BMC Genomics Software Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method Craig Burgler and Paul M Macdonald* BioMed Central Open Access Address: 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, USA Email: Craig Burgler - craig.burgler@mail.utexas.edu; Paul M Macdonald* - pmacdonald@mail.utexas.edu * Corresponding author Published: 08 June 2005 BMC Genomics 2005, 6:88 doi:10.1186/1471-2164-6-88 This article is available from: http://www.biomedcentral.com/1471-2164/6/88 Received: 07 December 2004 Accepted: 08 June 2005 © 2005 Burgler and Macdonald; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: 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. Background MicroRNAs (miRNAs) are an abundant evolutionarily conserved class of small (~22 nts) RNAs which play a sub- stantial gene regulatory role in plants and animals [1]. The first miRNA discovered, lin-4, was identified in a genetic screen focused on identifying genes involved in the hete- rochronic pathway in C. elegans [2]. The 22 nt lin-4 tran- script temporally negatively regulates translation of lin-14, apparently through antisense RNA-RNA interaction between the lin-4 transcript and multiple regions in the lin-14 3' UTR. Seven years later a second small RNA, let-7, was found, and it too acts in the heterochronic pathway in C. elegans [3]. let-7 represses translation of lin-41 in a tem- porally dependent manner, also through targeting com- plementary regions in the 3' UTR of the regulated gene [4]. let-7 transcripts are found in all bilaterians tested [5]. This discovery led to the understanding that miRNA-mediated Page 1 of 11 (page number not for citation purposes)