ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Bioinformatics
Transcriptome-Wide Prediction of Heat-Sensitive RNA Structures in Zea mays
Provisionally accepted
- Iowa State University of Science and Technology, Ames, United States
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As global temperatures rise, understanding the potential effects on agriculture and food security is critical. Plant heat stress responses are finely controlled at transcriptional and post-transcriptional levels, with RNA secondary structure now recognized as an important regulator in this process. To characterize and identify structure-function relationships in Zea mays, we applied the computational approach ScanFold to construct a transcriptome-wide database of RNA secondary structures and associated metrics. Using this database, analyzed at temperatures ranging from moderate (28°C) to extreme (42°C), we identified evolutionarily conserved RNA structures across the transcriptome that are sensitive to temperature-induced conformational switching. Focusing on two heat shock factors, ZmHsf04 and ZmHsf17, as a case study for thermotolerance in maize, our analysis yielded two key findings: many predicted structures are supported by significant sequence covariation, indicating evolutionary selection and likely functionality; and several structures of interest also exhibited extreme changes in conformation upon temperature increases. These identified structures in ZmHsf04 and ZmHsf17 may regulate gene expression through dynamic changes influencing processes like mRNA maturation, localization, expression, or alternative splicing—providing a rubric for understanding and approaching the future studies of the transcriptome-wide dataset. The transcriptome-wide dataset and methodology presented here provide a rapid and robust approach to facilitate research into plant abiotic stress response, offering a crucial first step in understanding the role of RNA structure in Zea mays heat response.
Keywords: Heat stress, Heat shock factors, covariation, ScanFold, RNA structure, Zea mays
Received: 19 Aug 2025; Accepted: 11 Nov 2025.
Copyright: © 2025 Eisenhauer, Dapour, Rouse and Moss. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Walter Moss, wmoss@iastate.edu
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