Yuan Chunhui, Meng Xianwen, Li Xue, Illing Nicola, Ingle Robert A, Wang Jingjing, Chen Ming
Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
Nucleic Acids Res. 2017 Jan 4;45(D1):D1009-D1014. doi: 10.1093/nar/gkw916. Epub 2016 Oct 7.
Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) which contains potential ceRNA target-target, and ceRNA target-mimic pairs from 26 plant species. For example, in Arabidopsis lyrata, 311 candidate ceRNAs are identified which could affect 2646 target-miRNA-target interactions. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target-target interactions from their own data.
RNA分子之间对微小RNA（miRNA）结合位点的竞争已成为真核基因表达调控的一种新机制。竞争性内源RNA（ceRNA）可以作为miRNA结合的诱饵，从而通过调控共享相同或相似微小RNA反应元件的其他RNA转录本的丰度形成ceRNA网络。尽管这种类型的RNA相互作用最初是在拟南芥中描述的，随后在动物模型中也被证明是活跃的，但目前还没有收集植物潜在ceRNA数据的数据库。我们开发了一个植物ceRNA数据库（PceRBase，http://bis.zju.edu.cn/pcernadb/index.jsp），其中包含来自26种植物的潜在ceRNA靶标-靶标对和ceRNA靶标-模拟物对。例如，在琴叶拟南芥中，鉴定出311个候选ceRNA，它们可能影响2646个靶标-miRNA-靶标相互作用。数据库中还存储了miRNA与其靶标mRNA转录本之间的预测配对结构、ceRNA对的表达水平以及相关的基因本体注释。通过网络界面可以方便地浏览和搜索感兴趣的特定基因。提供了用于ceRNA网络中基因可视化和富集分析的工具。此外，用户可以使用PceRBase从自己的数据中预测新的竞争性模拟物-靶标和靶标-靶标相互作用。
