Engineered riboregulators enable post-transcriptional control of gene expression (original) (raw)
References
Gesteland, R.F., Cech, T.R. & Atkins, J.F. The RNA World, edn. 2 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1999). Google Scholar
Eddy, S.R. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet.2, 919–929 (2001). ArticleCASPubMed Google Scholar
Kruger, K. et al. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell31, 147–157 (1982). ArticleCASPubMed Google Scholar
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The TNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell35, 849–857 (1983). ArticleCASPubMed Google Scholar
Doudna, J.A. & Cech, T.R. The chemical repertoire of natural ribozymes. Nature418, 222–228 (2002). ArticleCASPubMed Google Scholar
Steward, P., Molin, S. & Nordstrom, K. RNAs involved in copy-number control and incompatibility of plasmid R1. Proc. Natl. Acad. Sci. USA78, 6008–6012 (1981). Article Google Scholar
Wagner, E.G.H. & Simons, R.W. Antisense RNA control in bacteria, phages, and plasmids. Annu. Rev. Microbiol.48, 713–742 (1994). ArticleCASPubMed Google Scholar
Lee, R.C., Feinbaum, R.L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell75, 843–854 (1993). ArticleCASPubMed Google Scholar
Gottesman, S. Stealth regulation: biological circuits with small RNA switches. Genes Dev.16, 2829–2842 (2002). ArticleCASPubMed Google Scholar
Gelfand, M.S., Mironov, A.A., Jomantas, J., Kozlov, Y.I. & Perumov, D.A. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet.15, 439–442 (1999). ArticleCASPubMed Google Scholar
Winkler, W., Nahvi, A. & Breaker, R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature419, 952–656 (2002). ArticleCASPubMed Google Scholar
Johansson, J. et al. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell110, 551–561 (2002). ArticlePubMed Google Scholar
Mironov, A. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell111, 747–756 (2002). ArticleCASPubMed Google Scholar
Morita, M.T. et al. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Genes Dev.13, 655–665 (2002). Article Google Scholar
Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C. & Breaker, R.R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell113, 577–586 (2003). ArticleCASPubMed Google Scholar
Winkler, W., Nahvi, A., Roth, A., Collins, J.A. & Breaker, R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature428, 281–286 (2004). ArticleCASPubMed Google Scholar
Lease, R.A. & Belfort, M. A _trans_-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc. Natl. Acad. Sci. USA97, 9919–9924 (2000). ArticleCASPubMedPubMed Central Google Scholar
Majdalani, N., Hernandez, D. & Gottesman, S. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol. Microbiol.46, 813–826 (2002). ArticleCASPubMed Google Scholar
Opalinska, J.B. & Gewirtz, A.M. Nucleic–acid therapeutics: basic principles and recent applications. Nat. Rev. Drug Discov.1, 503–514 (2002). ArticleCASPubMed Google Scholar
Good, L. Translation repression by antisense sequences. Cell. Mol. LifeSci.60, 854–861 (2003). ArticleCAS Google Scholar
Ji, Y. et al. Identification of critical Staphylococcal gene using conditional phenotypes generated by antisense RNA. Science293, 2266–2269 (2001). ArticleCASPubMed Google Scholar
Dykxhoorn, D., Novina, C.D. & Sharp, P.A. Killing the messenger: Short RNAs that silence gene expression. Nat. Rev. Mol. Cell Biol.4, 457–467 (2003). ArticleCASPubMed Google Scholar
Engdahl, H.M., Lindell, M. & Wagner, E.G.H. Introduction of an RNA stability element at the 5′–end of an antisense RNA cassette increases the inhibition of target RNA translation. Antisense Nucleic A.11, 29–40 (2001). CAS Google Scholar
Morfeldt, E., Taylor, D., von Gabain, A. & Arvidson, S. Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII. EMBO J.14, 4569–4577 (1995). ArticleCASPubMedPubMed Central Google Scholar
Franch, T., Petersen, M., Wagner, E.G.H., Jacobsen, J.P. & Gerdes, K. Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J. Mol. Biol.294, 1115–1125 (1999). ArticleCASPubMed Google Scholar
Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraCI1-I2 regulatory elements. Nucleic Acids Res.25, 1203–1210 (1997). ArticleCASPubMedPubMed Central Google Scholar
Cormack, B.P., Valdivia, R.C. & Falkow, S. FACS-optimized mutants of the green fluorescent protein (GFP). Gene173, 33–38 (1996). ArticleCASPubMed Google Scholar
Hjalt, T.A.H. & Wagner, E.G.H. Bulged-out nucleotides protect an antisense RNA from RNase III cleavage. Nucleic Acids Res.23, 571–579 (1995). ArticleCASPubMedPubMed Central Google Scholar
Court, D. RNA processing and degradation by RNase III. Control of Messenger RNA Stability, (eds. Belasco, J. & Brawerman, G.) 71–116. (Academic Press, New York, 1993). Chapter Google Scholar
Rivas, E., Klein, R.J., Jones, T.A. & Eddy, S.R. Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr. Biol.11, 1369–1373 (2001). ArticleCASPubMed Google Scholar
Hasty, J., McMillen, D. & Collins, J.J. Engineered gene circuits. Nature420, 224–230 (2002). ArticleCASPubMed Google Scholar
Gardner, T.S., di Bernardo, D., Lorenz, D. & Collins, J.J. Inferring genetic networks and identifying compound mode of action via expression profiling. Science301, 102–105 (2003). ArticleCASPubMed Google Scholar
Bartel, D.P. & Szostak, J.W. Isolation of new ribozymes from a large pool of random sequences. Science261, 1411–1418 (1993). ArticleCASPubMed Google Scholar
Wilson, D.S. & Szostak, J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem.68, 611–647 (1999). ArticleCASPubMed Google Scholar
Ellington, A.D. & Szostak, J.W. In vitro selection of RNA molecules that bind specific ligands. Nature346, 818–822 (1990). ArticleCASPubMed Google Scholar
Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science249, 505–510 (1990). ArticleCASPubMed Google Scholar
Robertson, M.P. & Ellington, A.D. In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechnol.17, 62–66 (1999). ArticleCASPubMed Google Scholar
Faulhammer, D., Cukras, A.R., Lipton, R.J. & Landweber, L.F. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. USA97, 1385–1389 (2000). ArticleCASPubMedPubMed Central Google Scholar
Smith, H.O., Hutchison, C.A. III, Pfannkoch, C. & Venter, J.C. Generating a synthetic genome by whole genome assembly: φx174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA100, 15440–15445 (2003). ArticleCASPubMedPubMed Central Google Scholar
Tabor, J.J. & Ellington, A.D. Playing to win at DNA computation. Nat. Biotechnol.21, 1013–1015 (2003). ArticleCASPubMed Google Scholar
Stojanovic, M.N. & Stefanovic, D. A deoxyribozyme–based molecular automaton. Nat. Biotechnol.21, 1069–1074 (2003). ArticleCASPubMed Google Scholar
Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: A Laboratory Manual, edn. 2 (Cold Spring Harbor Laboratory Press, Plainview, New York, 1989). Google Scholar
Andersen, J.B. et al. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol.64, 2240–2246 (1998). CASPubMedPubMed Central Google Scholar
Ding, C. & Cantor, C.R. A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. Proc. Natl. Acad. Sci. USA100, 3059–3064 (2003). ArticleCASPubMedPubMed Central Google Scholar
Marky, L.A. & Breslauer, K.J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers26, 1601–1620 (1987). ArticleCASPubMed Google Scholar