ArticleBMC genomics2013
TE-array--a high throughput tool to study transposon transcription.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Epigenetic characterization of pseudogenes across human tissues.Genome research · 2026Article
- Measuring and interpreting transposable element expression.Nature reviews. Genetics · 2020Review
- Transposon Reactivation in the Germline May Be Useful for Both Transposons and Their Host Genomes.Cells · 2020Review
- Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.PLoS computational biology · 2019Article
- SQuIRE reveals locus-specific regulation of interspersed repeat expression.Nucleic acids research · 2019Article
- Article
- URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells.The Journal of biological chemistry · 2016Article
- TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.Bioinformatics (Oxford, England) · 2015Article
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Authors and funding
8 authors.
Funding
Abstract
backgroundAlthough 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.
resultsTo 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.
conclusionsOur 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.
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