Abstract
We created an accelerated version of MC-Fold called MC-Flashfold that allows us to compute large numbers of competing secondary structures including noncanonical base pairs. We visualize the base pairs in these sets using high quality intuitive dot plots and arc plots. Our new tools allow us to explore RNA dynamics by visualizing the competing structures in free energy bands. Here we describe how to use these tools to generate dot plots that reveal the postulated anti-terminator stem in the E. coli trp operon leader sequence. These plots show the anti-terminator hairpin loop during transcription and as a minor population of the full-length leader sequence. This is a case of switching RNA structure that had been originally postulated based on short dyad inverted repeats. Other switching RNA sequences can be analyzed by using our method.
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References
Leontis NB, Stombaugh J, Westhof E (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30(16):3497–3531
Parisien M, Major F (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452(7183):51–55. doi:10.1038/nature06684
Al-Hashimi HM, Walter NG (2008) RNA dynamics: it is about time. Curr Opin Struct Biol 18:321–329
Williamson JR (2000) Induced fit in RNA-protein recognition. Nat Struct Biol 7(10):834–837. doi:10.1038/79575
Dethoff EA, Petzold K, Chugh J, Casiano-Negroni A, Al-Hashimi HM (2012) Visualizing transient low-populated structures of RNA. Nature 491(7426):724–728. doi:10.1038/nature11498
Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6:26. doi:10.1186/1748-7188-6-26
Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, Dinse J, Lappe M (2011) CMView: interactive contact map visualization and analysis. Bioinformatics 27(11):1573–1574. doi:10.1093/bioinformatics/btr163
Pietal MJ, Szostak N, Rother KM, Bujnicki JM (2012) RNAmap2D—calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. BMC Bioinformatics 13:333. doi:10.1186/1471-2105-13-333
Dallaire P (2015) Une signature du polymorphisme structural d’acides ribonucléiques non-codants permettant de comparer leurs niveaux d’activités biochimiques. Université de Montréal, Montréal
Kolter R, Yanofsky C (1982) Attenuation in amino acid biosynthetic operons. Annu Rev Genet 16:113–134. doi:10.1146/annurev.ge.16.120182.000553
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Dallaire, P., Major, F. (2016). Exploring Alternative RNA Structure Sets Using MC-Flashfold and db2cm. In: Turner, D., Mathews, D. (eds) RNA Structure Determination. Methods in Molecular Biology, vol 1490. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6433-8_15
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DOI: https://doi.org/10.1007/978-1-4939-6433-8_15
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Publisher Name: Humana Press, New York, NY
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