Evidence is mounting that RNA modifications play essential roles in posttranscriptional regulation of gene expression. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. In plants, genome-wide identification of RNA modifications is largely limited to the model species Arabidopsis thaliana, while lacking in diverse non-model plants. Here, we present PRMdb, a plant RNA modification database, based on the analysis of thousands of RNA-seq, degradome-seq and small RNA-seq data from a wide range of plant species using the well-documented tool HAMR (high-throughput analysis of modified ribonucleotide). PRMdb provides a user-friendly interface that enables easy browsing and searching of the tRNA and mRNA modification data. We show that PRMdb collects high-confidence RNA modifications including novel RNA modification sites that can be validated by genomic PCR and reverse transcription PCR. In summary, PRMdb provides a valuable web resource for deciphering the epitranscriptomes in diverse plant species and will facilitate functional studies of RNA modifications in plants. RPMdb is available via http://www.biosequencing.cn/PRMdb/.

中文翻译：

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PRMdb：植物中预测的RNA修饰的信息库。

越来越多的证据表明，RNA修饰在基因表达的转录后调控中起着至关重要的作用。迄今为止，已经记录了超过150种由不同酶催化的RNA修饰。在植物中，RNA修饰的全基因组鉴定在很大程度上限于模式物种拟南芥，但缺少各种非模型工厂。在这里，我们介绍PRMdb，这是一种植物RNA修饰数据库，它基于使用证明充分的工具HAMR（高通量）对来自多种植物物种的数千种RNA-seq，degradome-seq和小RNA-seq数据的分析修饰的核糖核苷酸分析）。PRMdb提供了用户友好的界面，可轻松浏览和搜索tRNA和mRNA修饰数据。我们显示，PRMdb收集高可信度的RNA修饰，包括可以通过基因组PCR和逆转录PCR验证的新型RNA修饰位点。总之，PRMdb提供了宝贵的Web资源，可用于解密各种植物物种中的表观转录组，并将有助于植物中RNA修饰的功能研究。RPMdb可通过http://www.biosequencing.cn/PRMdb/获得。