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BMC Genomics. 2013 Dec 10;14:869. doi: 10.1186/1471-2164-14-869.

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

Author information

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. jboeke@jhmi.edu.

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.

PMID:
24325565
PMCID:
PMC3878892
DOI:
10.1186/1471-2164-14-869
[Indexed for MEDLINE]
Free PMC Article
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