Global N6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress.

Yinxiao Wang,Zhikang Li,Binying Fu,Wensheng Wang,Fengping Du,Yingbo Li,Jianlong Xu,Juan Wang,Xiuqin Zhao

doi:10.3390/ijms23042091

Abstract

N6-methyladenosine (m6A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m6A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m6A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m6A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m6A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m6A 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 m6A methylation levels only in the shoots or roots under salt stress, implying m6A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m6A modifications and gene expression changes revealed that m6A 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 m6A modifications on rice salt tolerance.

Highlights

Introduction2537 and 2304 differential m6 A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions
Academic Editors: Changning Liu, Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
On the basis of a comparative analysis of the RNA-seq data, we identified the differentially expressed genes (DEGs) in the shoots and roots under control and salt stress conditions

Summary

Introduction

2537 and 2304 differential m6 A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions These differential m6 A sites were largely regulated in a tissue-specific manner. Integrating analyses of m6 A modifications and gene expression changes revealed that m6 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 m6 A modifications on rice salt tolerance. M6 A is generated by the consensus sequence RRACH

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