Abstract
BackgroundDespite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined.ResultsHere we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated expression across broad classes of TEs. Despite this co-expression within tissues, there are individual TE loci that exhibit tissue-specific expression patterns, when compared across tissues. The core TE modules were negatively correlated with other gene modules that consisted of immune response genes in interferon signaling. KRAB Zinc Finger Proteins (KZFPs) were over-represented gene members of the TE modules, showing positive correlation across multiple tissues. But we did not find overlap between TE-KZFP pairs that are co-expressed and TE-KZFP pairs that are bound in published ChIP-seq studies.ConclusionsWe find unexpected variation in TE derived transcripts, within and across non-tumorous tissues. We describe a broad view of the RNA state for non-tumorous tissues exhibiting higher level of TE transcripts. Tissues with higher level of TE transcripts have a broad range of TEs co-expressed, with high expression of a large number of KZFPs, and lower RNA levels of immune genes.
Highlights
Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells
Given that the majority of the transposons transcribed and measured by Cap Analysis Gene Expression (CAGE) were not initiated at the canonical promoter in the 5′ of the transposon, and that they were enriched in the nuclear compartments, they likely do not reflect the autonomous transcription of active transposable elements that transport to the cytosol for retrotransposition
The results reported here are based on the STAR alignment allowing up to 200 multi-mapping of reads, with correction for potential read-thru transcripts based on the read-depths of the containing introns, as described unless specified otherwise
Summary
Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. Given that the majority of the transposons transcribed and measured by Cap Analysis Gene Expression (CAGE) were not initiated at the canonical promoter in the 5′ of the transposon, and that they were enriched in the nuclear compartments, they likely do not reflect the autonomous transcription of active transposable elements that transport to the cytosol for retrotransposition. Whether these TE derived transcripts have functional relevance need further studies. Observations include contribution to transcription start sites [19], source of transcription factor binding sites [22], source of long non-coding RNAs [23], active transcription during early development [24], and even critical function similar to long non-coding RNAs that guide chromatin-remodeling complexes to specific loci in the genome [25]
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