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Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq

Part of the Methods in Molecular Biology book series (MIMB,volume 2250)

Abstract

Active transposable elements (TEs) generate insertion polymorphisms that can be detected through genome resequencing strategies. However, these techniques may have limitations for organisms with large genomes or for somatic insertions. Here, we present a method that takes advantage of the extrachromosomal circular DNA (eccDNA) forms of actively transposing TEs in order to detect and characterize active TEs in any plant or animal tissue. Mobilome-seq consists in selectively amplifying and sequencing eccDNAs. It relies on linear digestion of genomic DNA followed by rolling circle amplification of circular DNA. Both active DNA transposons and retrotransposons can be identified using this technique.

Key words

  • Extrachromosomal circular DNA (eccDNA)
  • Plasmid safe
  • Rolling circle DNA amplification (RCA)
  • Phi29
  • Transposable elements (TEs)
  • Retrotransposons
  • Mobilome sequencing

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  • DOI: 10.1007/978-1-0716-1134-0_7
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Acknowledgments

This work was funded by IRD, a French ANR grant (ANR-13-JSV6-0002 “ExtraChrom”) and a EU Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 764965 (“EpiDiverse”) to M.M.

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Correspondence to Marie Mirouze .

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Lanciano, S., Zhang, P., Llauro, C., Mirouze, M. (2021). Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq. In: Cho, J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1134-0_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1133-3

  • Online ISBN: 978-1-0716-1134-0

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