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The origin of genomic N6-methyl-deoxyadenosine in mammalian cells

Nature Chemical Biology volume 16, pages 630–634 (2020)Cite this article

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Abstract

The proposal that N6-methyl-deoxyadenosine (m6dA) acts as an epigenetic mark in mammals remains controversial. Using isotopic labeling coupled to ultrasensitive mass spectrometry, we confirm the presence of low-level m6dA in mammalian DNA. However, the bulk of genomic m6dA originates from ribo-N6-methyladenosine, which is processed via the nucleotide-salvage pathway and misincorporated by DNA polymerases. Our results argue against m6dA acting as a heritable, epigenetic DNA mark in mammalian cells.

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Fig. 1: Slow DNA methylation kinetics of m6dA compared to m5dC.
Fig. 2: m6A ribonucleotide is converted into m6dA and misincorporated into gDNA.
Fig. 3: Not a DNA methyltransferase but ribo-m6A misincorporation generates m6dA.

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Data availability

The data supporting the findings of this study are available within the paper and its Supplementary Information file. Source Data for Figs. 1 and 2 are available online.

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Acknowledgements

We thank L. Schomacher for discussions, valuable suggestions, including experimental design and feedback during manuscript preparation. We thank M. Pradhan and G. Joshi for discussions, suggestions and critical reading of the manuscript. We are grateful for technical support by S. Ritz from the Institute of Molecular Biology Core Facility Microscopy.

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Authors and Affiliations

  1. Institute of Molecular Biology gGmbH, Mainz, Germany

    Michael U. Musheev, Anne Baumgärtner, Laura Krebs & Christof Niehrs

  2. Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany

    Christof Niehrs

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  1. Michael U. Musheev
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  2. Anne Baumgärtner
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Contributions

M.U.M. and C.N. designed the experiments. M.U.M., A.B. and L.K. performed the experiments. C.N. and M.U.M. wrote the manuscript. All authors were involved in discussions, planning the experiments and editing the manuscript.

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Correspondence to Michael U. Musheev or Christof Niehrs.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–13 and Tables 1–7

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Source Data Fig. 1c

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Source Data Fig. 2c–e

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Musheev, M.U., Baumgärtner, A., Krebs, L. et al. The origin of genomic N6-methyl-deoxyadenosine in mammalian cells. Nat Chem Biol 16, 630–634 (2020). https://doi.org/10.1038/s41589-020-0504-2

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  • DOI: https://doi.org/10.1038/s41589-020-0504-2

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