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The landscape, properties, and determinants of transcriptional activation of endogenous transposable elements in grapevine (Vitis vinifera L.)

ABSTRACT: Background: Transcriptional activation of structurally autonomous transposable elements (TEs) is a precursor to both autonomous and non-autonomous transposition in host genomes. However, the identification of those transcribed TE loci that are competent autonomous elements, their genomic locations and the specific conditions under which these loci can contribute to mobilisation of both autonomous and non-autonomous elements remains largely unknown. Results: A three-channel analysis pipeline was established to identified expressed TE loci. This pipeline is mainly comprised of three different existing tools (htseq-count, bedtools, and TEFingerprint) for mapped read quantification. Using Vitis vinifera embryogenic callus as a model, we exposed the callus to live cultures of an endemic grapevine yeast Hanseniaspora uvarum to determine the landscape and properties of expressed TE loci. In this system, only 1.7%-2.5% of total annotated TE loci were transcribed, of which 5%-10% of these were full-length (>90% length integrity). Collectively, these TE loci (including fragmented and structurally ‘autonomous’ loci) exhibited a significant tendency to be found within introns of expressed genes. This strong location bias towards expressed genes was also observed in Arabidopsis thaliana wild-type and ibm2, but not in ddm1. Moreover, in the grapevine model, differentially expressed TE loci tend to present similar expression pattern with co-localized differentially expressed genes. Nonetheless, utilizing Oxford Nanopore Technology (ONT) cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified full-length transcripts derived from structurally autonomous TE loci in our grapevine system, although the level of these transcripts was low. Conclusions: Our observations in the two disparate plant model systems reveal the closely connected transcriptional relationship between TEs and co-localized genes when the epigenetic silencing system is not compromised. Furthermore, we found that the stress treatment alone was not sufficient to induce large scale full length transcription from structurally intact TE loci, a precursor for mobilisation of non-autonomous and autonomous elements.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE175475 | GEO | 2022/05/05

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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The landscape, properties, and determinants of transcriptional activation of endogenous transposable elements in grapevine (Vitis vinifera L.)

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