PeTMbase: A database of plant endogenous target mimics (eTMs)

MicroRNAs (miRNA) are small endogenous RNA molecules, which regulate target gene expression at post-transcriptional level. Besides, miRNA activity can be controlled by a newly discovered regulatory mechanism called endogenous target mimicry (eTM). In target mimicry, eTMs bind to the corresponding miRNAs to block the binding of specific transcript leading to increase mRNA expression. Thus, miRNA-eTM-target-mRNA regulation modules involving a wide range of biological processes; an increasing need for a comprehensive eTM database arose. Except miRSponge with limited number of Arabidopsis eTM data no available database and/or repository was developed and released for plant eTMs yet. Here, we present an online plant eTM database, called PeTMbase (http://petmbase.org), with a highly efficient search tool. To establish the repository a number of identified eTMs was obtained utilizing from high-throughput RNA-sequencing data of 11 plant species. Each transcriptome libraries is first mapped to corresponding plant genome, then long non-coding RNA (lncRNA) transcripts are characterized. Furthermore, additional lncRNAs retrieved from GREENC and PNRD were incorporated into the lncRNA catalog. Then, utilizing the lncRNA and miRNA sources a total of 2,728 eTMs were successfully predicted. Our regularly updated database, PeTMbase, provides high quality information regarding miRNA:eTM modules and will aid functional genomics studies particularly, on miRNA regulatory networks.

MicroRNAs（miRNA）为一种小型内源性RNA分子，能够在转录后水平上调控靶基因的表达。此外，miRNA活性可通过一种新近发现的调控机制——内源性靶模拟（eTM）——进行调节。在靶模拟过程中，eTMs与相应的miRNAs结合，从而阻止特定转录本的结合，导致mRNA表达的增加。因此，miRNA-eTM-靶-mRNA调控模块涉及广泛的生物学过程，对构建全面的eTM数据库的需求日益增长。目前，除了miRSponge含有数量有限的拟南芥eTM数据外，尚无针对植物eTMs的数据库和/或存储库被开发并发布。在此，我们推出一个在线植物eTM数据库，命名为PeTMbase（http://petmbase.org），并配备了高效的搜索工具。为了建立该存储库，我们从11种植物的RNA测序数据中获取了大量已鉴定的eTMs。首先，将转录组文库映射到相应的植物基因组，然后对长非编码RNA（lncRNA）转录本进行特征化。此外，还将从GREENC和PNRD检索到的额外lncRNAs纳入lncRNA目录。随后，利用lncRNA和miRNA来源，成功预测出总计2,728个eTMs。我们定期更新的数据库PeTMbase提供了关于miRNA:eTM模块的高质量信息，并将有助于功能基因组学研究，尤其是miRNA调控网络的研究。