Collaborative Research: RESEARCH-PGR: Genetic and environmentally-induced functional variation in the rice RNA structurome


Sponsoring Agency
National Science Foundation


Ribonucleic acids (RNA) are essential molecules in living organisms, including in plants. RNA can serve roles as both an informational molecule (genetic code) and a functional molecule (perform and regulate chemical reactions). RNA can fold into complex shapes that can control whether it stays intact or is degraded. This in turn can control how a plant responds to environmental stresses it faces such as heat and cold. The research involves the development of new experimental technologies to investigate RNA structures one molecule at a time and new computational technologies of artificial intelligence wherein a computer learns patterns that can predict RNA structure and its variation. Rice is an important world-wide crop, and the research applies these technologies to rice varieties that are grown in different parts of the world. There are thousands of different varieties of rice adapted to local environments and their RNAs often differ from each other by relatively few changes. Some of these changes will alter the shape of the RNA and thus the response of that rice variety to stress. A major goal of these studies is to identify those changes that alter RNA shape and thereby affect temperature tolerance. Once identified, these shape-shifters could be engineered into specific rice varieties to breed crops more resistant to stress. Aspects of the research will involve high school students and their teachers, and research results and methods will be disseminated in public outreach activities.

RNA structure is a primary determinant of gene expression. Individual copies of the same transcript can take on different structures as influenced by their microenvironment, but methods have been lacking to categorize this diversity. Single nucleotide polymorphisms (SNPs) also can affect RNA structure as “riboSNitches”; however, riboSNitches have not been studied in plants, and their conditionality on environmental conditions has not been assessed. Using rice (Oryza sativa) as the primary model system, the proposed research will develop new wet bench and computational approaches that will allow categorization of the mRNA “pan-structurome,” its consequent impacts on gene expression, and its functional association with respect to local climate conditions in rice landraces. Training will be provided to postdoctoral fellows, graduate students, undergraduates, and high school students and teachers. Broader Impacts will include development of the Oryza CLIMtools webtool to relate rice genotypes with climate variables and to identify beneficial structural haplotypes for use in development of elite rice cultivars. Impact will be broadened through technology including enhanced browser-based RNA structure-reactivity visualization and publicly available instructional screencasts. Collaborations with PUI Swarthmore College will engage undergraduate researchers in computational aspects of the project. Local high school students will perform whole plant physiological experiments, engaging a future generation of biologists and chemists. Finally, the 23rd Penn State Plant Biology Symposium, on RNA biology, will be organized, which will promote the global field of post-transcriptional gene regulation.

This award was co-funded by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences.

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.