Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis

Guanqun Wang, Haoxuan Li, Chang Ye, Kayla He, Shun Liu, Bochen Jiang, Ruiqi Ge, Boyang Gao, Jiangbo Wei, Yutao Zhao, Aixuan Li, Di Zhang, Jianhua Zhang and Chuan He ()
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Guanqun Wang: The University of Chicago
Haoxuan Li: The University of Chicago
Chang Ye: The University of Chicago
Kayla He: The University of Chicago
Shun Liu: The University of Chicago
Bochen Jiang: The University of Chicago
Ruiqi Ge: The University of Chicago
Boyang Gao: The University of Chicago
Jiangbo Wei: The University of Chicago
Yutao Zhao: The University of Chicago
Aixuan Li: Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Di Zhang: Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Jianhua Zhang: Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
Chuan He: The University of Chicago

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-48941-7

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