Skip to main content
SpringerLink
Log in

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

  • Protocol
  • First Online:
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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Kubo S, del Seleme MC, Soifer HS et al (2006) L1 retrotransposition in nondividing and primary human somatic cells. PNAS 103:8036–8041. https://doi.org/10.1073/pnas.0601954103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Muotri AR, Chu VT, Marchetto MCN et al (2005) Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435:903–910. https://doi.org/10.1038/nature03663

    Article  CAS  PubMed  Google Scholar 

  3. Coufal NG, Garcia-Perez JL, Peng GE et al (2009) L1 retrotransposition in human neural progenitor cells. Nature 460:1127–1131. https://doi.org/10.1038/nature08248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Xie W, Donohue RC, Birchler JA (2013) Quantitatively increased somatic transposition of transposable elements in Drosophila strains compromised for RNAi. PLoS One 8:e72163. https://doi.org/10.1371/journal.pone.0072163

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Li W, Prazak L, Chatterjee N et al (2013) Activation of transposable elements during aging and neuronal decline in Drosophila. Nat Neurosci 16:529–531. https://doi.org/10.1038/nn.3368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Chang Y-H, Keegan RM, Prazak L, Dubnau J (2019) Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies. PLoS Biol 17:e3000278. https://doi.org/10.1371/journal.pbio.3000278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Treiber CD, Waddell S (2020) Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome. Genome Res 30:1559. https://doi.org/10.1101/gr.259200.119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Treiber CD, Waddell S (2017) Resolving the prevalence of somatic transposition in Drosophila. eLife 6:e28297. https://doi.org/10.7554/eLife.28297

    Article  PubMed  PubMed Central  Google Scholar 

  9. Yang N, Srivastav SP, Rahman R et al (2022) Transposable element landscapes in aging Drosophila. PLoS Genet 18:e1010024. https://doi.org/10.1371/journal.pgen.1010024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Siudeja K, Nassari S, Gervais L et al (2015) Frequent somatic mutation in adult intestinal stem cells drives neoplasia and genetic mosaicism during aging. Cell Stem Cell 17:663–674. https://doi.org/10.1016/j.stem.2015.09.016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Riddiford N, Siudeja K, van den Beek M et al (2021) Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells. Genome Res 31(8):1419–1432. https://doi.org/10.1101/gr.268441.120

    Article  PubMed  PubMed Central  Google Scholar 

  12. Siudeja K, van den Beek M, Riddiford N et al (2021) Unraveling the features of somatic transposition in the Drosophila intestine. The EMBO J:e106388. https://doi.org/10.15252/embj.2020106388

  13. Rahman R, Chirn G, Kanodia A et al (2015) Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res 43:10655–10672. https://doi.org/10.1093/nar/gkv1193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Tauc HM, Tasdogan A, Pandur P (2014) Isolating intestinal stem cells from adult Drosophila midguts by FACS to study stem cell behavior during aging. J Vis Exp:e52223. https://doi.org/10.3791/52223

  15. Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401–415

    Article  CAS  PubMed  Google Scholar 

  16. Feng Q, Moran JV, Kazazian HH, Boeke JD (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87:905–916. https://doi.org/10.1016/S0092-8674(00)81997-2

    Article  CAS  PubMed  Google Scholar 

  17. Ewing AD, Smits N, Sanchez-Luque FJ et al (2020) Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Mol Cell 80:915–928.e5. https://doi.org/10.1016/j.molcel.2020.10.024

    Article  CAS  PubMed  Google Scholar 

  18. Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. https://doi.org/10.1093/bioinformatics/bty191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Stocker H, Gallant P (2008) Getting started. In: Dahmann C (ed) Drosophila: methods and protocols. Humana Press, Totowa, pp 27–44

    Chapter  Google Scholar 

  20. Partridge L, Green A, Fowler K (1987) Effects of egg-production and of exposure to males on female survival in Drosophila melanogaster. J Insect Physiol 33:745–749. https://doi.org/10.1016/0022-1910(87)90060-6

    Article  Google Scholar 

  21. Partridge L, Prowse N (1997) The effects of reproduction on longevity and fertility in male Drosophila melanogaster. J Insect Physiol 43:501–512. https://doi.org/10.1016/s0022-1910(97)00014-0

    Article  CAS  PubMed  Google Scholar 

  22. Reiff T, Jacobson J, Cognigni P et al (2015) Endocrine remodelling of the adult intestine sustains reproduction in Drosophila. eLife 4:e06930. https://doi.org/10.7554/eLife.06930

    Article  PubMed  PubMed Central  Google Scholar 

  23. Ahmed SMH, Maldera JA, Krunic D et al (2020) Fitness trade-offs incurred by ovary-to-gut steroid signalling in Drosophila. Nature 584:415–419. https://doi.org/10.1038/s41586-020-2462-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. O’Neill K, Brocks D, Hammell MG (2020) Mobile genomics: tools and techniques for tackling transposons. Philos Trans R Soc B: Biol Sci 375:20190345. https://doi.org/10.1098/rstb.2019.0345

    Article  CAS  Google Scholar 

  25. Mohamed M, Dang NT-M, Ogyama Y et al (2020) A transposon story: from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford nanopore. Cell 9. https://doi.org/10.3390/cells9081776

  26. Han S, Dias GB, Basting PJ et al (2022) Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line. bioRxiv:2022.01.04.471818

    Google Scholar 

  27. Wang L, Zeng X, Ryoo HD, Jasper H (2014) Integration of UPRER and oxidative stress signaling in the control of intestinal stem cell proliferation. PLoS Genet 10:e1004568. https://doi.org/10.1371/journal.pgen.1004568

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

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).

Author information

Authors and Affiliations

  1. Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Paris, France

    Marius van den Beek, Natalia Rubanova & Katarzyna Siudeja

  2. The Pennsylvania State University, University Park, PA, USA

    Marius van den Beek

Authors
  1. Marius van den Beek
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Natalia Rubanova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Katarzyna Siudeja
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Katarzyna Siudeja .

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

Rights and permissions

Reprints and permissions

Copyright information

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

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

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

Download citation

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

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation