Current technical advancements in plant epitranscriptomic studies

The growth and development of plants are the result of the interplay between the internal developmental programming and plant–environment interactions. Gene expression regulations in plants are made up of multi‐level networks. In the past few years, many studies were carried out on co‐ and post‐transcriptional RNA modifications, which, together with the RNA community, are collectively known as the “epitranscriptome.” The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third‐generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant–environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi‐omics investigations using the recent technical advancements. Core Ideas The epitranscriptome is an additional regulatory layer in plant growth and development. Third‐generation sequencing technologies facilitate more comprehensive epitranscriptomic profiling. RNA modifications could lead to systemic changes in gene expressions in response to environmental fluctuations. Integration of multi‐omics data provides new insights into gene regulatory networks.