The In Vivo Rice RNA Structurome in Abiotic Stress Sensing and Response

Project: Research project

Project Details


PI: Philip C. Bevilacqua (Penn State University)

CoPIs: David H. Mathews (University of Rochester) and Sarah M. Assmann (Penn State University)

Rice is a staple food for more than 1/3 of the world's population and the second most important crop in terms of global production. Given global population growth, limited resources of fresh water, and global warming, it is very important to develop stress-tolerant varieties of rice. This research has the potential to advance both basic and applied knowledge regarding how RNA structure regulates expression of diverse genes in response to abiotic stresses, information that may useful for crop improvement. In addition to the training of students and postdoctoral associates, this project will provide summer training for underrepresented high school students in math and sciences in collaboration with the SEECoS program ( at Penn State. This project will also contribute to a new training program for ethics at Penn State and to an ethics module on Genetic Manipulation. All project outcomes will be made available to the public. Sequence data will be available at and through long term repositories such as the NCBI-SRA, Galaxy, and the Single Nucleotide Resolution Nucleic Acid Structure Mapping (SNRNASM; Biological materials generated in this project will be available on request or through the Dale Bumpers National Rice Resource Center.

When plants are subjected to drought, molecular crowding within cells is enhanced and osmolyte and K+ concentrations increase. Likewise, when plants are stressed from temperature, RNAs in cells are thermodynamically affected. Taken together, these observations suggest that drought and temperature regulate RNA folding, and that RNA structure may play a central role in regulating gene expression and stress tolerance in rice. To evaluate the contribution of RNA structural changes to the regulation of gene expression in rice, this project will leverage, advance and apply recently developed in vivo and computational tools to reveal, on a genome-wide basis, how RNA folds in vivo in rice during drought and temperature stress.

Effective start/end date6/1/145/31/20


  • National Science Foundation: $2,971,699.00


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