Conserved noncoding elements influence the transposable element landscape in<i>Drosophila</i>

Manee, Manee M.; Jackson, John; Bergman, Casey M.

doi:10.1101/257907

Cited by 3 publications

(3 citation statements)

References 65 publications

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“…Similar analyses in D. melanogaster show that TEs are underrepresented in CNSs compared to the rest of the genome, however, there was no difference in population frequency of TEs in or outside of CNSs (Manee et al 2018). Our results suggest that important TE effects on genes extend not only to direct gene disruption and methylation-mediated gene silencing, but also to disruption of regulatory sequence.…”

Section: Selection Against Gene Disruption Regulates Te Numberssupporting

confidence: 77%

Transposable elements are important contributors to standing variation in gene expression inCapsella grandiflora

Uzunović

Josephs

Stinchcombe

et al. 2018

Preprint

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Transposable elements (TEs) make up a significant portion of eukaryotic genomes and are important drivers of genome evolution. However, the extent to which TEs affect phenotypic variation on a genome-wide scale in comparison with other types of variants is still unclear. We characterised TE insertion polymorphisms and their effects on gene expression in 124 wholegenome sequences from a single population of Capsella grandiflora, and contrasted this with the effects of rare single nucleotide polymorphisms (SNPs). The frequency of insertions was negatively correlated with distance to genes, as well as density of conserved non-coding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare SNPs contribute equally to up-and down-regulation, but have a weaker effect than TEs. Taken together, these results imply that TEs are a significant contributor to gene expression variation and are more likely than rare SNPs to cause extreme changes in gene expression.

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Section: Selection Against Gene Disruption Regulates Te Numberssupporting

confidence: 77%

Transposable elements are important contributors to standing variation in gene expression inCapsella grandiflora

Uzunović

Josephs

Stinchcombe

et al. 2018

Preprint

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“…We restricted our analysis to normal recombination regions since low recombination regions have high reference TE content which reduces the ability to predict non-reference TE insertions (Bergman et al . 2006; Manee et al . 2018).…”

Section: Methodsmentioning

confidence: 99%

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

Han

Dias

Basting

et al. 2022

Preprint

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Animal cell lines cultured for extended periods often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In Drosophila, many established cell lines also exhibit massive proliferation of transposable elements (TEs) relative to wild-type flies. To better understand the role of transposition during long-term animal somatic cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. Relative to comparable data from inbred whole flies, WGAs for S2R+ were highly fragmented and generated variable estimates of TE content across sequencing and assembly technologies. We therefore developed a novel WGA-independent bioinformatics method called "TELR" that identifies, locally assembles, and estimates allele frequency of TEs from long-read sequence data (https://github.com/bergmanlab/telr). Application of TELR to a ~130x PacBio dataset for S2R+ revealed many haplotype-specific TE insertions that arose by somatic transposition in cell culture after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TE copies within the S2R+ genome, which revealed that proliferation of different TE families during cell line evolution in vitro can be driven by single or multiple source lineages. Our work provides a model for the analysis of TEs in complex heterozygous or polyploid genomes that are not amenable to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.

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“…Our analysis was restricted to normal recombination regions since low recombination regions have high reference TE content which reduces the ability to predict non-reference TE insertions (Bergman et al . 2006; Manee et al . 2018).…”

Section: Methodsmentioning

confidence: 99%

Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sub-lines

Han

Dias

Basting

et al. 2021

Preprint

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Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element (TE) content than whole flies, but whether this increase in TE content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here we sequence the genomes of 25 sub-lines of Drosophila S2 cells and show that TE insertions provide abundant markers for the phylogenetic reconstruction of diverse sub-lines in a model animal cell culture system. Analysis of DNA copy number evolution across S2 sub-lines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using TE insertions. Analysis of TE insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for sub-line identity.

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Conserved noncoding elements influence the transposable element landscape inDrosophila

Cited by 3 publications

References 65 publications

Transposable elements are important contributors to standing variation in gene expression inCapsella grandiflora

Transposable elements are important contributors to standing variation in gene expression inCapsella grandiflora

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sub-lines

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