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Unique features of the m6A methylome in Arabidopsis thaliana.

Luo GZ, MacQueen A, Zheng G, Duan H, Dore LC, Lu Z, Liu J, Chen K, Jia G, Bergelson J, He C - Nat Commun (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA [2] Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.

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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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.
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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.

Mentions: We next analyzed the distribution of m6A in the whole transcriptome for both strains of A. thaliana. We determined the distribution of m6A reads along transcripts in the m6A-IP and non-IP (input) samples, respectively. Intriguingly, we found that reads from m6A-IP are highly enriched around the start codon, stop codon and within 3′ UTRs in both strains (Fig. 2a and Supplementary Fig. 5). The prevalence of m6A-IP reads around the start codon has not been observed in mammals or yeast.


Unique features of the m6A methylome in Arabidopsis thaliana.

Luo GZ, MacQueen A, Zheng G, Duan H, Dore LC, Lu Z, Liu J, Chen K, Jia G, Bergelson J, He C - Nat Commun (2014)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4248235&req=5

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.
Mentions: We next analyzed the distribution of m6A in the whole transcriptome for both strains of A. thaliana. We determined the distribution of m6A reads along transcripts in the m6A-IP and non-IP (input) samples, respectively. Intriguingly, we found that reads from m6A-IP are highly enriched around the start codon, stop codon and within 3′ UTRs in both strains (Fig. 2a and Supplementary Fig. 5). The prevalence of m6A-IP reads around the start codon has not been observed in mammals or yeast.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA [2] Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.

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.

Show MeSH