Mockly Sophie, Seitz Hervé
IGH (CNRS and University of Montpellier), Montpellier, France.
Methods Mol Biol. 2019;1970:291-314. doi: 10.1007/978-1-4939-9207-2_16.
MicroRNAs and their Argonaute protein partners constitute the RISC complex, which can repress specific target mRNAs. The identification of microRNA targets is of central importance, and various experimental and computational methods have been developed over the last 15 years. Most experimental methods are based on the assumption that mRNAs which interact physically with the RISC complex constitute regulatory targets and, similarly, some computational methods only aim at predicting physical interactors for RISC. Besides specific limitations, which we discuss for each method, the mere concept of assuming a functional role for every detected molecular event is likely to identify many deceptive interactions (i.e., interactions that really exist at the molecular scale, but without controlling any biological function at the macroscopic scale).In order to select biologically important interactions, some computational tools interrogate the phylogenetic conservation of microRNA/mRNA interactions, thus theoretically selecting only biologically relevant targets. Yet even comparative genomics can yield false positives.Conceptual and technical limitations for all these techniques tend to be overlooked by the scientific community. This review sums them up, emphasizing on the implications of these issues on our understanding of microRNA biology.
微小RNA及其AGO蛋白伴侣构成RNA诱导沉默复合体（RISC），该复合体可抑制特定的靶标信使核糖核酸（mRNA）。微小RNA靶标的鉴定至关重要，在过去15年里已开发出各种实验和计算方法。大多数实验方法基于这样的假设，即与RISC复合体发生物理相互作用的mRNA构成调控靶标，同样，一些计算方法仅旨在预测RISC的物理相互作用分子。除了我们针对每种方法所讨论的特定局限性外，仅仅假设每个检测到的分子事件都具有功能作用这一概念，很可能会识别出许多具有误导性的相互作用（即那些在分子水平确实存在，但在宏观水平上不控制任何生物学功能的相互作用）。为了选择具有生物学重要性的相互作用，一些计算工具会研究微小RNA/mRNA相互作用的系统发育保守性，从而理论上仅选择具有生物学相关性的靶标。然而，即使是比较基因组学也可能产生假阳性结果。科学界往往忽视了所有这些技术在概念和技术上的局限性。本综述对这些局限性进行了总结，强调了这些问题对我们理解微小RNA生物学的影响。
