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TEs and host genome (Coord. E Lerat)

Identification and analysis of TE sequence variants in Drosophila genomes

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The goal of this project is to explore different Drosophila species to characterize and analyze their TE copies, to have a large view of the TE dynamics inside different Drosophila sequenced genome species. At first, we have decided to focused on the melanogaster subgroup, comprising D. melanogaster, D. simulans, D. sechellia, D. yakuba, D. santomea, and D. erecta, whose genomes are sequenced, before extending it to all sequenced Drosophila species. In some TE families, sequence variants are present in D. simulans and D. sechellia, and several families seemed to have been horizontally transmitted between the species. We thus will determine if the existence of sequence variants exist for more families and in more species by undertaking evolutionary analyses of the TEs present in those genomes. The mechanisms of horizontal transfer (HT) is a way for TEs to escape the host-defense mechanisms and to invade new genomes. The invasion of a genome often result in a burst of transposition caused by the lack of specific defenses against this new TE. Understanding the mechanisms and the dynamics of the HT of TEs is thus primordial in the study of TEs. We are currently investigating the occurrence of HT and their underlying mechanisms in the phylogeny of the 19 drosophila genomes available using bioinformatics approaches.

People involved : E. Lerat,L. Modolo
Collaborators : Franck Picard (LBBE),

Evolutionary dynamics of transposable elements in Diptera

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Eukaryotic genomes consist largely of repeated sequences, including transposable elements TEs. In many species, the content in TEs appears to be strongly positively correlated with genome size. Processes that govern the accumulation of TEs in their genomes are still poorly understood. The project is to use genomes recently sequenced in insects, and more specifically in the Diptera order to address the question of a phylogenetic point of view. Is it possible to associate TEs’ activity with changes in genome size during their evolution ? Diptera exhibit huge variations in genome size, cover a long phylogenetic distance and have the advantage of being widely sequenced. The aim is to evaluate the evolutionary dynamics of TEs on the phylogeny of Diptera and identify a potential tendency to expansion / contraction of the genome in different branches of the phylogeny.

People involved : A. Haudry, E. Lerat

Influence of TEs on histone marks changes associated with tumor in human

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Transposable elements (TEs) are particularly abundant in the human genome as they constitute 40% of its sequence. We have previously shown that the presence of TEs in the vicinity of genes may affect their expression under different conditions. One question is whether this effect is related to epigenetic changes, specifically post-translational modifications of histones, which are known to be involved in gene regulation. Using Chip-seq data informing on histone marks for the entire genome in different tissues (cancerous and healthy) and the complete annotation of the human genome, it is possible to look for links between the presence of TEs and specific histone changes. This project aims to identify potential (i) associations between TE families and particular histone marks, (ii) tissue-specific histone modifications, (iii) differences in histone modifications associated to the cancerous state of a given tissue.

People involved : E. Lerat, A. Haudry