Transposons: a blessing curse

Dubin, Manu; Scheid, Ortrun Mittelsten; Becker, Claude

doi:10.1016/j.pbi.2018.01.003

Cited by 165 publications

(157 citation statements)

References 49 publications

Supporting

Mentioning

155

Contrasting

Unclassified

Order By: Relevance

“…TE de-repression in response to stress is widely shared across eukaryotes (Bundo et al 2014; Van Meter et al 2014; Voronova et al 2014; Romero-Soriano and Guerreiro 2016; Ryan et al 2016; Zovoilis et al 2016; Huang et al 2017; Hummel et al 2017; Shpyleva et al 2018). De-repression of TEs under stress usually impacts TE transcription levels and can increase transpositional activity (Dubin et al 2018). The impact of stress on TEs is often mediated through changes in the epigenetic state of the genome ( i.e.…”

Section: Introductionmentioning

confidence: 99%

Stress-driven transposable element de-repression dynamics in a fungal pathogen

Fouché

Badet

Oggenfuss

et al. 2019

Preprint

View full text Add to dashboard Cite

Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity, however the regulatory mechanisms underlying de-repression are poorly understood. Key unresolved questions are whether different types of stress differentially induce TE activity and whether different TEs respond differently to the same stress. Plant pathogens are excellent models to dissect the impact of stress on TEs, because lifestyle transitions on and off the host impose exposure to a variety of stress conditions. We analyzed the TE expression landscape of four well-characterized strains of the major wheat pathogenZymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including MITE and LTR-Gypsyelements, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e.different strains harboring the same TEs) were major predictors of de-repression dynamics under stress. Genomic defenses inducing point mutations in repetitive regions were largely ineffective to prevent TE de-repression. Consistent with TE de-repression being governed by epigenetic effects, we found that gene expression profiles under stress varied significantly depending on the proximity to the closest TEs. The unexpected complexity in TE responsiveness to stress across genetic backgrounds and genomic locations shows that species harbor substantial genetic variation to control TEs.

show abstract

Section: Introductionmentioning

confidence: 99%

Stress-driven transposable element de-repression dynamics in a fungal pathogen

Fouché

Badet

Oggenfuss

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Thanks to the regulatory elements they carry, TEs have also the capacity to confer environmental responsiveness to neighboring genes (e.g. Makarevitch et al 2015; Horváth et al 2017; Dubin et al 2018). Hence, the duality of TEs, seen either as purely deleterious or as powerful drivers of rapid adaptive evolution has not been resolved today and the way natural selection is acting on TEs and how they accumulate in host genomes remain important questions in evolutionary genomics (Hua-Van et al 2011; Lisch 2013; Casacuberta and González 2013).…”

Section: Introductionmentioning

confidence: 99%

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Legrand

Caron

Maumus

et al. 2018

Preprint

View full text Add to dashboard Cite

2Transposable elements (TEs) have initially been viewed as pure genomic parasites but are now 3 recognized as central genome architects and powerful agents of rapid adaptation. A proper 4 evaluation of their evolutionary significance has been hampered by the paucity of short scale 5 phylogenetic comparisons between closely related species. Here, we characterized the dynamics 6 of TE accumulation at the micro-evolutionary scale by comparing two closely related plant 7 species, Arabidopsis lyrata and A. halleri. Joint genome annotation in these two outcrossing 8 species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' 9 insertion histories. Identification of rare segregating insertions suggests that diverse TE families 10 contribute to the ongoing dynamics of TE accumulation in the two species. TE fragments that 11 have been maintained in both species, i.e. those that are orthologous, tend to be located on 12 average closer to genes than those that are retained in one species only. Moreover, compared to 13 non-orthologous TE insertions, those that are orthologous tend to produce fewer short 14 interfering RNAs, are less heavily methylated when found within or adjacent to genes and these 15 tend to have lower expression levels. These findings suggest that long-term retention of TE 16 insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of 17 removing TE insertions when they are close to genes. Overall, our results indicate a rapid 18 evolutionary dynamics of the TE landscape in these two outcrossing species, with an important

show abstract

“…A positive association between expression variation and TE insertions has been reported for Drosophila (Osada et al ., ). TE insertions can affect the expression of flanking genes in a variety of ways, either by disrupting or providing regulatory elements, such as promoters and enhancers (Dubin et al ., ), or by affecting the epigenetic status of the local chromatin region (Song and Cao, ).…”

Section: Discussionmentioning

confidence: 99%

Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties

et al. 2019

View full text Add to dashboard Cite

Summary The transcriptional regulatory structure of plant genomes is still relatively unexplored, and little is known about factors that influence expression variation in plants. We used a genetic system consisting of 10 heterozygous grape varieties with high consanguinity and high haplotypic diversity to: (i) identify regions of haplotype sharing through whole‐genome resequencing and single‐nucleotide polymorphism (SNP) genotyping; (ii) analyse gene expression through RNA‐seq in four stages of berry development; and (iii) associate gene expression variation with genetic and epigenetic properties. We found that haplotype sharing in and around genes was positively correlated with similarity in expression and was negatively correlated with the fraction of differentially expressed genes. Genetic and epigenetic properties of the gene and the surrounding region showed significant effects on the extent of expression variation, with negative associations for the level of gene body methylation and mean expression level, and with positive associations for nucleotide diversity, structural diversity and ratio of non‐synonymous to synonymous nucleotide diversity. We also observed a spatial dependency of covariation of gene expression among varieties. These results highlight relevant roles for cis‐acting factors, selective constraints and epigenetic features of the gene, and the regional context in which the gene is located, in the determination of expression variation. Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA385116; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA392287; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA373967 (released upon publication); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA490160 (released upon publication); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA265039; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA265040.

show abstract

Transposons: a blessing curse

Cited by 165 publications

References 49 publications

Stress-driven transposable element de-repression dynamics in a fungal pathogen

Stress-driven transposable element de-repression dynamics in a fungal pathogen

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties

Contact Info

Product

Resources

About