High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq.
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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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
Citation
DOI
Publication Date
Volume
Start / End Page
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