PRMD：一个用于植物 RNA 修饰的综合数据库。

PRMD: an integrated database for plant RNA modifications.

机构信息

State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.

Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan, 610041, China.

出版信息

Nucleic Acids Res. 2024 Jan 5;52(D1):D1597-D1613. doi: 10.1093/nar/gkad851.

DOI:10.1093/nar/gkad851

PMID:37831097

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10768107/

Abstract

The scope and function of RNA modifications in model plant systems have been extensively studied, resulting in the identification of an increasing number of novel RNA modifications in recent years. Researchers have gradually revealed that RNA modifications, especially N6-methyladenosine (m6A), which is one of the most abundant and commonly studied RNA modifications in plants, have important roles in physiological and pathological processes. These modifications alter the structure of RNA, which affects its molecular complementarity and binding to specific proteins, thereby resulting in various of physiological effects. The increasing interest in plant RNA modifications has necessitated research into RNA modifications and associated datasets. However, there is a lack of a convenient and integrated database with comprehensive annotations and intuitive visualization of plant RNA modifications. Here, we developed the Plant RNA Modification Database (PRMD; http://bioinformatics.sc.cn/PRMD and http://rnainformatics.org.cn/PRMD) to facilitate RNA modification research. This database contains information regarding 20 plant species and provides an intuitive interface for displaying information. Moreover, PRMD offers multiple tools, including RMlevelDiff, RMplantVar, RNAmodNet and Blast (for functional analyses), and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (for displaying data). Furthermore, PRMD is freely available, making it useful for the rapid development and promotion of research on plant RNA modifications.

摘要

在模式植物系统中，RNA 修饰的范围和功能已经得到了广泛的研究，近年来鉴定出了越来越多的新型 RNA 修饰。研究人员逐渐揭示出，RNA 修饰，特别是 N6-甲基腺苷（m6A），作为植物中最丰富和研究最广泛的 RNA 修饰之一，在生理和病理过程中具有重要作用。这些修饰改变了 RNA 的结构，影响其分子互补性和与特定蛋白质的结合，从而产生各种生理效应。对植物 RNA 修饰的日益关注，使得 RNA 修饰及其相关数据集的研究成为必要。然而，目前缺乏一个方便且集成的数据库，该数据库具有综合注释和直观的植物 RNA 修饰可视化功能。在这里，我们开发了 Plant RNA Modification Database（PRMD；http://bioinformatics.sc.cn/PRMD 和 http://rnainformatics.org.cn/PRMD）来促进 RNA 修饰研究。该数据库包含 20 种植物物种的信息，并提供了一个直观的界面来显示信息。此外，PRMD 还提供了多个工具，包括 RMlevelDiff、RMplantVar、RNAmodNet 和 Blast（用于功能分析），以及 mRNAbrowse、RNAlollipop、JBrowse 和 Integrative Genomics Viewer（用于显示数据）。此外，PRMD 是免费提供的，这使其成为研究植物 RNA 修饰的快速发展和推广的有用工具。