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Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

Nature Structural & Molecular Biology volume 23, pages 2430 (2016) | Download Citation

  • A Correction to this article was published on 23 March 2017

Abstract

Methylation of cytosine deoxynucleotides generates 5-methylcytosine (m5dC), a well-established epigenetic mark. However, in higher eukaryotes much less is known about modifications affecting other deoxynucleotides. Here, we report the detection of N6-methyldeoxyadenosine (m6dA) in vertebrate DNA, specifically in Xenopus laevis but also in other species including mouse and human. Our methylome analysis reveals that m6dA is widely distributed across the eukaryotic genome and is present in different cell types but is commonly depleted from gene exons. Thus, direct DNA modifications might be more widespread than previously thought.

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Acknowledgements

M.J.K. was supported by a Long-Term Human Frontiers Fellowship (LT000149/2010-l), a Medical Research Council (MRC) grant (G1001690) and an Isaac Newton Trust Fellowship (RG76588). This work was sponsored by a Biotechnology and Biological Sciences Research Council grant (BB/M022994/1 to J.B.G. and M.J.K.). The laboratory of J.B.G. is funded by Wellcome Trust grant 101050/Z/13/Z (J.B.G.) and is supported by Gurdon Institute core grants, namely a Wellcome Trust Core Grant (092096/Z/10/Z) and a Cancer Research UK grant (C6946/A14492). C.R.B. and G.E.A. are funded by a Wellcome Trust Core Grant (092096/Z/10/Z). A.S.H.C. and C.F. are funded by the MRC Cancer Unit core grant. We are grateful to D. Simpson and R. Jones-Green for preparing X. laevis eggs and oocytes, F. Miller for providing us with M. musculus tissue, T. Dyl for X. laevis eggs and D. rerio samples (all researchers from Gurdon Institute, University of Cambridge), and members of J.B.G.'s laboratory for their critical comments. We thank U. Ruether (Entwicklungs- und Molekularbiologie der Tiere, Heinrich Heine Universitaet Duesseldorf) for providing us with M. musculus kidney DNA. We also thank J. Ahringer, S. Jackson, A. Bannister and T. Kouzarides (Gurdon Institute, University of Cambridge) for critical input and advice, and M. Sciacovelli and E. Gaude (MRC Cancer Unit, University of Cambridge) for suggestions.

Author information

Author notes

    • Charles R Bradshaw
    • , George E Allen
    •  & Ana S H Costa

    These authors contributed equally to this work.

Affiliations

  1. Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.

    • Magdalena J Koziol
    • , Charles R Bradshaw
    • , George E Allen
    •  & John B Gurdon
  2. Department of Zoology, University of Cambridge, Cambridge, UK.

    • Magdalena J Koziol
    •  & John B Gurdon
  3. Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK.

    • Ana S H Costa
    •  & Christian Frezza

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Contributions

A.S.H.C. performed all UHPLC-MS/MS analyses. M.J.K. conceived the study, designed and performed all experiments, analyzed the data, supervised all research and wrote the paper. C.R.B. and G.E.A. performed the bioinformatic analyses, developed ideas and helped to generate figures and to write the paper. C.F. advised on and supervised all UHPLC-MS/MS analyses, and both A.S.H.C. and C.F. helped to design UHPLC-MS/MS studies and to write the paper. J.B.G. assisted with writing the paper and supervised all research.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Magdalena J Koziol.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–5 and Supplementary Tables 1, 3 and 4

  2. 2.

    Supplementary Data Set 1

    Uncropped images for dot blots shown in Figure 1b,g

Excel files

  1. 1.

    Supplementary Table 2

    Dataset of all m6dA peaks identified by comparing m6dA Ab DIP-seq with input-seq samples from X. laevis and M. musculus biological replicates

  2. 2.

    Supplementary Table 5

    Data set of all m6dA peaks identified by comparing m6dA Ab DIP-seq, m6dA Ab* DIP-seq, m6dA Ab** DIP-seq with input-seq and IgG-seq samples from X. laevis testis biological replicates

  3. 3.

    Supplementary Table 6

    Data set of all m6dA peaks identified in Dam+ and Dam E. coli

  4. 4.

    Supplementary Table 7

    Data set of enrichment values found in X. laevis m6dA peaks for all 256 4bp motifs

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DOI

https://doi.org/10.1038/nsmb.3145

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