Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method.
Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method.
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DOI：
10.1186/1471-2164-6-88
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发表时间：
2005-06-08
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影响因子：
4.4
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中科院分区：
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microRNAs（miRNAs）是动物体内一种重要的转录调控因子。已经鉴定了数百种动物miRNAs，但只有少数靶点是已知的。预测miRNA的翻译调节靶点具有挑战性，因为与靶mRNA的相互作用通常通过不完全和中断的碱基配对发生。此外，管理这种相互作用的规则也没有完全定义。MovingTargets是一个软件程序，允许研究人员预测一组满足可调整的生物学约束的miRNA靶标。我们使用MovingTargets在果蝇中识别了一组83个高可能性的miRNA靶标，所有这些靶标都遵循严格的生物学约束。我们在培养的细胞中测试并验证了其中3个预测，包括果蝇let-7同源物的目标。此外，我们利用MovingTargets的灵活性，通过放松生物学约束来鉴定和验证靶向tramtrack的miRNA，该基因也已知受到依赖于RNA结合蛋白Musashi的翻译控制。MovingTargets是一个灵活的工具，用于准确预测果蝇中的miRNA靶点。MovingTargets可用于使用所有果蝇miRNA和潜在靶点对miRNA靶点进行全基因组搜索，或者可用于对靶向特定基因的miRNA进行集中搜索。此外，用于定义miRNA靶标的一组生物学约束的值是可调节的，允许软件结合用于表征miRNA靶标的规则，因为这些规则是通过实验确定和解释的。
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. 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. 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.