The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses

Abstract

Background N6-methyladenosine (m6A) 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 m6A in the regulation of several major human viral diseases have already been reported. However, the patterns and functions of m6A distribution in plant disease bursting remain largely unknown. Results We analyse the high-quality m6A methylomes in rice plants infected with two devastating viruses. We find that the m6A methylation is mainly associated with genes that are not actively expressed in virus-infected rice plants. We also detect different m6A 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 m6A 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 m6A methylated. The level of m6A methylation is tightly associated with its relative expression levels. Conclusions We revealed the dynamics of m6A 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 m6A modifications in interactions between plant and viruses, especially in regulating the expression of genes involved in key pathways.

Profiling of N6-Methyladenosine (m6A) Modification Landscape in Response to Drought Stress in Apple (Malus prunifolia (Willd.) Borkh)

“…Since m 6 A methylation has been widely reported to be involved in regulating biological processes in plants [ 24 , 25 , 28 , 31 , 33 , 62 ], we performed gene ontology (GO) enrichment analyses of m 6 A-containing genes in control- and drought-treated M. prunifolia seedlings. As shown in Figure 2 a,b, the m 6 A-containing genes in M. prunifolia under control and drought were significantly enriched in a number of pathways: (1) RNA processing: RNA processing, RNA splicing, ncRNA (metabolic) processing, and tRNA (metabolic) processing; (2) others: RNA 3′-end processing, mRNA transport, histone modification, regulation of gene expression, chromosome (chromatin) organization, and DNA methylation or demethylation; (3) development: flower development, fruit development, and post-embryonic development; (4) stress: response to abiotic stimulus, response to osmotic stress, response to heat, response to temperature stimulus, response to salt stress, response to stimulus, response to abiotic stimulus, response to metal ion, immune response, protein folding, and fatty acid metabolic process.…”

“…Compared with wild-type Arabidopsis , the alkbh6 mutant plants exhibit low survival rates under abiotic stresses, including salt, drought, and heat stresses [ 30 ]. Increased levels of m 6 A methylation have been observed in rice plants’ response to viral infection [ 31 ]. In maize, m 6 A hypomethylation under drought stress has a favorable function in drought response [ 32 ].…”

Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection

“…Specifically, total RNA was extracted and fragmented into approximately 200 nucleotide-long fragments. These fragments were incubated and purified as previous reported [ 15 ]. m 6 A-seq was performed on the Illumina HiSeq platform at Shanghai OE Biotech Co., Ltd.…”

“…In tobacco, the global m 6 A level was reduced under Tobacco mosaic virus (TMV) infection, probably associated with decreased m 6 A methyltransferase and increased demethylase expression [ 14 ]. Furthermore, m 6 A levels in susceptible rice increased in response to Rice black-streaked dwarf virus (RBSDV) and Rice stripe virus (RSV) infection, as m 6 A methylation mainly depends on genes which are not actively expressed in virus-infected rice plants via m 6 A-seq analyses [ 15 ]. In wheat, the transcriptome-wide m 6 A profile of two varieties with different resistance to Wheat yellow mosaic virus (WYMV) revealed that many genes related to plant defense responses and plant-pathogen interaction significantly changed in both m 6 A and mRNA levels [ 16 ].…”

RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering

“…These findings implied that the multifaceted effects of m 6 A modification on mRNA expression may depend on the position of m 6 A peaks in gene structure. The specific feature of m 6 A distribution in tea leaves is closely related to gene expression, and it is conserved among several important crops, including rice [36], strawberry [13], and apple [37].…”