    CAS  PubMed  Google Scholar 

  38. Soukup, G.A. & Breaker, R.R. Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA 96, 3584–3589 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Robertson, M.P. & Ellington, A.D. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechnol. 17, 62–66 (1999).

    Article  CAS  PubMed  Google Scholar 

  40. Robertson, M.P. & Ellington, A.D. In vitro selection of nucleoprotein enzymes. Nat. Biotechnol. 19, 650–655 (2001).

    Article  CAS  PubMed  Google Scholar 

  41. Vaish, N.K. et al. Monitoring post-translational modification of proteins with allosteric ribozymes. Nat. Biotechnol. 20, 810–815 (2002).

    Article  CAS  PubMed  Google Scholar 

  42. Atsumi, S., Ikawa, Y., Shiraishi, H. & Inoue, T. Design and development of a catalytic ribonucleoprotein. EMBO J. 20, 5453–5460 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Hartig, J.S. et al. Protein-dependent ribozymes report molecular interactions in real time. Nat. Biotechnol. 20, 717–722 (2002).

    Article  CAS  PubMed  Google Scholar 

  44. Robertson, M.P., Knudsen, S.M. & Ellington, A.D. In vitro selection of ribozymes dependent on peptides for activity. RNA 10, 114–127 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Najafi-Shoushtari, S.H., Mayer, G. & Famulok, M. Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. Nucleic Acids Res. 32, 3212–3219 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Breaker, R.R. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13, 31–39 (2002).

    Article  CAS  PubMed  Google Scholar 

  47. Wu, A.M. & Senter, P.D. Arming antibodies: prospects and challenges for immunoconjugates. Nat. Biotechnol. 23, 1137–1146 (2005).

    Article  CAS  PubMed  Google Scholar 

  48. Homann, M. & Goringer, H.U. Combinatorial selection of high affinity RNA ligands to live African trypanosomes. Nucleic Acids Res. 27, 2006–2014 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Shangguan, D. et al. Aptamers evolved from live cells as effective molecular probes for cancer study. Proc. Natl. Acad. Sci. USA 103, 11838–11843 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Lupold, S.E., Hicke, B.J., Lin, Y. & Coffey, D.S. Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res. 62, 4029–4033 (2002).

    CAS  PubMed  Google Scholar 

  51. Chu, T.C. et al. Aptamer:toxin conjugates that specifically target prostate tumor cells. Cancer Res. 66, 5989–5992 (2006).

    Article  CAS  PubMed  Google Scholar 

  52. Farokhzad, O.C. et al. Nanoparticle-aptamer bioconjugates: a new approach for targeting prostate cancer cells. Cancer Res. 64, 7668–7672 (2004).

    Article  CAS  PubMed  Google Scholar 

  53. Farokhzad, O.C. et al. Targeted nanoparticle-aptamer bioconjugates for cancer chemotherapy in vivo. Proc. Natl. Acad. Sci. USA 103, 6315–6320 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Chu, T.C., Twu, K.Y., Ellington, A.D. & Levy, M. Aptamer mediated siRNA delivery. Nucleic Acids Res. 34, e73 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. McNamara, J.O. II, et al. Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat. Biotechnol. 24, 1005–1015 (2006).

    Article  CAS  PubMed  Google Scholar 

  56. Werstuck, G. & Green, M.R. Controlling gene expression in living cells through small molecule-RNA interactions. Science 282, 296–298 (1998).

    Article  CAS  PubMed  Google Scholar 

  57. Grate, D. & Wilson, C. Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg. Med. Chem. 9, 2565–2570 (2001).

    Article  CAS  PubMed  Google Scholar 

  58. Harvey, I., Garneau, P. & Pelletier, J. Inhibition of translation by RNA-small molecule interactions. RNA 8, 452–463 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Hanson, S., Bauer, G., Fink, B. & Suess, B. Molecular analysis of a synthetic tetracycline-binding riboswitch. RNA 11, 503–511 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Suess, B. et al. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res. 31, 1853–1858 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Hanson, S., Berthelot, K., Fink, B., McCarthy, J.E. & Suess, B. Tetracycline-aptamer-mediated translational regulation in yeast. Mol. Microbiol. 49, 1627–1637 (2003).

    Article  CAS  PubMed  Google Scholar 

  62. Kim, D.S., Gusti, V., Pillai, S.G. & Gaur, R.K. An artificial riboswitch for controlling pre-mRNA splicing. RNA 11, 1667–1677 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Suess, B., Fink, B., Berens, C., Stentz, R. & Hillen, W. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res. 32, 1610–1614 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Desai, S.K. & Gallivan, J.P. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc. 126, 13247–13254 (2004).

    Article  CAS  PubMed  Google Scholar 

  65. Kertsburg, A. & Soukup, G.A. A versatile communication module for controlling RNA folding and catalysis. Nucleic Acids Res. 30, 4599–4606 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Thompson, K.M., Syrett, H.A., Knudsen, S.M. & Ellington, A.D. Group I aptazymes as genetic regulatory switches. BMC Biotechnol. [online] 2, 21 (2002).

    Article  Google Scholar 

  67. Yen, L. et al. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431, 471–476 (2004).

    Article  CAS  PubMed  Google Scholar 

  68. Yen, L., Magnier, M., Weissleder, R., Stockwell, B.R. & Mulligan, R.C. Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries. RNA 12, 797–806 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Isaacs, F.J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22, 841–847 (2004).

    Article  CAS  PubMed  Google Scholar 

  70. Lease, R.A., Cusick, M.E. & Belfort, M. Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc. Natl. Acad. Sci. USA 95, 12456–12461 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Bayer, T.S. & Smolke, C.D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 23, 337–343 (2005).

    Article  CAS  PubMed  Google Scholar 

  72. An, C.I., Trinh, V.B. & Yokobayashi, Y. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 12, 710–716 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. SenGupta, D.J. et al. A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. USA 93, 8496–8501 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Sengupta, D.J., Wickens, M. & Fields, S. Identification of RNAs that bind to a specific protein using the yeast three-hybrid system. RNA 5, 596–601 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Saha, S., Ansari, A.Z., Jarrell, K.A. & Ptashne, M. RNA sequences that work as transcriptional activating regions. Nucleic Acids Res. 31, 1565–1570 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Buskirk, A.R., Kehayova, P.D., Landrigan, A. & Liu, D.R. In vivo evolution of an RNA-based transcriptional activator. Chem. Biol. 10, 533–540 (2003).

    Article  CAS  PubMed  Google Scholar 

  77. Buskirk, A.R., Landrigan, A. & Liu, D.R. Engineering a ligand-dependent RNA transcriptional activator. Chem. Biol. 11, 1157–1163 (2004).

    Article  CAS  PubMed  Google Scholar 

  78. Elowitz, M.B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).

    Article  CAS  PubMed  Google Scholar 

  79. Gardner, T.S., Cantor, C.R. & Collins, J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).

    Article  CAS  PubMed  Google Scholar 

  80. Levskaya, A. et al. Synthetic biology: engineering Escherichia coli to see light. Nature 438, 441–442 (2005).

    Article  CAS  PubMed  Google Scholar 

  81. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R. & Shapiro, E. An autonomous molecular computer for logical control of gene expression. Nature 429, 423–429 (2004).

    Article  CAS  PubMed  Google Scholar 

  82. Stojanovic, M.N. & Stefanovic, D. A deoxyribozyme-based molecular automaton. Nat. Biotechnol. 21, 1069–1074 (2003).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We would like to thank M. Levy for help with figure preparation.

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  1. the Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, 1 University Station/A4800, University of Texas at Austin, Austin, 78712, Texas, USA

    Eric A Davidson & Andrew D Ellington

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Correspondence to Andrew D Ellington.

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A.E. is a founder of Archemix, which works on therapeutic applications of aptamers.

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Davidson, E., Ellington, A. Synthetic RNA circuits. Nat Chem Biol 3, 23–28 (2007). https://doi.org/10.1038/nchembio846

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