TE-array-a high throughput tool to study transposon transcription

Veena P. Gnanakkan, Andrew E. Jaffe, Lixin Dai, Jie Fu, Sarah J. Wheelan, Hyam I. Levitsky, Jef D. Boeke, Kathleen H. Burns

Research output: Contribution to journalArticle

Abstract

Background: Although transposable element (TE) derived DNA accounts for more than half of mammalian genomes and initiates a significant proportion of RNA transcripts, high throughput methods are rarely leveraged specifically to detect expression from interspersed repeats. Results: To characterize the contribution of transposons to mammalian transcriptomes, we developed a custom microarray platform with probes covering known human and mouse transposons in both sense and antisense orientations. We termed this platform the " TE-array" and profiled TE repeat expression in a panel of normal mouse tissues. Validation with nanoString® and RNAseq technologies demonstrated that TE-array is an effective method. Our data show that TE transcription occurs preferentially from the sense strand and is regulated in highly tissue-specific patterns. Conclusions: Our results are consistent with the hypothesis that transposon RNAs frequently originate within genomic TE units and do not primarily accumulate as a consequence of random 'read-through' from gene promoters. Moreover, we find TE expression is highly dependent on the tissue context. This suggests that TE expression may be related to tissue-specific chromatin states or cellular phenotypes. We anticipate that TE-array will provide a scalable method to characterize transposable element RNAs.

Original languageEnglish (US)
Article number869
JournalBMC genomics
Volume14
Issue number1
DOIs
StatePublished - Dec 10 2013

Keywords

  • Endogenous retrovirus
  • Expression microarray
  • L1 LINE
  • Mobile DNA
  • SINE

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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