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

Publication ,  Chapter
Wang, L; Kim, EY; Cho, J
January 2021

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.

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DOI

Publication Date

January 2021

Volume

2250

Start / End Page

103 / 110

Related Subject Headings

  • Terminal Repeat Sequences
  • Sequence Analysis, DNA
  • Reverse Transcription
  • Retroelements
  • Plants
  • High-Throughput Nucleotide Sequencing
  • Genome, Plant
  • Evolution, Molecular
  • Developmental Biology
  • 3404 Medicinal and biomolecular chemistry
 

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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. (Vol. 2250, pp. 103–110). https://doi.org/10.1007/978-1-0716-1134-0_9
Wang, Ling, Eun Yu Kim, and Jungnam Cho. “High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq.,” 2250:103–10, 2021. https://doi.org/10.1007/978-1-0716-1134-0_9.
Wang, Ling, et al. High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq. Vol. 2250, 2021, pp. 103–10. Epmc, doi:10.1007/978-1-0716-1134-0_9.

DOI

Publication Date

January 2021

Volume

2250

Start / End Page

103 / 110

Related Subject Headings

  • Terminal Repeat Sequences
  • Sequence Analysis, DNA
  • Reverse Transcription
  • Retroelements
  • Plants
  • High-Throughput Nucleotide Sequencing
  • Genome, Plant
  • Evolution, Molecular
  • Developmental Biology
  • 3404 Medicinal and biomolecular chemistry