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Computational Methods for the Discovery and Annotation of Viral Integrations

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Book cover piRNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2509))

Abstract

The transfer of genetic material between viruses and eukaryotic cells is pervasive. Somatic integrations of DNA viruses and retroviruses have been linked to persistent viral infection and genotoxic effects. Integrations into germline cells, referred to as Endogenous Viral Elements (EVEs), can be co-opted for host functions. Besides DNA viruses and retroviruses, EVEs can also derive from nonretroviral RNA viruses, which have often been observed in piRNA clusters. Here, we describe a bioinformatic framework to annotate EVEs in a genome assembly, study their widespread occurrence and polymorphism and identify sample-specific viral integrations using whole genome sequencing data.

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Author information

Authors and Affiliations

  1. Department of Biology and Biotechnology, University of Pavia, Pavia, Italy

    Umberto Palatini, Elisa Pischedda & Mariangela Bonizzoni

Authors
  1. Umberto Palatini
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  2. Elisa Pischedda
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  3. Mariangela Bonizzoni
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Corresponding author

Correspondence to Mariangela Bonizzoni .

Editor information

Editors and Affiliations

  1. Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan

    Nicholas F. Parrish

  2. Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan

    Yuka W. Iwasaki

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Palatini, U., Pischedda, E., Bonizzoni, M. (2022). Computational Methods for the Discovery and Annotation of Viral Integrations. In: Parrish, N.F., Iwasaki, Y.W. (eds) piRNA. Methods in Molecular Biology, vol 2509. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2380-0_18

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  • DOI: https://doi.org/10.1007/978-1-0716-2380-0_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2379-4

  • Online ISBN: 978-1-0716-2380-0

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