Abstract
Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.
In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs. We verify the performance of our algorithms for joint structure and binding site prediction on a set of known interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform all competitive approaches.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alkan, C., Karakoc, E., Nadeau, J.H., Sahinalp, S.C., Zhang, K.: RNA-RNA interaction prediction and antisense RNA target search. Journal of Computational Biology 13(2), 267–282 (2006)
Andronescu, M., Zhang, Z.C., Condon, A.: Secondary structure prediction of interacting RNA molecules. J. Mol. Biol. 345, 987–1001 (2005)
Bernhart, S.H., Tafer, H., Mückstein, U., Flamm, C., Stadler, P.F., Hofacker, I.L.: Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol. 1, 3 (2006)
Busch, A., Richter, A.S., Backofen, R.: IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, page btn544 (2008)
Chitsaz, H., Salari, R., Sahinalp, S.C., Backofen, R.: A partition function algorithm for two interacting nucleic acid strands. Bioinformatics 25(12) (2009)
Dimitrov, R.A., Zuker, M.: Prediction of hybridization and melting for double-stranded nucleic acids. Biophysical Journal 87, 215–226 (2004)
Hackermller, J., Meisner, N.C., Auer, M., Jaritz, M., Stadler, P.F.: The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene 345, 3–12 (2005)
Kato, Y., Akutsu, T., Seki, H.: A grammatical approach to rna-rna interaction prediction. Pattern Recogn. 42(4), 531–538 (2009)
Markham, N.R., Zuker, M.: UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol. 453, 3–31 (2008)
McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105–1119 (1990)
Meisner, N.C., Hackermller, J., Uhl, V., Aszdi, A., Jaritz, M., Auer, M.: mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure. Chembiochem. 5, 1432–1447 (2004)
Mückstein, U., Tafer, H., Hackermüller, J., Bernhart, S.H., Hernandez-Rosales, M., Vogel, J., Stadler, P.F., Hofacker, I.L.: Translational control by RNA-RNA interaction: Improved computation of RNA-RNA binding thermodynamics. Bioinformatics Research and Development 13, 114–127 (2008)
Mückstein, U., Tafer, H., Hackermüller, J., Bernhart, S.H., Stadler, P.F., Hofacker, I.L.: Thermodynamics of RNA-RNA binding. Bioinformatics 22, 1177–1182 (2006)
Pervouchine, D.D.: IRIS: intermolecular RNA interaction search. Genome Inform. 15, 92–101 (2004)
Rehmsmeier, M., Steffen, P., Hochsmann, M., Giegerich, R.: Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507–1517 (2004)
Wagner, E.G., Flrdh, K.: Antisense RNAs everywhere? Trends Genet. 18, 223–226 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Salari, R., Backofen, R., Sahinalp, S.C. (2009). Fast Prediction of RNA-RNA Interaction. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_22
Download citation
DOI: https://doi.org/10.1007/978-3-642-04241-6_22
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04240-9
Online ISBN: 978-3-642-04241-6
eBook Packages: Computer ScienceComputer Science (R0)