Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.
Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
Bioinformatics. 2019 Dec 1;35(23):4922-4929. doi: 10.1093/bioinformatics/btz358.
Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous tissues. Therefore, it is necessary to detect D in RNA for further understanding its functional roles. Since wet-experimental techniques for the aim are time-consuming and laborious, it is urgent to develop computational models to identify D modification sites in RNA.
We constructed a predictor, called iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. The final model could produce the overall accuracy of 96.18% with the area under the receiver operating characteristic curve of 0.9839 in jackknife cross-validation test. Furthermore, we performed a series of validations from several aspects and demonstrated the robustness and reliability of the proposed model.
A user-friendly web-server called iRNAD can be freely accessible at http://lin-group.cn/server/iRNAD, which will provide convenience and guide to users for further studying D modification.
二氢尿嘧啶核苷 (D) 是一种常见的真核生物、细菌和少数古菌中的 RNA 转录后修饰。这种修饰可以促进单个核苷酸碱基的构象灵活性。并且其水平在癌组织中增加。因此，有必要在 RNA 中检测 D 以进一步了解其功能作用。由于针对这一目标的湿实验技术既耗时又费力，因此迫切需要开发计算模型来识别 RNA 中的 D 修饰位点。
我们构建了一个名为 iRNAD 的预测器，用于识别 RNA 序列中的 D 修饰位点。在这个预测器中，来自五个物种的 RNA 样本由核苷酸化学性质和核苷酸密度编码。支持向量机用于执行分类。最终模型在 Jackknife 交叉验证测试中产生了 96.18%的总体准确率，接收者操作特征曲线下的面积为 0.9839。此外，我们从多个方面进行了一系列验证，证明了所提出模型的稳健性和可靠性。
一个名为 iRNAD 的用户友好型网络服务器可在 http://lin-group.cn/server/iRNAD 上免费访问，该服务器将为用户进一步研究 D 修饰提供便利和指导。
