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Open Access Highly Accessed Methodology article

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

Veena P Gnanakkan1, Andrew E Jaffe2, Lixin Dai3, Jie Fu4, Sarah J Wheelan45, Hyam I Levitsky467, Jef D Boeke1348* and Kathleen H Burns1489*

Author Affiliations

1 The Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building (MRB) Room 469, Baltimore, MD 21205, USA

2 The Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD, USA

3 Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Broadway Research Building, Room 339, Baltimore, MD 21205, USA

4 Department of Oncology, The Johns Hopkins University School of Medicine, Bunting Blaustein Cancer Research Building, Suite 4M51, 1650 Orleans St, Baltimore, MD 21287, USA

5 Department of Biostatistics, The Bloomberg School of Public Health, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

6 Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

7 Department of Urology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

8 High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

9 Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

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BMC Genomics 2013, 14:869  doi:10.1186/1471-2164-14-869

Published: 10 December 2013

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.

Keywords:
Mobile DNA; Expression microarray; L1 LINE; Endogenous retrovirus; SINE