Transcriptome-Wide N6-Methyladenosine (m6A) Profiling of Susceptible and Resistant Wheat Varieties Reveals the Involvement of Variety-Specific m6A Modification Involved in Virus-Host Interaction Pathways.

Tian-Ye Zhang,Hai-Chao Hu,Fan Zhang,Zhi-Qing Chen,Shi-Qi Gao,Long He,Zi-Qiong Wang,Peng Liu,Peng Jin,Jian Yang,Miao-Ze Xu,Jian-Ping Chen

doi:10.3389/fmicb.2021.656302

Tian-Ye Zhang, Hai-Chao Hu + Show 10 more

Open Access

https://doi.org/10.3389/fmicb.2021.656302

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Abstract

N6-methyladenosine (m6A) methylation is the most prevalent internal modification of post-transcriptional modifications in mRNA, tRNA, miRNA, and long non-coding RNA in eukaryotes. m6A methylation has been proven to be involved in plant resistance to pathogens. However, there are no reports on wheat (Triticum aestivum) m6A transcriptome-wide map and its potential biological function in wheat resistance to wheat yellow mosaic virus (WYMV). To the best of our knowledge, this study is the first to determine the transcriptome-wide m6A profile of two wheat varieties with different resistances to WYMV. By analyzing m6A-sequencing (m6A-seq) data, we identified 25,752 common m6A peaks and 30,582 common m6A genes in two groups [WYMV-infected resistant wheat variety (WRV) and WYMV-infected sensitive wheat variety (WSV)], and all these peaks were mainly enriched in 3′ untranslated regions and stop codons of coding sequences. Gene Ontology analysis of m6A-seq and RNA-sequencing data revealed that genes that showed significant changes in both m6A and mRNA levels were associated with plant defense responses. Kyoto Encyclopedia of Genes and Genomes analysis revealed that these selected genes were enriched in the plant–pathogen interaction pathway. We further verified these changes in m6A and mRNA levels through gene-specific m6A real-time quantitative PCR (RT-qPCR) and normal RT-qPCR. This study highlights the role of m6A methylation in wheat resistance to WYMV, providing a solid basis for the potential functional role of m6A RNA methylation in wheat resistance to infection by RNA viruses.

Highlights

RNA molecules are crucial in all living organisms, playing significant roles in passing genetic information and regulating several biological processes (Fu et al, 2014)
The accumulation of wheat yellow mosaic virus (WYMV) was detected in the total RNA extracted from WRV and WSV leaves by qRT-PCR assay using CP-specific primers
M6A Methylation in WYMV Infection accumulation of WYMV was significantly increased in WSV than that in WRV (Supplementary Figure 1). These samples were used for transcriptome-wide m6A-seq and RNA-sequencing (RNA-seq) using the Illumina NovaseqTM 6000

Summary

Introduction

RNA molecules are crucial in all living organisms, playing significant roles in passing genetic information and regulating several biological processes (Fu et al, 2014). The m6A modification can be dynamically regulated by m6A demethylases, called m6A erasers, including fat mass and obesity-associated protein (FTO) and ALKB homolog 5 (ALKBH5), to maintain the m6A modification in a dynamic balance (Jia et al, 2011; Zheng et al, 2013; Liu et al, 2014) Another series of m6A-binding proteins (readers), such as YTHDF2 and YTHDF3, which belong to the YT521-B homology domain family, can bind to m6A-modified cellular RNAs to carry out the biological function of methylation (Zhang et al, 2010; Dominissini et al, 2012; Xu et al, 2014, 2015). The m6A modification can efficiently control gene expression, plant development, and physiological processes

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