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.