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Transposable element mobilization, its control and impact

TEs are potentially powerful endogenous mutagens and epimutagens. However, the dynamics as well as the determinants of TE mobilization are largely unknown for most eukaryotic species and so is the contribution of this process to the generation of phenotypic variation. Using genome sequencing data for 211 A. thaliana accessions taken from across the globe we identified thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We also showed using this population genomics approach that the composition and activity of the so-called ’mobilome’ vary extensively between accessions in relation to climate and genetic factors. Recent TE insertions are distributed evenly across the chromosomes, with no overt bias and we provided evidence that those located within the gene-rich chromosome arms are subjected to strong purifying selection. Finally, we showed that loci controlling adaptive responses to the environment are the most frequent carriers of the transpositions we observed, suggesting that TE mobilization is a potent source of genetic diversity with important consequences for rapid adaptation.

We now wish to determine the contribution of TE mobilization to the rapid generation of adaptive phenotypes in two distinct contexts, that of colonizing populations of A. thaliana and that of domestication and improvement of tomato. As TEs are exquisitely sensitive to the environment, we are also investigating the impact of climate change on TE activity using the genome sequences publically available for over one thousand A. thaliana accessions taken from across the globe. Finally, we are also exploiting the epiRIL population we developed in A. thaliana to investigate experimentally the transgenerational dynamics of TE mobilization when DNA methylation is compromised. Following TE mobilization generation after generation, we are thus able to measure precisely the effect on the expression of the nearby genes of all new TE insertions, before and after they become epigenetically silenced.

A) Association between annual temperature range and TE copy number (CN ; red circles) for the LTR-retroelement ATCOPIA78 in A. thaliana accessions collected from across the globe. B) Circos representation of new insertion events detected in epiRILs for the DNA transposon ATENSPM3. The external bars represent the density of new TE insertions within WT- and ddm1-derived intervals (green and red, respectively).