The dynamics of N(6)-methyladenine RNA modification in interactions between rice and plant viruses

BACKGROUND: N(6)-methyladenosine (m(6)A) is the most common RNA modification in eukaryotes and has been implicated as a novel epigenetic marker that is involved in various biological processes. The pattern and functional dissection of m(6)A in the regulation of several major human viral diseases have already been reported. However, the patterns and functions of m(6)A distribution in plant disease bursting remain largely unknown. RESULTS: We analyse the high-quality m(6)A methylomes in rice plants infected with two devastating viruses. We find that the m(6)A methylation is mainly associated with genes that are not actively expressed in virus-infected rice plants. We also detect different m(6)A peak distributions on the same gene, which may contribute to different antiviral modes between rice stripe virus or rice black-stripe dwarf virus infection. Interestingly, we observe increased levels of m(6)A methylation in rice plant response to virus infection. Several antiviral pathway-related genes, such as RNA silencing-, resistance-, and fundamental antiviral phytohormone metabolic-related genes, are also m(6)A methylated. The level of m(6)A methylation is tightly associated with its relative expression levels. CONCLUSIONS: We revealed the dynamics of m(6)A modification during the interaction between rice and viruses, which may act as a main regulatory strategy in gene expression. Our investigations highlight the significance of m(6)A modifications in interactions between plant and viruses, especially in regulating the expression of genes involved in key pathways. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02410-2.