Fast and effective prediction of microRNA/target duplexes
Top Cited Papers
- 21 September 2004
- journal article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 10 (10) , 1507-1517
- https://doi.org/10.1261/rna.5248604
Abstract
MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a few targets are known. In contrast to plant miRNAs, which usually bind nearly perfectly to their targets, animal miRNAs bind less tightly, with a few nucleotides being unbound, thus producing more complex secondary structures of miRNA/target duplexes. Here, we present a program, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs. In general, the program finds the energetically most favorable hybridization sites of a small RNA in a large RNA. Intramolecular hybridizations, that is, base pairings between target nucleotides or between miRNA nucleotides are not allowed. For large targets, the time complexity of the algorithm is linear in the target length, allowing many long targets to be searched in a short time. Statistical significance of predicted targets is assessed with an extreme value statistics of length normalized minimum free energies, a Poisson approximation of multiple binding sites, and the calculation of effective numbers of orthologous targets in comparative studies of multiple organisms. We applied our method to the prediction of Drosophila miRNA targets in 3′UTRs and coding sequence. RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/).Keywords
This publication has 34 references indexed in Scilit:
- A discipline of dynamic programming over sequence dataScience of Computer Programming, 2004
- Computational identification of microRNA targetsDevelopmental Biology, 2004
- Prediction of Mammalian MicroRNA TargetsCell, 2003
- Identification of Drosophila MicroRNA TargetsPLoS Biology, 2003
- Discovery of genes with highly restricted expression patterns in theDrosophilawing disc using DNA oligonucleotide microarraysDevelopment, 2003
- Micro-RNAsThe Journal of cell biology, 2002
- An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegansScience, 2001
- Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology, 1999
- A dynamic programming algorithm for RNA structure prediction including pseudoknots 1 1Edited by I. TinocoJournal of Molecular Biology, 1999
- The Cold Shock Domain Protein LIN-28 Controls Developmental Timing in C. elegans and Is Regulated by the lin-4 RNACell, 1997