Technological frontiers driving new insights in plant RNA biology

Abstract

Recent technological innovations in high-throughput sequencing have reshaped our understanding of plant RNA biology, revealing complex regulatory layers beyond primary genetic sequences. In this mini-review, we highlight how emerging methodologies ranging from nascent RNA profiling to direct long-read sequencing have uncovered novel roles for non-coding RNAs, enhancer elements, alternative splicing/polyadenylation, and epitranscriptomic marks in RNA transcriptional control and stress adaptation. For each technique driving these fundamental advances, we provide a brief overview outlining the methodologies and their respective advantages and limitations, guiding the optimal tool for future RNA research. Finally, we propose how integrating these technologies into combinatorial studies will advance a unified, system-wide model of plant RNA dynamics, as well as the potential to resolve co-occurring RNA modifications in the context of an epitranscriptomic “epi-code” governing post-transcriptional fate. Bridging these molecular mechanisms will be crucial for understanding phenotypic plasticity and enabling targeted (epi)transcriptomic engineering to develop climate-resilient crops.