Shinde Harshraj, Dudhate Ambika, Kadam Ulhas S, Hong Jong Chan
Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States.
Sequencing and Genome Discovery Center, Stowers Institute for Medical Research, Kansas City, MO, United States.
Front Plant Sci. 2023 Mar 1;14:1132959. doi: 10.3389/fpls.2023.1132959. eCollection 2023.
RNA methylation is an important post-transcriptional modification that influences gene regulation. Over 200 different types of RNA modifications have been identified in plants. In animals, the mystery of RNA methylation has been revealed, and its biological role and applications have become increasingly clear. However, RNA methylation in plants is still poorly understood. Recently, plant science research on RNA methylation has advanced rapidly, and it has become clear that RNA methylation plays a critical role in plant development. This review summarizes current knowledge on RNA methylation in plant development. Plant writers, erasers, and readers are highlighted, as well as the occurrence, methods, and software development in RNA methylation is summarized. The most common and abundant RNA methylation in plants is N6-methyladenosine (mA). In Arabidopsis, mutations in writers, erasers, and RNA methylation readers have affected the plant's phenotype. It has also been demonstrated that methylated TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1-messenger RNA moves from shoot to root while unmethylated TCTP1-mRNA does not. Methylated RNA immunoprecipitation, in conjunction with next-generation sequencing, has been a watershed moment in plant RNA methylation research. This method has been used successfully in rice, Arabidopsis, Brassica, and maize to study transcriptome-wide RNA methylation. Various software or tools have been used to detect methylated RNAs at the whole transcriptome level; the majority are model-based analysis tools (for example, MACS2). Finally, the limitations and future prospects of methylation of RNA research have been documented.
RNA甲基化是一种重要的转录后修饰，可影响基因调控。在植物中已鉴定出200多种不同类型的RNA修饰。在动物中，RNA甲基化的奥秘已被揭示，其生物学作用和应用也越来越清晰。然而，植物中的RNA甲基化仍知之甚少。最近，关于植物RNA甲基化的科学研究进展迅速，并且已经明确RNA甲基化在植物发育中起关键作用。本文综述了目前关于植物发育中RNA甲基化的知识。重点介绍了植物中的“书写者”“擦除者”和“阅读者”，并总结了RNA甲基化的发生、方法和软件开发。植物中最常见且含量丰富的RNA甲基化是N6-甲基腺苷（m6A）。在拟南芥中，“书写者”“擦除者”和RNA甲基化“阅读者”的突变会影响植物的表型。还证明了甲基化的翻译控制肿瘤蛋白1信使核糖核酸从地上部分移动到根部，而未甲基化的TCTP1-mRNA则不会。甲基化RNA免疫沉淀结合下一代测序，是植物RNA甲基化研究中的一个分水岭。该方法已成功用于水稻、拟南芥、甘蓝和玉米，以研究全转录组范围的RNA甲基化。已使用各种软件或工具在全转录组水平检测甲基化RNA；大多数是基于模型的分析工具（例如MACS2）。最后，记录了RNA甲基化研究的局限性和未来前景。
