Collaborative research: understanding the role of the RNA covalent modification, dihydrouridine, in maintaining photosynthesis and metabolism under stress in plants

The National Science Foundation Division of Biological Infrastructure awarded Boyce Thompson Institute for Plant Research Inc. $686,065 on July 15, 2026, under the Biological Sciences program (CFDA 47.074) to investigate the role of dihydrouridine (DHU), an RNA covalent modification, in maintaining photosynthesis and metabolism under drought and heat stress in plants. The project applies genomic, transcriptomic, machine-learning, and AI-assisted methods to understand how DHU targets messenger RNAs associated with photosynthesis and metabolism for rapid degradation during environmental stress, and to characterize DHU's interactions with other RNA chemical modifications. By elucidating the mechanisms of DHU-mediated stress tolerance, the work aims to identify targets for developing resilient agricultural systems. The project also addresses workforce development, providing undergraduate students with training in computational and RNA biology. Performance runs through June 30, 2029, at Ithaca, New York.

Abstract

At the cellular level, plants utilize a number of approaches to control their response to changes in their environment. One such approach is to modify messenger rnas (mrnas) with chemical modifications that influence mrna stability, structure, localization within the cell, and ultimately function. This project is investigating a newly discovered mrna modification, dihydrouridine (DHU), that appears to target highly abundant mrnas associated with photosynthesis and metabolism for rapid degradation during drought and heat stress, and environments at multiple levels. This work will use a number of cutting-edge genomic and transcriptomic techniques, as well as machine-learning and AI-assisted methods, to better understand the impact that DHU has on mrnas, particularly in the context of other RNA chemical modifications (rcms). By uncovering the mechanism by which DHU influences environmental stress tolerance, this project addresses a fundamental challenge for plant stress tolerance and offers new targets for the development of resilient agricultural systems. Because the machinery associated with adding DHU to mrna is present in yeast and humans, this work may provide valuable insights that extend to human health, as well as uncover broader rules about this modification and its interaction with the full suite of eukaryote-shared rcms. Beyond fundamental and applied scientific discovery, the project serves the public interest by advancing biotechnology innovation and supporting education, particularly for undergraduate students with minimal exposure to computational and RNA biology. These education and mentoring efforts will prepare a technologically literate scientific workforce ready to make the next great fundamental discoveries. Organisms must remodel their transcriptomes to adequately, and accurately, respond to changes in their environment. While transcriptional control is well characterized, post-transcriptional regulation in the form of RNA covalent modifications remains largely unexplored. Dihydrouridine (DHU), a conserved RCM traditionally associated with trnas, has recently been identified as a functional modification on mrnas encoding core photosynthesis and metabolic proteins in arabidopsis and sorghum. However, characterizing DHU?s place in the epitranscriptome is currently hindered by low-resolution detection methods that rely on reverse transcription errors and cannot capture modification stoichiometry or the presence of multiple rcms on the same transcript. This proposal addresses these challenges by utilizing oxford nanopore technologies direct RNA-sequencing (ONT DRS) to detect DHU-modified bases at single nucleotide resolution across a tissue and stress transcriptome atlas in arabidopsis. Furthermore, this proposal uses transcriptome-wide approaches to define how DHU influences mrna structure, function, and degradation. In addition, this work will connect DHU presence to mrna stability at the transcript level, alongside other well-known rcms. Lastly, this project will use RNA and protein immunoprecipitation followed by mass spectrometry to identify the machinery responsible for specificity of deposition and regulation. The proposed work will generate critical resources for the plant science community, including open-source ML algorithms for detecting DHU in ONT DRS data, a time-resolved ONT DRS mrna decay dataset that allows for RCM-mrna decay interrogations, a full transcript ONT DRS tissue and stress transcriptome atlas for the model species, arabidopsis, and RCM-aware structural models for arabidopsis mrnas under control and heat conditions. 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.- subawards are not planned for this award.