Transcriptome-wide high-throughput deep m6A-seq reveals unique differential m6A methylation patterns between three organs in Arabidopsis thaliana

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.

Post-transcriptional gene regulation by mRNA modifications

“…m 6 A deposition is also positively correlated with the abundance of a large fraction of A. thaliana transcripts, suggesting that it has regulatory roles in plant gene expression 51 . Another study found that m 6 A patterns differ between plant organs, suggesting that m 6 A affects organogenesis and has cell-type specific functions 145 . Numerous homologues of mammalian m 6 A demethylases and the YT521-B homology (YTH) domain reader proteins exist in plant genomes.…”

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

“…m 6 A is found within a conserved consensus sequence (G/A)(G/A) A CU (with a preference for (G/A)G A CU) in different eukaryotes (Horowitz et al ., 1984; Narayan & Rottman, 1988; Dominissini et al ., 2012; Meyer et al ., 2012; Luo et al ., 2014; Wan et al ., 2015). However, only a subset of potential sites is actually modified and the mechanisms underlying the specificity of writing are not yet understood.…”

mRNA N6-methyladenosine methylation of postnatal liver development in pig

“…N 6 -methyladenosine (m 6 A) is one of the most prevalent modifications of eukaryotic mRNAs [4] with conserved topology across yeast [5], Arabidopsis thaliana [6, 7], Drosophila [8], mouse and human [9, 10]. Most of the m 6 A sites share a similar consensus m 6 A motif, RRm 6 ACH, where R represents a purine and H represents a non-guanine base [9].…”

“…Genes with m 6 A methylation mainly enriched in biologically important pathways, such as regulation of gene expression, differentiation and metabolism [6, 7, 9]. Nonetheless, m 6 A methylation profiles and functions in tissue at postnatal developmental stages have rarely been investigated.…”