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Detection of A-to-I Hyper-edited RNA Sequences

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RNA Editing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2181))

Abstract

Following A-to-I editing of double-stranded RNA (dsRNA) molecules, sequencing reactions interpret the edited inosine (I) as guanosine (G). For this reason, current methods to detect A-to-I editing sites work to align RNA sequences to their reference DNA sequence in order to reveal A-to-G mismatches. However, areas with heavily edited reads produce dense clusters of A-to-G mismatches that hinder alignment, and complicate correct identification of the sites. The presented approach employs prudent alignment and examination of excessive mismatch events, enabling high-accuracy detection of hyper-edited reads and sites.

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Acknowledgments

The authors thank H.T. Porath and the Levanon laboratory members for fruitful discussions. EYL was supported by the International Collaboration Grant from the Jacki and Bruce Barron Cancer Research Scholars’ Program, a partnership of the Israel Cancer Research Fund and City of Hope, as supported by The Harvey L. Miller Family Foundation [grant number 205467].

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Authors and Affiliations

  1. Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel

    Roni Cohen-Fultheim & Erez Y. Levanon

Authors
  1. Roni Cohen-Fultheim
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  2. Erez Y. Levanon
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Editors and Affiliations

  1. Department of Biosciences, Biotechnology and Biopharmaceutics, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, University of Bari “Aldo Moro”, Bari, Italy, Bari, Italy

    Ernesto Picardi

  2. Department of Biosciences, Biotechnology and Biopharmaceutics, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, University of Bari “Aldo Moro”, Bari, Italy, Bari, Italy

    Graziano Pesole

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Cohen-Fultheim, R., Levanon, E.Y. (2021). Detection of A-to-I Hyper-edited RNA Sequences. In: Picardi, E., Pesole, G. (eds) RNA Editing. Methods in Molecular Biology, vol 2181. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0787-9_13

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  • DOI: https://doi.org/10.1007/978-1-0716-0787-9_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0786-2

  • Online ISBN: 978-1-0716-0787-9

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