Structure under stress: conserved RNA structure in plant interaction with the environment.

Plants have evolved sophisticated molecular mechanisms to sense and respond to their environment. There has been growing realization that RNA structure is a key player in this process, such as acting as sensor of temperature changes and nutrient availability, modulator of immune response, and regulator of diverse stress-response pathways (reviewed in Zhang and Ding, 2025). It is now possible to interrogate in vivo RNA secondary structure at nucleotide resolution across the entire transcriptome, which has enabled unprecedented insights into their biological function. However, the evolutionary conservation of functional RNA structures is still poorly understood in plants. Indeed, most reports either do not attempt to assess structural conservation or do not apply appropriate methods. Hence, it is difficult to know whether and how findings in model plants can be translated to crop improvement. This Opinion article briefly discusses previous attempts to assess RNA structural conservation in plants and proposes the need for more rigorous, structure-aware approaches.