In vivo RNA structure influences the translation and stability of plant long non-coding RNAs

Long non-coding RNAs (lncRNAs) regulate numerous biological processes in plants, including development and stress responses. Although previous studies have mainly examined their sequences and transcriptional activity, other essential aspects, such as in vivo RNA secondary structure and post-transcriptional regulation, remain poorly understood in plants. Here, we comprehensively characterized lncRNA features, including length, sequence composition, conservation, and in vivo secondary structure, in two representative species: Arabidopsis thaliana (dicot) and durum wheat (monocot). While lncRNAs show limited conservation across the plant kingdom, their sequences display moderate conservation within evolutionary clades. We further identified conserved RNA structural motifs that form stable folds in vivo. Comparative genome-wide analyses of post-transcriptional regulation revealed that plant lncRNAs vary widely in translation efficiency and RNA stability, with RNA structure emerging as a major determinant of both processes. Moreover, transcriptome-wide analyses uncovered structural motifs associated with translation and stability, predominantly enriched at the 3' ends of plant lncRNAs. Together, these findings provide a comprehensive framework for understanding plant lncRNA features and reveal a central role of RNA structure in shaping their post-transcriptional regulation.