EAGER: Revealing the function of the epitranscriptome in plant pathogen defense

该项目将探索RNA修饰在植物防御病原体中的作用。在包括植物和动物在内的真核生物中，通过甲基化修饰RNA是普遍的，并且对于生存力是必不可少的，但是这种修饰的功能在很大程度上是未知的。使用模式植物拟南芥进行的初步研究发现，植物病原体反应的调节与RNA甲基化水平之间存在令人惊讶的可能联系。该项目旨在通过进行一系列全基因组分析来直接测试这种联系。该研究将产生大型复杂的数据集，这些数据集将使用利用高性能计算能力的工具进行分析。这些工具将在实验室和课堂上使用，为学生和博士后提供RNA生物学，计算科学和生物信息学的跨学科培训。这项研究的结果有可能改变我们对植物对病原体攻击反应的分子基础的理解，从而有助于未来抗病原体植物的发展。真核生物蛋白编码信使RNA（mRNA）最普遍的内部共价修饰是腺苷在N6位的甲基化[N6-甲基腺苷（m6 A）]。这是一个基本的修改，但其功能还没有得到很好的理解。拟南芥中的全转录组研究揭示了已知参与调节植物对真菌或细菌感染的反应的基因的mRNA中m6 A水平的变化。这一观察结果导致了一种假设，即真菌和细菌感染可能通过重新编程m6 A修饰来调节植物的所谓表转录组，这反过来又改变了RNA二级结构和RNA-蛋白质相互作用。为了测试这一想法，将从用模拟真菌（几丁质）或细菌（flg 22）感染的化合物处理的正常和m6 A缺陷植物中分离RNA，并将全面分析RNA以测量对m6 A水平和位置、全局RNA二级结构、RNA-蛋白质相互作用、RNA丰度和剪接的影响。 所有的数据，网络访问的基因组分析工具和数据管理系统将通过一个项目网站和长期的基因组学储存库，方便更广泛的研究界访问。这项研究将在两个传统上不同的领域的交叉点提供前所未有的新见解，即，RNA介导的调节和植物-病原体相互作用，因此应该在这个跨学科的接口为未来的发展奠定了基础。

This project will explore the role of RNA modification in plant defense against pathogens. In eukaryotes, including plants and animals, modification of RNAs by methylation is widespread and essential for viability, but the function of such modifications is largely unknown. Preliminary research using the model plant, Arabidopsis thaliana, uncovered a surprising possible link between regulation of the plant pathogen response and levels of RNA methylation. This project aims to test the link directly by conducting a series of genome-wide analyses. The research will produce large, complex datasets that will be analyzed with tools that leverage high performance computing capabilities. These tools will be used in both the laboratory and the classroom to provide students and postdocs with interdisciplinary training in RNA biology, computational science, and bioinformatics. The outcome of the research has the potential to transform our understanding of the molecular basis for plant responses to pathogen attack and could thereby contribute to future development of pathogen resistant plants. The most prevalent internal covalent modification of eukaryotic protein-coding messenger RNA (mRNA) is methylation of adenosine at the N6 position [N6-methyladenosine (m6A)]. This is an essential modification, but its function is not well understood. Transcriptome-wide studies in Arabidopsis revealed variation in m6A levels in mRNAs from genes known to be involved in regulating plant responses to fungal or bacterial infection. This observation led to the hypothesis that fungal and bacterial infection may regulate the plant's so-called epitranscriptome by reprogramming m6A modification, which in turn alters RNA secondary structure and RNA-protein interactions. To test this idea, RNA will be isolated from normal and m6A-deficient plants treated with compounds that mimic fungal (chitin) or bacterial (flg22) infection, and the RNA will be analyzed comprehensively to measure effects on m6A levels and locations, global RNA secondary structure, RNA-protein interactions, RNA abundance, and splicing. All of the data, web-accessible genome analytical tools, and data management systems will be made readily accessible to the broader research community through a project website and through long-term genomics repositories. This research will provide unprecedented new insights at the intersection of two traditionally disparate fields, i.e., RNA-mediated regulation and plant-pathogen interactions, and thus should set the stage for future developments at this interdisciplinary interface.