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 journalArticlepeer-review

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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