Exploring the CeRNA landscape in plants: advances, methods, and challenges

From animals to plants, the proposed competing endogenous RNAs (ceRNAs) mechanism has expanded our understanding of gene regulation, suggesting a complex "communication network" involving RNA molecules. In plant gene regulation, ceRNAs studies are increasingly uncovering new insights into the precision and complexity of the mechanisms controlling gene expression. Research suggests that ceRNAs may play critical fine-tuning roles in plant life activities, ranging from growth and development to stress responses. However, plant ceRNAs appear to differ from animal ceRNAs in terms of sequence characteristics, interaction modes, and functions. This review provides an overview on the research conducted to date on plant ceRNAs, revealing key differences between animals and plants and summarizing the progress in research on the relationships between ceRNAs and stress responses (e.g., drought, salinity, and disease) as well as signal transduction and hormone regulation. Moreover, research methods that combine cutting-edge technologies (such as single-cell sequencing and spatial transcriptomics) with multi-omics tools to comprehensively investigate plant ceRNAs are discussed. Our analysis indicates that ceRNAs networks are characterized by plant-specific features, posing distinct research challenges. These range from the limited predictive accuracy of existing bioinformatics tools to the difficulties in functional validation within complex plant tissues. To overcome these hurdles, we propose that future research must prioritize the creation of plant-optimized prediction models and the integration of multi-omics data within a spatially resolved context. Ultimately, unraveling plant ceRNAs networks will not only fill a critical knowledge gap in post-transcriptional regulation, but also unlock novel strategies for crop improvement.