High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS)

  • Arundhati Bakshi
  • Muhammad B. Ekram
  • Joomyeong KimEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1908)


High-throughput targeted repeat element bisulfite sequencing (HT-TREBS) is designed to assay the methylation level of individual retrotransposon loci of a targeted family, in a locus-specific manner, and on a genome-wide scale. Briefly, genomic DNA is sheared and ligated to Ion Torrent A adaptors (with methylated cytosines), followed by bisulfite-conversion, and amplification with primers designed to bind the targeted retrotransposon. Since the primers carry the Ion Torrent P1 adaptor as a 5′-extension, the amplified library is ready to be size-selected and sequenced on a next-generation sequencing platform. Once sequenced, each retrotransposon is mapped to a particular genomic locus, which is achieved through ensuring at least a 10-bp overlap with flanking unique sequence, followed by the calculation of methylation levels of the mapped retrotransposon using a BiQ Analyzer HT. A complete protocol for library construction as well as the bioinformatics for HT-TREBS is described in this chapter.

Key words

DNA methylation Repeat elements Retrotransposons Long terminal repeat Endogenous retrovirus ERV SINE LINE Long interspersed element Short interspersed element Alu HT-TREBS 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Arundhati Bakshi
    • 1
  • Muhammad B. Ekram
    • 1
  • Joomyeong Kim
    • 1
    Email author
  1. 1.Department of Biological SciencesLouisiana State UniversityBaton RougeUSA

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