Saçar Demirci Müşerref Duygu, Yousef Malik, Allmer Jens
Faculty of Life and Natural Sciences, Department of Bioinformatics, Abdullah Gul University, Kayseri, Turkey.
Department of Community Information Systems, Zefat Academic College, Zefat, Israel.
Methods Mol Biol. 2019;1912:175-196. doi: 10.1007/978-1-4939-8982-9_7.
Proteins have a strong influence on the phenotype and their aberrant expression leads to diseases. MicroRNAs (miRNAs) are short RNA sequences which posttranscriptionally regulate protein expression. This regulation is driven by miRNAs acting as recognition sequences for their target mRNAs within a larger regulatory machinery. A miRNA can have many target mRNAs and an mRNA can be targeted by many miRNAs which makes it difficult to experimentally discover all miRNA-mRNA interactions. Therefore, computational methods have been developed for miRNA detection and miRNA target prediction. An abundance of available computational tools makes selection difficult. Additionally, interactions are not currently the focus of investigation although they more accurately define the regulation than pre-miRNA detection or target prediction could perform alone. We define an interaction including the miRNA source and the mRNA target. We present computational methods allowing the investigation of these interactions as well as how they can be used to extend regulatory pathways. Finally, we present a list of points that should be taken into account when investigating miRNA-mRNA interactions. In the future, this may lead to better understanding of functional interactions which may pave the way for disease marker discovery and design of miRNA-based drugs.
蛋白质对表型有强大影响，其异常表达会导致疾病。微小RNA（miRNA）是短RNA序列，可在转录后调节蛋白质表达。这种调节由miRNA驱动，miRNA在更大的调节机制中充当其靶标mRNA的识别序列。一个miRNA可以有许多靶标mRNA，一个mRNA可以被许多miRNA靶向，这使得通过实验发现所有miRNA-mRNA相互作用变得困难。因此，已经开发了用于miRNA检测和miRNA靶标预测的计算方法。大量可用的计算工具使得选择变得困难。此外，相互作用目前并非研究重点，尽管它们比单独的前体miRNA检测或靶标预测更准确地定义调节作用。我们定义了一种包括miRNA来源和mRNA靶标的相互作用。我们提出了计算方法，可用于研究这些相互作用以及如何利用它们扩展调节途径。最后，我们列出了在研究miRNA-mRNA相互作用时应考虑的要点。未来，这可能会更好地理解功能相互作用，为疾病标志物发现和基于miRNA的药物设计铺平道路。
