Abstract
N(6)-methyladenosine (m(6)A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m(6)A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m(6)A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m(6)A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m(6)A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m(6)A 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 m(6)A methylation levels only in the shoots or roots under salt stress, implying m(6)A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m(6)A modifications and gene expression changes revealed that m(6)A 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 m(6)A modifications on rice salt tolerance.