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Recognition and silencing of a new transposable element

ABSTRACT: Genomes constantly face threats from transposable elements (TEs) and other genomic parasites. While the silencing of existing TE has been well studied, little is known about how cells recognize new invading TEs that they have not previously encountered. Here we explore this question by inserting a foreign sequences into S. pombe. Our data revealed that the newly invading TE tj1 is recognized and targeted for silencing by RNAi and heterochromatin. The efficiency of recognition, as well as the degree and stability of silencing, depends on the copy number and insertion location of the TE. We demonstrated that RNA, rather than DNA, is sensed, and that the efficiency of TE recognition correlates with levels of RNA antisense to the TE, generated from upstream transcripts. We also show that various genes of non-transposable nature can initiate silencing. Our data show that silencing may not require recognition of specific elements in the transposon by the host defense systems, and suggest that disruption of host transcription patterns can trigger recognition of TE.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE249616 | GEO | 2026/04/16

REPOSITORIES: GEO

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Project description:Background: Transposable elements (TEs) represent a substantial fraction of the genomes, playing a major role in evolution, as sources of genetic variability. To fully appraise the role of TE in the acquisition of genetic novelty in genome evolution, we must also consider the impact of their own transcriptional activity. Results: We studied impact of TE transcriptional activity on gene using high-throughput RNA-Seq sequencing in Drosophila melanogaster. TEs, which turn out to be expressed in euchromatin as well as in heterochromatin, interact with genes at different levels. The observed transcription from TEs involve canonical or non-canonical transcription start sites (TSSs) distributed along their sequence. We also find evidences for potential bidirectional transcription from the TE promoter regions where the antisense transcript is co-opted by the host genome as TSSs of a gene. We found that active TEs seem to accumulate in the 5' upstream regions of the genes, and possibly provide an alternative transcript of the nearby gene. Indeed, predominantly, the TE transcript is collinear and overlapping the gene. Apart from the 5' upstream regions, we also found that most active TEs are transcribed on the gene transcript strand. Conversely, few transcripts from TE are anti sense with respect to the gene. This suggests that they have a disruptive action and are counter-selected. The only exceptions are for TEs located into introns, where they could provide another complex way of gene regulation, and in the 3' downstream region, where other mechanisms akin to siRNAs could take place. Finally, we noted several cases where the cryptic TSS is located on TE fragments corresponding to a low complexity sequence. Frequently these TE fragments appear to be over-represented when close to genes, suggesting a possible selected role. Conclusion: Altogether, these results suggest that active transposable elements influence host gene transcription. It is likely that some features of transposable elements have been exaptated in order to enrich the genes repertoire by opening routes to sub- or neo-functionalization. Examination of the transcription produced by transposable elements in D. melanogaster

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Recognition and silencing of a new transposable element

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