The stationary nature of plants leaves them vulnerable to environmental stresses such as heat and drought. Thus, plants have evolved many mechanisms to recognize and respond to such stresses by turning on and off specific sets of genes in response to certain conditions. Part of this control includes regulating RNA levels, which are intermediary molecules made from reading the DNA of genes. Traditionally, scientists believed that the activity of RNA was controlled only by the sequence of the DNA, but recent discoveries have shown that the stability of the RNA molecules is also highly controlled. Recently, it was discovered that this control of RNA stability can be achieved through the addition or removal of small molecules, such as methyl groups, to the individual bases that make up RNA molecules. This new form of regulation, called epitranscriptomics, is largely unexplored in plants and is potentially valuable for improving crops, such as rice, to better tolerate heat and drought stress. This project aims to characterize all these modifications to RNA and identify those that may improve plant tolerance to environmental stresses. To accomplish this goal, the project will leverage and pioneer advances in RNA isolation and sequencing as well as new computational tools to analyze large amounts of sequencing data. These methods and tools will be made available for other science groups so that they can rapidly apply the same techniques to their research questions.

Plants have developed numerous regulatory mechanisms to recognize and subsequently direct precise transcriptome regulation to properly respond to abiotic stressors. However, the mechanisms responsible for directing eukaryotic transcriptome reprogramming during stress response are still quite unclear. Significant recent attention has revealed that post-transcriptional processes are just as important to plant gene expression regulation as transcriptional regulation. Covalent RNA nucleotide chemical modifications (e.g. methylation) have been found to have significant post-transcriptional regulatory effects that are both widespread and physiologically relevant. However, understanding of the roles RNA covalent modifications (the ?epitranscriptome?) play in post-transcriptional regulation of the plant transcriptome is in its infancy, especially when considering cereal crops. These modifications are likely to have a direct impact on yield, quality, and tolerance to various stresses. The project addresses this significant gap using a combination of genomic, evolutionary, and bioinformatics approaches together with new analytical software packages and web-based tools. The result will be important, new mechanistic insights, resources for studying the functions of RNA covalent modifications and potentially new ways to develop more stress resistant crop plants. Finally, this team will develop a data life-cycle management, analysis, and visualization system for epitranscriptomics data and their analysis within the EPIC-CoGe framework. In addition to the broader impacts that our new findings will have on the fields of RNA epitranscriptomics and cereal crop improvement, a novel training program will be developed that will prepare the next generation of epitranscriptomics researchers for the future of biology as a data-driven science.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Clifford Weil
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University of Pennsylvania
United States
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