Detection technologies for RNA modifications and their applications in plants

Chemical modifications of RNA molecules play diverse regulatory roles in gene expression by influencing RNA biogenesis, stability, and translation. Emerging evidence indicates that RNA modifications in plants have functional significance for enhancing crop performance, stress resistance, and agricultural productivity. Recent advances in quantitative mapping of RNA modifications at the single-base level have highlighted the critical roles of RNA modifications in regulating RNA metabolism and translation in mammals. However, our understanding of the regulatory roles of these chemical modifications at the single-base level remains limited in plants, hindering deeper insights into their biological significance. This gap can be attributed to the limited use of advanced base-resolution detection technologies in plant research. Here, we systematically review both conventional and base-resolution methods that have been used to detect RNA modifications in mammals and plants. We highlight the implications of RNA modifications at the single-base level, and discuss how modification levels could be manipulated during crop improvement and breeding to regulate RNA metabolism and translation without altering amino acid sequences.