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High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq

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

Abstract

Extrachromosomal linear DNA (eclDNA) is the reverse-transcribed cDNA intermediate derived from long terminal repeat (LTR) transposable elements (TEs) (Cho et al., Nat Plants 5:26–33, 2018). Given that the eclDNAs are the final intermediate of LTR-TE life cycle prior to integration to the host chromosomes, their presence is considered a strong indication of active LTR retrotransposons (Cho et al., Nat Plants 5:26–33, 2018; Lanciano et al., PLoS Genet 13:e1006630, 2017). Here, we describe a method of amplification of LTR extrachromosomal DNA followed by sequencing (ALE-seq) which determines the 5′ LTR sequences of eclDNAs. Briefly, ALE-seq consists of two steps of amplification, in vitro transcription of adaptor-ligated eclDNAs and subsequent reverse transcription to cDNAs primed at the conserved primer binding site (PBS) (Cho et al., Nat Plants 5:26–33, 2018). ALE-seq allows the high-throughput identification of novel LTR-TEs which are active in plants that could be potentially useful for crop biotechnology.

Key words

  • LTR-TE
  • eclDNA
  • ALE-seq

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  • DOI: 10.1007/978-1-0716-1134-0_9
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References

  1. Cho J, Benoit M, Catoni M et al (2018) Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. Nat Plants 5:26–33. https://doi.org/10.1038/s41477-018-0320-9

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Acknowledgment

This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB27030209) and the National Natural Science Foundation of China (31970518) granted to J.C.

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Correspondence to Jungnam Cho .

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Wang, L., Kim, E.Y., Cho, J. (2021). High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-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_9

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_9

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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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