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Natural variation in RNA m6A methylation and its relationship with translational status.

ABSTRACT: N6-methyladenosine (m6A) is the most abundant modification of eukaryotic messenger RNA. Although m6A has been demonstrated to affect almost all aspects of RNA metabolism, its global contribution to the post-transcriptional balancing of translational efficiency remains elusive in plants. In this study, we performed a parallel analysis of the transcriptome-wide mRNA m6A distribution and polysome profiling in two maize (Zea mays) inbred lines to assess the global correlation of m6A modification with translational status. m6A sites are widely distributed in thousands of protein-coding genes, confined to a consensus motif and primarily enriched in the 3' untranslated regions, and highly coordinated with alternative polyadenylation usage, suggesting a role of m6A modification in regulating alternative polyadenylation site choice. More importantly, we identified that the m6A modification shows multifaceted correlations with the translational status depending on its strength and genic location. Moreover, we observed a substantial intraspecies variation in m6A modification, and this natural variation was shown to be partly driven by gene-specific expression and alternative splicing. Together, these findings provide an invaluable resource for ascertaining transcripts that are subject to m6A modification in maize and pave the way to a better understanding of natural m6A variation in mediating gene expression regulation.

ORGANISM(S): Zea mays

PROVIDER: GSE124543 | GEO | 2019/09/16

REPOSITORIES: GEO

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Project description:Heterosis, also known as hybrid vigor, has been extensively utilized to increase productivity in crop, yet the underlying molecular mechanisms remain largely elusive. Recent studies have reported that in addition to mRNA transcription, epigenetic variations in DNA methylation, small RNAs and histone modifications also contribute to heterosis. However, the operative mode of post-transcriptional regulation on gene expression such as RNA m6A methylation and translational efficiency in heterosis has never been explored. In this study, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize (Zea mays) F1 hybrid B73×Mo17 and its two parental lines B73 and Mo17 to ascertain contributions of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and the distribution configuration of m6A maintained unchanged, a greater number of genes have gained m6A modification in hybrid compared to parent lines. m6A modification and translational efficiency exhibited greater variations between hybrid and parents as compared with observed variation of mRNA abundance. In hybrid, the vast majority of genes with m6A modification exhibited non-additive expression pattern, the percentage of which was exceedingly higher than that of differential genes at mRNA abundance and translation efficiency levels. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulations on gene expression adopt divergent approaches to participate in the formation of heterosis in hybrid. Overall, the integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation on gene expression in maize hybrid, and pave new avenues for exploring molecular mechanisms underlying hybrid vigor.

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Natural variation in RNA m6A methylation and its relationship with translational status.

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