Abstract
Backgroundm6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, differential m6A patterns between organs have not been well characterized.ResultsOver two-third of the transcripts in Arabidopsis are modified by m6A. In contrast to a recent observation of m6A enrichment in 5′ mRNA, we find that m6A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m6A methylation extent compared to their transcript level. The 290 highly methylated transcripts are mainly associated with transporters, stress responses, redox, regulation factors, and some non-coding RNAs. On average, the proportion of transcripts showing differential methylation between two plant organs is higher than that showing differential transcript levels. The transcripts with extensively higher m6A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m6A may be another important contributor to organ differentiation in Arabidopsis. Highly expressed genes are relatively less methylated and vice versa, and different RNAs have distinct m6A patterns, which hint at mRNA fate. Intriguingly, most of the transposable element transcripts maintained a fragmented form with a relatively low transcript level and high m6A methylation in the cells.ConclusionsThis is the first study to comprehensively analyze m6A patterns in a variety of RNAs, the relationship between transcript level and m6A methylation extent, and differential m6A patterns across organs in Arabidopsis.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0839-2) contains supplementary material, which is available to authorized users.
Highlights
Over 100 types of chemical modifications have been discovered in RNAs from all of the living species [1, 2]
This is the first study to comprehensively analyze m6A patterns in a variety of RNAs, the relationship between transcript level and m6A methylation extent, and differential m6A patterns across organs in Arabidopsis
The aim of the RNA immunoprecipitation (RIP) experiment for the RNA sequencing based on m6A RNA immunoprecipitation (m6A-seq) study was to pull down the RNA of interest containing m6A modification through application of m6A antibody to the randomly fragmented RNA pool. m6A-seq is a recently reported technology integrating the powers of both RIP and high-throughput RNA sequencing for transcriptome-wide analysis of m6A
Summary
Over 100 types of chemical modifications have been discovered in RNAs from all of the living species [1, 2]. This study aimed to: (1) comprehensively and transcriptome-wide characterize the m6A distributing patterns in numerous types of RNAs in Arabidopsis; (2) analyze the relationship between the transcript level and the m6A modification extent in the Arabidopsis transcriptome; (3) characterize differential patterns of the m6A methylation among leaves, flowers, and roots; and (4) discuss new functions of m6A modification in the transcripts extensively modified by m6A from the clues of the potential biological functions in these transcripts. This is the first study to comprehensively analyze m6A differential patterns across organs in plants. This study opens up a new avenue to greatly understand the transcriptome-wide patterns of m6A modification in different RNAs, relationship between m6A methylation extent and gene transcript level, and m6A differential patterns across organs in plants
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