Salt‐stress priming enhances the tolerance of plants against subsequent exposure to a similar stress. Priming‐induced transcriptomic reprogramming is mediated by multiple epigenetic mechanisms, the best known of which is histone modifications. However, not much is known about other epigenetic responses. In this study, salt‐stress priming resulted in global DNA hypomethylation in the leaves of soybean seedlings. The DNA methyltransferase activities in primed seedlings were reduced, contributing to the overall DNA hypomethylation. Genes associated with the hypomethylated DNA regions in primed seedlings also showed a higher mean level of the active histone mark, histone 3 lysine 4 trimethylation (H3K4me3), and a lower mean level of the repressive histone mark, H3K4me2. Transcriptomic analyses supported that DNA hypomethylation played a role in fine‐tuning the chromatin status in primed seedlings to potentiate gene expressions. Motif and transcriptional network analyses revealed that DNA hypomethylation may facilitate the responses mediated by key transcription factors in the abscisic acid (ABA)‐dependent pathway. A pre‐treatment using a DNA methyltransferase inhibitor, 5‐azacytidine, could enhance salt tolerance in non‐primed soybean seedlings, similar to the priming effect, suggesting the role of DNA hypomethylation in salt‐stress priming. Overall, this research furthers our understanding of the epigenetic mechanisms involved in salt‐stress priming in soybean.

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.