Impact Of Transposable Elements On Transcriptome: The Example Of Drosophila melanogaster

We studied transposable elements (TEs) impact on gene transcription using high-throughput sequencing (RNA-Seq). TEs, which turn out to be expressed in euchromatin as well as in heterochromatin, interact with genes at different levels.

First, active TEs seem to accumulate in the 5' upstream regions of the genes, possibly providing an alternative transcript of the nearby gene. Indeed, in some cases, the TE transcript is co-linear and overlapping to the gene.

Second, apart from the 5' upstream regions, most active TEs seem transcribed on the same strand as the gene. Conversely, few anti-sense-TEs with respect to the gene are observed. This suggests that anti-sense TEs insertions have a disruptive action and are counter-selected. The only exceptions are when the TEs are located in introns, where they could provide another complex way of regulating the gene, and in the 3' downstream region, where other mechanisms akin to siRNAs could take place.

Third, we noted several cases where a non-canonical transcriptional start site (TSS) is present on the TE. This cryptic-TSS is located on specific TE fragments that appear to be selected among other TE fragments when close to genes.

All together, these results suggest that the active transposable elements influence the transcription in the host genome. It is likely that some features of transposable elements have been exaptated in order to enrich some genes, and possibly acquire new functions.