UMR CNRS 5558 Laboratoire de Biométrie et Biologie Évolutive

• Research Projects
  • + - schema

    TEs and intra/inter species variation

    TEs and genome host

    TEs and invasive species

  • TEs and intra/inter species variation (Coordinator : M. Fablet)
    • + - Transposable element dynamics and variability between and within species

      

      Transposable elements are found in the genomes of virtually all living organisms, but their proportions and activities vary greatly between and within species. In order to understand TE dynamics, we focus on wild-type strains of Drosophila melanogaster and D. simulans, two closely related species which have a three-fold difference in their TE content. In particular, we explore variability in epigenetic TE regulation in relationship to variability in TE dynamics and content. One of the major defense mechanisms against TEs in Drosophila is an RNA interference machinery based on a particular class of small RNAs : piwi-interacting small RNAs (piRNAs). We are currently investigating the link between differences in TE and piRNA content between different populations and species of Drosophila using available genomes and NGS data. We focus on tirant, an endogenous retrovirus which activity varies between wild-type strains of D.simulans : while tirant is either inactive and embedded in heterochromatin in most strains, or it displays post-transcriptionaly silenced euchromatic copies, we identified one strain in which tirant behaves as an endogenous retrovirus and increases in copy number. We use this system of three-type wild-type strains to decipher the dynamics of tirant, with an emphasis on the regulation by piRNAs. People involved : M. Fablet, C. Vieira, L. Modolo Collaborators : Abdou Akkouche et Séverine Chambeyron (Institute of Human Genetics, Montpellier, France), Christophe Terzian (Infections et Rétrovirus Endogènes, Lyon, France)

    • + - Transposable elements and hybrids incompatibility

       

      It has been postulated in the literature that TE may be some how implicated in hybrid incompatibility, or that they are associated with speciation events. At the intra species level, this was typically shown in the case of the hybrid digenesis in Drosophila, in which several different TEs may be involved. We are addressing this question with two different models. One consists in the analysis of hybrids from D. mojavensis and D. arizonae. This two species diverged less the 1 Mya and it is still possible to produce hybrids in the laboratory. We are analyzing the dynamics of TEs in the hybrids versus the parental lines. People involved : C. Vieira, H. Lopez Collaborators : Vincent Lacroix (LBBE), Claudia Carareto and Elias Carnelossi (Department of Biology ; UNESP—São Paulo State University ; São Paulo, Brazil)

  • TEs and genome host (Coordinator : E. Lerat).
    • + - Identification and analysis of TE sequence variants in Drosophila genomes

      

      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

      

      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

      

      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, L. Gregoire, A. Haudry

  • TEs and invasive species (Coordinator : M. Boulesteix).
    • + - The genetic basis of adaptation to new environments : the Asian tiger mosquito case

      

      Aedes albopictus (the Asian tiger mosquito) is an invasive species. From its cradle in Asia it has colonized Europe, America and Africa during the last 30 years, mainly through intercontinental trade in used automobile tires where females lay their eggs. In France its range at first limited to the South East is rapidly expanding. The goal of our project is to understand if the success of the colonizing populations of A. albopictus is due to particular genetic characteristics that distinguishes them from the Asian populations. To answer this question we are comparing Asian and recently established populations by genotyping individuals at thousands of markers, TEs-based or not, distributed throughout the genome, taking advantage of the most recently developed sequencing technologies. People involved : M. Boulesteix, C. Vieira and C. Goubert Collaborators : Claire Valiente-Moro and Patrick Mavingui (UMR 5557) ; Frédéric Simard and Didier Fontenille (MIVEGEC), Grégory L’Ambert (EID-MIVEGEC)

• What’s new ?
  • + - Abdou’s new paper in EMBO Reports !

    Akkouche A, Grentzinger T, Fablet M, Armenise C, Burlet N, Braman V, Chambeyron S. , Vieira C Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells (2013), EMBO reports : in press

  • + - New people….

    
     Emanuel is comming from Spain and Mexico, is doing is M2 in an Erasmus Mundus Program. He will be working with repetitive sequences from Schistosoma mansoni

     Bianca is a PhD student from Rio de Janeiro. She will stay for 6 moths. She has this nice Drosophila lines selected for wing shape, and she will be looking for the activity of TE

• Want to join us ?
  • + - Proposition stage M1/M2 (2012-2013) Intégration du rétrovirus endogène tirant dans la lignée germinal de la drosophile. Analyse de populations naturelles.

    Lors d’une infection par un rétrovirus, lorsque les cellules infectées appartiennent à la lignée germinale de l’hôte, les séquences rétrovirales peuvent être intégrées de façon stable dans le génome, et être alors transmises de génération en génération, comme un gène cellulaire. Ces séquences sont appelées rétrovirus endogènes, par opposition aux rétrovirus exogènes, qui se transmettent par infection d’un individu à l’autre. Ainsi, 8% de notre ADN correspond à des séquences de rétrovirus endogènes, vestiges d’anciennes infections virales, aujourd’hui totalement intégrés à notre génome. La plupart de ces séquences sont totalement inactives, tandis que certaines ont été domestiquées par notre génome et sont aujourd’hui de véritables gènes indispensables au bon fonctionnement de notre organisme. Ce phénomène d’endogénisation de rétrovirus peut ainsi avoir des conséquences importantes sur le fonctionnement et l’évolution du génome hôte. La manière dont les rétrovirus s’intègrent initialement dans la lignée germinale est peu connue, et la rareté de ce phénomène reflète l’existence d’une barrière à l’infection. Dans le but de comprendre les mécanismes à l’origine de l’endogénisation de ces séquences, notre équipe travaille sur tirant, un rétrovirus endogène de drosophile, qui a la particularité de n’être actif que dans quelques populations naturelles africaines de Drosophila simulans.

    Hybridation in ARN du rétrovirus endogène tirant sur des ovaires de drosophile (Photo A. Akkouche).

    Dans ce cadre, l’objectif du travail de recherche sera de décrire la localisation des protéines structurales de tirant par des techniques d’imagerie cellulaire. Cette description permettra d’analyser l’assemblage des particules virales de tirant. Cette recherche se fera sur des populations naturelles qui présentent différents stades d’infection du rétrovirus, avec des lignées saines et des lignées infectées. Il s’agit d’un travail de biologie moléculaire pour lequel l’étudiant réalisera des constructions avec protéine fusion (GFP, YFP), qu’il étudiera par expression transitoire en culture cellulaire et également par transgénèse, en colocalisation avec des marqueurs cellulaires.

    Contact : M. Fablet (fablet@biomserv.univ-lyon1.fr) ou C. Vieira (vieira@biomserv.univ-lyon1.fr) LBBE UMR 5558, Equipe Eléments transposables, évolution, populations

  • + - stages

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+Publications -Publications