Gong Jing, Liu Chunjie, Liu Wei, Xiang Yu, Diao Lixia, Guo An-Yuan, Han Leng
Department of Bioinformatics and Systems Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China.
Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA.
Nucleic Acids Res. 2017 Jan 4;45(D1):D79-D84. doi: 10.1093/nar/gkw835. Epub 2016 Sep 19.
RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome. To provide a useful resource for the functional effects of RNA editing in long noncoding RNAs (lncRNAs), we systematically analyzed the A-to-I editing sites in lncRNAs across human, rhesus, mouse, and fly, and observed an appreciable number of RNA editing sites which can significantly impact the secondary structures of lncRNAs and lncRNA-miRNA interactions. All the data were compiled into LNCediting, a user-friendly database (http://bioinfo.life.hust.edu.cn/LNCediting/). LNCediting provides customized tools to predict functional effects of novel editing sites in lncRNAs. We hope that it will become an important resource for exploring functions of RNA editing sites in lncRNAs.
RNA编辑是一种广泛存在的转录后机制，它可以使RNA转录本中的特定核苷酸序列发生单个碱基变化。RNA编辑事件可导致错义密码子改变以及mRNA中可变剪接的调控，还可导致非编码RNA及其结合位点的修饰。最近的计算研究从下一代测序（NGS）中准确检测到了超过200万个A-to-I RNA编辑位点。然而，这些RNA编辑位点中的绝大多数功能未知，且位于基因组的非编码区域。为了为长链非编码RNA（lncRNA）中RNA编辑的功能效应提供有用资源，我们系统分析了人类、恒河猴、小鼠和果蝇lncRNA中的A-to-I编辑位点，并观察到相当数量的RNA编辑位点会显著影响lncRNA的二级结构以及lncRNA与miRNA的相互作用。所有数据都被整合到LNCediting中，这是一个用户友好型数据库（http://bioinfo.life.hust.edu.cn/LNCediting/）。LNCediting提供了定制工具来预测lncRNA中新型编辑位点的功能效应。我们希望它将成为探索lncRNA中RNA编辑位点功能的重要资源。
