RNA-based regulation beyond microRNAs: Emerging layers of post-transcriptional control in plants

Plant gene expression is regulated by multilayered post-transcriptional mechanisms that extend beyond the well-characterized microRNA pathway. Although miRNAs play central roles in controlling mRNA stability and translation, recent advances in transcriptomics and RNA biology have uncovered additional regulatory layers that significantly expand the complexity of plant PTR. These include long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), diverse classes of small interfering RNAs (siRNAs), tRNA-derived fragments, epitranscriptomic RNA modifications, and RNA-binding proteins. Collectively, these components influence RNA processing, stability, translation, and genome integrity, thereby shaping plant development and stress adaptation. This review synthesizes current knowledge on these non-miRNA RNA-based regulatory mechanisms, with emphasis on their molecular functions and biological significance. Importantly, we highlight the emerging view that these pathways operate within an interconnected regulatory network rather than as isolated mechanisms. Understanding this integrated framework provides new insights into plant adaptive plasticity and offers potential avenues for crop improvement under changing environmental conditions.