Global N-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress.

N-methyladenosine (mA) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of mA on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in mA methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the mA methylation in the shoots ( value < 0.05). Additionally, 2537 and 2304 differential mA sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential mA sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased mA methylation levels only in the shoots or roots under salt stress, implying mA may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of mA modifications and gene expression changes revealed that mA changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of mA modifications on rice salt tolerance.