Transcriptome-wide high-throughput deep m ⁶A-seq reveals unique differential m ⁶A methylation patterns between three organs in Arabidopsis thaliana

Abstract

Background

m ⁶A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m ⁶A patterns in Arabidopsis have been assayed recently. However, differential m ⁶A patterns between organs have not been well characterized.

Results

Over two-third of the transcripts in Arabidopsis are modified by m ⁶A. In contrast to a recent observation of m ⁶A enrichment in 5′ mRNA, we find that m ⁶A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m ⁶A 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 m ⁶A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m ⁶A 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 m ⁶A 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 m ⁶A methylation in the cells.

Conclusions

This is the first study to comprehensively analyze m ⁶A patterns in a variety of RNAs, the relationship between transcript level and m ⁶A methylation extent, and differential m ⁶A patterns across organs in Arabidopsis.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0839-2) contains supplementary material, which is available to authorized users.