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Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing

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Transposable Elements

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

Abstract

The extent of transposable element (TE) mobilization in different somatic tissues and throughout diverse species is not well understood. Somatic transposition is often challenging to study as it generates de novo TE insertions that represent rare genetic variants present in heterogenous tissues. Here, we describe experimental approaches that can be applied to address TE mobility in somatic tissues with the use of short- and long-read whole-genome DNA sequencing. Focusing on the analysis of the Drosophila melanogaster intestinal and head tissues, we provide instructions on how to design, perform, and validate experiments that aim at detecting somatic transposition. In addition to providing examples of protocols, this chapter intends to deliver general experimental guidelines that may be adapted to other fly tissues or to other species.

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Acknowledgments

The authors would like to thank Allison Bardin for her support and guidance in developing the presented protocols and for the comments on the manuscript. We would also like to acknowledge Sonia Lameiras for optimizing low DNA input Illumina WGS sequencing. This work was supported by Inserm (K.S.) and ANR SoMuSeq-STEM (ANR-16-CE13-0012) to Allison J. Bardin and Nicolas Servant (salaries of NR and MvdB).

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Correspondence to Katarzyna Siudeja .

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van den Beek, M., Rubanova, N., Siudeja, K. (2023). Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing. 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_14

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  • DOI: https://doi.org/10.1007/978-1-0716-2883-6_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

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