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Published June 7, 2024 | Version v1
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Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis

Creators

  • 1. University of Chicago
  • 2. Hong Kong Baptist University

Description

N6-methyladenosine (m6A) plays critical roles in regulating mRNA metabolism. However, comprehensive m6A methylomes in different plant tissues with single-base precision have yet to be reported. Here, we present transcriptome-wide m6A maps at single-base resolution in different tissues of rice and Arabidopsis using m6A-SAC-seq. Our analysis uncovers a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis. The evolutionarily conserved m6A sites in rice and Arabidopsis ortholog gene pairs are involved in controlling tissue development, photosynthesis and stress response. We observe an overall mRNA stabilization effect by 3' UTR m6A sites in certain plant tissues. Like in mammals, a positive correlation between the m6A level and the length of internal exons is also observed in plant mRNA, except for the last exon. Our data suggest an active m6A deposition process occurring near the stop codon in plant mRNA. In addition, the MTA-installed plant mRNA m6A sites correlate with both translation promotion and translation suppression, depicting a more complicated regulatory picture. Our results therefore provide in-depth resources for relating single-base resolution m6A sites with functions in plants and uncover a suppression-activation model controlling m6A biogenesis across species.

Data availability

All data supporting the findings of this study are available in the main text or the Supplementary Data. The rice SAC-seq data and Arabidopsis SAC-seq data generated in this study have been deposited in the Gene Expression Omnibus database under the GEO numbers of GSE243722 and GSE245738, respectively. Source data are provided with this paper.

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Additional details

Identifiers

DOI
10.1038/s41467-024-48941-7
Other
oai:uchicago.tind.io:12695

Funding

Margot and Tom Pritzker Foundation
Unorthodox Philanthropy
Harborview Foundation
Bill & Melinda Gates Agricultural Innovations (Gates Ag One)

UChicago Information

Division(s)
Biological Sciences Division, Physical Sciences Division
Department(s)
Biochemistry and Molecular Biology, Chemistry
Center(s) or Institute(s)
Institute for Biophysical Dynamics