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Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

Nature Chemical Biology volume 12, pages 311–316 (2016)Cite this article

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Abstract

N1-Methyladenosine (m1A) is a prevalent post-transcriptional RNA modification, yet little is known about its abundance, topology and dynamics in mRNA. Here, we show that m1A is prevalent in Homo sapiens mRNA, which shows an m1A/A ratio of ∼0.02%. We develop the m1A-ID-seq technique, based on m1A immunoprecipitation and the inherent ability of m1A to stall reverse transcription, as a means for transcriptome-wide m1A profiling. m1A-ID-seq identifies 901 m1A peaks (from 600 genes) in mRNA and noncoding RNA and reveals a prominent feature, enrichment in the 5′ untranslated region of mRNA transcripts, that is distinct from the pattern for N6-methyladenosine, the most abundant internal mammalian mRNA modification. Moreover, m1A in mRNA is reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, we show that m1A methylation responds dynamically to stimuli, and we identify hundreds of stress-induced m1A sites. Collectively, our approaches allow comprehensive analysis of m1A modification and provide tools for functional studies of potential epigenetic regulation via the reversible and dynamic m1A methylation.

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Figure 1: m1A-ID-seq utilizes an m1A antibody and a biochemical demethylation reaction to enrich and identify high-confidence m1A sites.
Figure 2: m1A-ID-seq reveals the topology of m1A in the human transcriptome.
Figure 3: m1A in RNA is reversible by ALKBH3.
Figure 4: m1A is dynamically regulated by different stimuli.

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Acknowledgements

The authors would like to thank G. Jia and C. Zhang for assistance with recombinant ALKBH3 protein. This work was supported by the National Basic Research Foundation of China (no. 2014CB964900) and the National Natural Science Foundation of China (nos. 21472009 and 21522201).

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Author notes

  1. Xiaoyu Li and Xushen Xiong: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China

    Xiaoyu Li, Xushen Xiong, Kun Wang, Lixia Wang, Xiaoting Shu, Shiqing Ma & Chengqi Yi

  2. Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China

    Xiaoyu Li, Xushen Xiong, Kun Wang, Lixia Wang, Xiaoting Shu, Shiqing Ma & Chengqi Yi

  3. Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China

    Xushen Xiong, Xiaoting Shu & Shiqing Ma

  4. Department of Chemical Biology, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China

    Chengqi Yi

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Contributions

X.L., X.X. and C.Y. conceived the project, designed the experiments and wrote the manuscript. X.L. performed the experiments with the help of K.W., L.W. and X.S.; X.X. designed and performed the bioinformatics analysis; S.M. participated in discussion. All authors commented on and approved the paper.

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Correspondence to Chengqi Yi.

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Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Table 1 and Supplementary Figures 1–18. (PDF 2385 kb)

Supplementary Data Set 1

Contains the following four sheets: (1) m1A peaks of wild-type HEK293T cells, (2) m1A peaks of ALKBH3-KO cells, (3) H2O2-induced m1A, and (4) serum starvation-induced m1A. (XLSX 654 kb)

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Li, X., Xiong, X., Wang, K. et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat Chem Biol 12, 311–316 (2016). https://doi.org/10.1038/nchembio.2040

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