Abstract
BackgroundMicroRNAs (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.ResultsMovingTargets 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.ConclusionMovingTargets 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.
Highlights
MicroRNAs mediate a form of translational regulation in animals
A striking feature of the set of predicted miRNA targets is the disproportionate fraction of mRNAs that encode transcription factors (13 of 41 genes with known function) or have assigned roles in neural processes (7 of 41). [41] noted a similar enrichment for transcription factors and neural genes in predicted miRNA targets in Drosophila
The combination of a conserved 3' UTR database and the MovingTargets algorithm allowed us to predict 83 miRNA targets that meet stringent biological constraints based on features of the probable or proven interactions between individual miRNAs and the mRNAs under their control
Summary
MicroRNAs (miRNAs) mediate a form of translational regulation in animals. The 22 nt lin-4 transcript 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. Let-7 represses translation of lin-41 in a temporally dependent manner, through targeting complementary regions in the 3' UTR of the regulated gene [4]. Several hundred miRNAs have since been identified in a variety of plants and animals through cloning and computational methods, including 78 miRNAs in Drosophila [6]. Many of these miRNAs are expressed in a temporal or tissue-specific dependent manner [1]
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