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Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules

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Transposable Elements

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2607))

Abstract

During their proliferation and the host’s concomitant attempts to suppress it, LINE-1 (L1) retrotransposons give rise to a collection of heterogeneous ribonucleoproteins (RNPs); their protein and RNA compositions remain poorly defined. The constituents of L1-associated macromolecules can differ depending on numerous factors, including, for example, position within the L1 life cycle, whether the macromolecule is productive or under suppression, and the cell type within which the proliferation is occurring. This chapter describes techniques that aid the capture and characterization of protein and RNA components of L1 macromolecules from tissues that natively express them. The protocols described have been applied to embryonal carcinoma cell lines that are popular model systems for L1 molecular biology (e.g., N2102Ep, NTERA-2, and PA-1 cells), as well as colorectal cancer tissues. N2102Ep cells are given as the use case for this chapter; the protocols should be applicable to essentially any tissue exhibiting endogenous L1 expression with minor modifications.

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Acknowledgments

This work was supported in-part by National Institutes of Health grants R01GM126170 and P41GM109824.

Author information

Authors and Affiliations

  1. European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands

    Luciano H. Di Stefano, Leila J. Saba & John LaCava

  2. Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA

    Mehrnoosh Oghbaie, Hua Jiang & John LaCava

  3. Institute for Systems Genetics, NYU Langone Health, New York, NY, USA

    Wilson McKerrow

  4. GENYO. Centro de Genómica e Investigación Oncológica: Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain

    Maria Benitez-Guijarro

  5. Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA

    Martin S. Taylor

Authors
  1. Luciano H. Di Stefano
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  2. Leila J. Saba
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  3. Mehrnoosh Oghbaie
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  4. Hua Jiang
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  5. Wilson McKerrow
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  6. Maria Benitez-Guijarro
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  7. Martin S. Taylor
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  8. John LaCava
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Corresponding author

Correspondence to John LaCava .

Editor information

Editors and Affiliations

  1. Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK

    Miguel R. Branco

  2. School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK

    Alexandre de Mendoza Soler

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Di Stefano, L.H. et al. (2023). Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules. In: Branco, M.R., de Mendoza Soler, A. (eds) Transposable Elements. Methods in Molecular Biology, vol 2607. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2883-6_12

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  • DOI: https://doi.org/10.1007/978-1-0716-2883-6_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

  • eBook Packages: Springer Protocols

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