A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

Mohamed, Mourdas; Dang, Nguyet Thi-Minh; Ogyama, Yuki; Burlet, Nelly; Mugat, Bruno; Boulesteix, Matthieu; Mérel, Vincent; Veber, Philippe; Salces-Ortiz, Judit; Séverac, Dany; Pélisson, Alain; Vieira, Cristina; Sabot, François; Fablet, Marie; Chambeyron, Séverine

doi:10.3390/cells9081776

Cited by 40 publications

(84 citation statements)

References 72 publications

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“…The abundance of ZAM in these ovarian cell lines is more than 10-fold higher than fly strains where ZAM has been mobilized because of deletions in the flamenco piRNA locus ( Leblanc et al 1999 ; Zanni et al . 2013 ) or because of multigenerational knockdown of the piRNA effector protein piwi ( Barckmann et al 2018 ; Mohamed et al 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

et al. 2021

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Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabelling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of LTR retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.

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Section: Resultsmentioning

confidence: 99%

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

et al. 2021

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“…Thus, by the use of long-read sequencing we put forward a novel methodology for detecting somatic TE activity. A similar approach has very recently been proposed to map rare TE germline variants in Drosophila (Mohamed et al, 2020) and to perform epigenomic profiling and non-referenced TE mapping in human datasets (Ewing et al, 2020), further showing that long-read sequencing will certainly gain popularity in the field. As our results obtained with this technology are highly consistent with our results obtained with short-read sequencing of neoplastic clones, we believe the singleton reads detected with long-read sequencing are very likely de novo somatic events.…”

Section: Somatic Retrotransposition In the Fly Intestinementioning

confidence: 99%

Unraveling the features of somatic transposition in the Drosophila intestine

et al. 2021

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Transposable elements (TEs) play a significant role in evolution, contributing to genetic variation. However, TE mobilization in somatic cells is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we have mapped hundreds of highconfidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, applying Oxford Nanopore longread sequencing technology we provide evidence for tissue-specific differences in retrotransposition. Comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are enriched in genic regions and in transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown features underlying somatic TE mobility in vivo.

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“…The present datasets are RNA-seq and ChIP-seq for H3K4me3 and H3K9me3 marks, and were prepared from ovarian samples. They were analyzed in parallel with already published data produced from the same drosophila strains: ovarian piRNA repertoires and genome assemblies based on Oxford Nanopore long read sequencing (Mohamed et al 2020). For RNA-seq and ChIP-seq, TE-derived reads were analyzed at the TE family level, and gene-derived reads were analyzed in relation to TE insertions inside or nearby the genes (therefore restricted to the TE insertions included within the gray bubbles).…”

Section: Introductionmentioning

confidence: 99%

A quantitative, genome-wide analysis inDrosophilareveals transposable elements’ influence on gene expression is species-specific

Fablet

Salces-Ortiz

Jacquet

et al. 2022

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Transposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They are controlled by the host through the targeting of silencing epigenetic marks, which may affect the chromatin structure of neighboring sequences, including genes. In this study, we used transcriptomic and epigenomic high-throughput data produced from ovarian samples of Drosophila melanogaster and Drosophila simulans wild-type strains, in order to finely quantify the influence of TE insertions on gene RNA levels and histone marks (H3K4me3 and H3K9me3) enrichments. We find general, negative impacts of TE insertions on gene RNA levels and H3K4me3 enrichments, which intensity varies according to the localization of the TE insertion. We also uncover that TE insertions within exons are associated with a reduction in H3K9me3 enrichments, which we propose is associated with TE splicing out. Overall, we find that gene RNA and histone mark levels show contrasted dependencies on TE insertions regarding the species. The fold-decrease in TE-carrying gene proportions between extreme expression classes is 2.6 in D. melanogaster and 1.8 in D. simulans, while it is strongly contrasted between extreme classes of H3K4me3 enrichments: 4.4 in D. melanogaster and 19.2 in D. simulans. This provide a new light on the considerable natural variability provided by TEs, which may be associated with contrasted adaptive and evolutionary potentials.

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A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

Cited by 40 publications

References 72 publications

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

Unraveling the features of somatic transposition in the Drosophila intestine

A quantitative, genome-wide analysis inDrosophilareveals transposable elements’ influence on gene expression is species-specific

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