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Accurate detection of m6A RNA modifications in native RNA sequences

Huanle Liu, Oguzhan Begik, Morghan C Lucas, Christopher E. Mason, Schraga Schwartz, John S. Mattick, Martin A. Smith, Eva Maria Novoa
doi: https://doi.org/10.1101/525741
Huanle Liu
1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
2Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
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Oguzhan Begik
1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
2Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
3St-Vincent’s Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
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Morghan C Lucas
1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
4Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Christopher E. Mason
5Department of Physiology and Biophysics, Weill Cornell Medicine, New York 10021, NY, USA
6The Feil Family Brain and Mind Institute, Weill Cornell Medicine, New York 10021, NY, USA
7The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York 10021, NY, USA
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Schraga Schwartz
8Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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John S. Mattick
2Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
3St-Vincent’s Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
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Martin A. Smith
3St-Vincent’s Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
9Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia
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Eva Maria Novoa
1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
2Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
3St-Vincent’s Clinical School, UNSW Sydney, Darlinghurst, NSW, 2010, Australia
4Universitat Pompeu Fabra (UPF), Barcelona, Spain
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  • For correspondence: eva.novoa@crg.eu
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ABSTRACT

The field of epitranscriptomics has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here we show that using Oxford Nanopore Technologies, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Our results open new avenues to investigate the universe of RNA modifications with single nucleotide resolution, in individual RNA molecules.

  • LIST OF ABBREVIATIONS

    (m6A)
    N6-methlyadenosine
    (m1A)
    N1-methyladenosine
    (5hmc)
    5-hydroxymethylcytosine
    (ONT)
    Oxford Nanopore Technologies
    (SVM)
    Support Vector Machine
    (IVT)
    In vitro transcription
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted January 21, 2019.
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    Accurate detection of m6A RNA modifications in native RNA sequences
    Huanle Liu, Oguzhan Begik, Morghan C Lucas, Christopher E. Mason, Schraga Schwartz, John S. Mattick, Martin A. Smith, Eva Maria Novoa
    bioRxiv 525741; doi: https://doi.org/10.1101/525741
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    Accurate detection of m6A RNA modifications in native RNA sequences
    Huanle Liu, Oguzhan Begik, Morghan C Lucas, Christopher E. Mason, Schraga Schwartz, John S. Mattick, Martin A. Smith, Eva Maria Novoa
    bioRxiv 525741; doi: https://doi.org/10.1101/525741

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