Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method

dc.creatorBurgler, Craigen
dc.creatorMacdonald, Paul M.en
dc.date.accessioned2014-12-15T17:10:09Zen
dc.date.available2014-12-15T17:10:09Zen
dc.date.issued2005-06-08en
dc.descriptionAuthors are with the Section of Molecular Cell and Developmental Biology, Institute for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station A-4800, Austin, TX 78712-0159, USAen
dc.description.abstractBackground: MicroRNAs (miRNAs) mediate a form of translational regulation in animals. Hundreds of animal miRNAs have been identified, but only a few of their targets are known. Prediction of miRNA targets for translational regulation is challenging, since the interaction with the target mRNA usually occurs via incomplete and interrupted base pairing. Moreover, the rules that govern such interactions are incompletely defined. -- Results: MovingTargets is a software program that allows a researcher to predict a set of miRNA targets that satisfy an adjustable set of biological constraints. We used MovingTargets to identify a high-likelihood set of 83 miRNA targets in Drosophila, all of which adhere to strict biological constraints. We tested and verified 3 of these predictions in cultured cells, including a target for the Drosophila let-7 homolog. In addition, we utilized the flexibility of MovingTargets by relaxing the biological constraints to identify and validate miRNAs targeting tramtrack, a gene also known to be subject to translational control dependent on the RNA binding protein Musashi. -- Conclusion: MovingTargets is a flexible tool for the accurate prediction of miRNA targets in Drosophila. MovingTargets can be used to conduct a genome-wide search of miRNA targets using all Drosophila miRNAs and potential targets, or it can be used to conduct a focused search for miRNAs targeting a specific gene. In addition, the values for a set of biological constraints used to define a miRNA target are adjustable, allowing the software to incorporate the rules used to characterize a miRNA target as these rules are experimentally determined and interpreted.en
dc.description.catalogingnotepmacdonald@mail.utexas.eduen
dc.description.departmentInstitute for Cellular and Molecular Biologyen
dc.description.sponsorshipen
dc.identifier.Filename1471-2164-6-88en
dc.identifier.citationBurgler, Craig, and Paul M. Macdonald. “Prediction and Verification of microRNA Targets by MovingTargets, a Highly Adaptable Prediction Method.” BMC Genomics 6, no. 1 (June 8, 2005): 88. doi:10.1186/1471-2164-6-88.en
dc.identifier.doidoi:10.1186/1471-2164-6-88en
dc.identifier.urihttp://hdl.handle.net/2152/27838en
dc.language.isoEnglishen
dc.publisherBMC Genomicsen
dc.rightsAdministrative deposit of works to UT Digital Repository: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access at http://www.biomedcentral.com. The public license is specified as CC-BY: http://creativecommons.org/licenses/by/4.0/. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en
dc.subjectmicroRNAen
dc.subjectMovingTargetsen
dc.subjectadaptable prediction methoden
dc.subjectmiRNAsen
dc.titlePrediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction methoden
dc.typeOtheren
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