Brief Communication | Published:

Mapping DNA methylation with high-throughput nanopore sequencing

Nature Methods volume 14, pages 411413 (2017) | Download Citation

Abstract

DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer's ionic current signal. We map three cytosine variants and two adenine variants. The results show that our model is sensitive enough to detect changes in genomic DNA methylation levels as a function of growth phase in Escherichia coli.

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Acknowledgements

Research reported in this publication was supported by the National Human Genome Research Institute of the US National Institutes of Health under award numbers HG006321 (M.A.), HG007827 (M.A.) and 5U54HG007990 (B.P.).

Author information

Author notes

    • Arthur C Rand
    • , Miten Jain
    •  & Jordan M Eizenga

    These authors contributed equally to this work.

Affiliations

  1. Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.

    • Arthur C Rand
    • , Miten Jain
    • , Jordan M Eizenga
    • , Audrey Musselman-Brown
    • , Hugh E Olsen
    • , Mark Akeson
    •  & Benedict Paten

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Contributions

B.P. conceived of the experiments. B.P. and M.A. directed the research. A.C.R. implemented the models and performed analysis. M.J. and H.E.O. performed the sequencing experiments and performed sequence data analysis. J.M.E. implemented the HDP model and Gibbs sampler. A.M.-B. performed initial experiments. All authors contributed to writing the manuscript.

Competing interests

M.A. is a consultant to Oxford Nanopore Technologies.

Corresponding author

Correspondence to Benedict Paten.

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    Supplementary Figures 1–5, Supplementary Tables 1–3, Supplementary Note and Supplementary Discussion

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    Supplementary Software

    SignalAlign software

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DOI

https://doi.org/10.1038/nmeth.4189

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