Quantification of LINE-1 RNA Expression from Bulk RNA-seq Using L1EM

Methods Mol Biol. 2023:2607:115-126. doi: 10.1007/978-1-0716-2883-6_7.

Abstract

LINE-1 retrotransposons have the potential to cause DNA damage, contribute to genome instability, and induce an interferon response. Thus, accurate measurements of their expression, especially in disease contexts where genome instability and the interferon response are relevant, are of particular importance. Illumina-based bulk RNA sequencing remains the most abundant datatype for measuring gene expression. However, "active" expression from its own internal promoter is only one source of LINE-1 aligning reads in an RNA-seq experiment. With about half a million LINE-1 sequences scattered throughout the genome, many are incorporated into other transcripts that have nothing to do with LINE-1 activity. We call this "passive" co-transcription. Here we will describe how to use L1EM, a computational method that separates active from passive LINE-1 expression at the locus-specific level.

Keywords: Co-transcription; L1; LINE-1; RNA-seq; Short reads; Transposable elements.

MeSH terms

  • Antiviral Agents*
  • Exome Sequencing
  • Genomic Instability
  • Humans
  • Interferons*
  • RNA / genetics
  • RNA-Seq

Substances

  • Interferons
  • Antiviral Agents
  • RNA