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. 2014 Nov 28:5:5630.
doi: 10.1038/ncomms6630.

Unique features of the m6A methylome in Arabidopsis thaliana

Guan-Zheng Luo #  1   2 , Alice MacQueen #  3 , Guanqun Zheng #  1   2 , Hongchao Duan  4 , Louis C Dore  1   2 , Zhike Lu  1   2 , Jun Liu  4 , Kai Chen  1   2 , Guifang Jia  4 , Joy Bergelson  3 , Chuan He  1   2   4
Affiliations

Unique features of the m6A methylome in Arabidopsis thaliana

Guan-Zheng Luo et al. Nat Commun. .

Abstract

Recent discoveries of reversible N(6)-methyladenosine (m(6)A) methylation on messenger RNA (mRNA) and mapping of m(6)A methylomes in mammals and yeast have revealed potential regulatory functions of this RNA modification. In plants, defects in m(6)A methyltransferase cause an embryo-lethal phenotype, suggesting a critical role of m(6)A in plant development. Here, we profile m(6)A transcriptome-wide in two accessions of Arabidopsis thaliana and reveal that m(6)A is a highly conserved modification of mRNA in plants. Distinct from mammals, m(6)A in A. thaliana is enriched not only around the stop codon and within 3'-untranslated regions, but also around the start codon. Gene ontology analysis indicates that the unique distribution pattern of m(6)A in A. thaliana is associated with plant-specific pathways involving the chloroplast. We also discover a positive correlation between m(6)A deposition and mRNA abundance, suggesting a regulatory role of m(6)A in plant gene expression.

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Figures

Figure 1
Figure 1. Overview of m6A methylome in A. thaliana
(a) The m6A/A ratio of mRNA isolated from each A. thaliana strain. Error bars are calculated as the standard deviation from three replicates. PAR values are displayed below the strain names. (b) Numbers of strain-specific and common m6A peaks. (c) Examples of m6A peaks conserved between Can-0 and Hen-16. Orange color represents IP reads while blue color represents input reads. The purple color comes from mixing orange with blue. (d) The RRACH conserved sequence motif for m6A-containing peak regions.
Figure 2
Figure 2. Distribution pattern of m6A peaks along transcripts
(a) Accumulation of m6A-IP reads along transcripts. Each transcript is divided into 3 parts: 5′ UTRs, CDs and 3′ UTRs. (b) The m6A peak distribution within different gene contexts. Left panel: total genes with m6A peaks; right panel: genes conserved in human and Arabidopsis. (c) The m6A peak distribution along a metagene. Enrichment scores are calculated as. n: number of peaks belonging to each category; N: number of total peaks; p:proportion of each category within the genome by length. *P<2.2e-16, **P<1e-30. P-values are determined by Chi-squared test. (d) An example of homologous genes with m6A peaks conserved in human and A. thaliana.
Figure 3
Figure 3. Functional annotation of genes with m6A
(a) GO enrichment analysis of all the genes with m6A peaks. GO categories are maintained by Gene Ontology Consortium. P-values are calculated using the DAVID tool. (b) Percentages of subgroups of genes divided by the position pattern of m6A peaks. (c) Percentages of genes characterized as chloroplast-related for each subgroup. *P<6.0e-25, **P<5.2e-18. P-values are calculated using the DAVID tool. (d) Examples of chloroplast genes with m6A peaks at both the start and stop codon. The m6A-IP peaks are indicated by arrows.
Figure 4
Figure 4. Dynamic m6A peaks in two Arabidopsis strains
Different colors illustrate the accumulation of m6A-IP reads from two accessions.
Figure 5
Figure 5. Relationship between m6A peaks and mRNA level
(a) Differentially expressed mRNAs in Can-0 and Hen-16. Genes with Can-0-specific m6A peaks are highlighted in orange, and genes with Hen-0-specific m6A peaks are highlighted in blue. (b) The ratio of mRNA expression levels in two samples containing strain-specific m6A peaks. Genes are divided to two categories (PeakStart and PeakStop) according to the peak positions. (c) Fraction of genes belonging to each subgroup defined by the m6A distribution pattern. Genes are sorted by expression levels. (d) Cumulative distribution of mRNA expression changes between the mta mutant and WT for m6A modified genes (red) and non-target genes (blue). P-values are calculated by two-sided Mann-Whitney test.
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References

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