Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China.
Comput Biol Med. 2012 Jan;42(1):1-7. doi: 10.1016/j.compbiomed.2011.10.001. Epub 2011 Oct 29.
There are two main mechanisms of miRNA-mediated gene silencing: either mRNA degradation or translational repression. However, the precise mechanism of target mRNAs regulated by miRNA remains unclear. As a complementary approach to experiment, a computational method was proposed to recognize the mechanism of miRNA-mediated gene silencing in human. We have analyzed extensive features correlated with miRNA-mediated silencing mechanism of mRNA. It is found that, the duplex structure, the number of binding sites and the structural accessibility of target site region are effective factors in determining whether a target mRNA is cleaved or only translationally inhibited. An SVM-based classifier was constructed to predict the regulation mode of miRNA based on these informative features. The results indicated that the approach proposed is effective in distinguishing whether a target mRNA is cleaved or translationally inhibited in human. Furthermore, the web server microDoR (http://reprod.njmu.edu.cn/microdor) has been developed and is freely available for users.
存在两种 miRNA 介导的基因沉默的主要机制：mRNA 降解或翻译抑制。然而，miRNA 调控的靶 mRNA 的精确机制仍不清楚。作为实验的补充方法，提出了一种计算方法来识别人类 miRNA 介导的基因沉默的机制。我们分析了与 miRNA 介导的 mRNA 沉默机制相关的广泛特征。结果发现，双链结构、结合位点的数量和靶位点区域的结构可及性是决定靶 mRNA 是否被切割或仅被翻译抑制的有效因素。基于这些信息特征，构建了基于 SVM 的分类器来预测 miRNA 的调控模式。结果表明，该方法可有效区分靶 mRNA 在人类中是被切割还是被翻译抑制。此外，还开发了一个名为 microDoR（http://reprod.njmu.edu.cn/microdor）的网络服务器，可供用户免费使用。
