The French congress on transposable elements was initiated after Christian Biémont (Laboratory “Biométrie et Biologie Évolutive”, Lyon, France) and Pierre Capy (Laboratory “Evolution, Génomes et Spéciation”, Gif/Yvette, France) had the idea in the 1990s. They wanted to federate all the French researchers working in different fields, but interested in transposable elements (TEs) and other mobile genetic elements. The first edition was held in 1991 in Gif/Yvette (France), hosted by Pierre Capy and Alain Bucheton (IGH, Montpellier, France). Since then, the congress has taken place in a different city each year, each time hosted by a different laboratory from the French TE community. This year, the 17th edition of the congress was hosted by our group “Transposable Elements, Evolution and Populations” from the laboratory “Biométrie et Biologie Évolutive” in Lyon. The particular aim of the congress is to bring together researchers working from very different areas, from molecular biology, molecular evolution and population genetics to bioinformatics, and studying a broad spectrum of organisms. All participants have in common the study of TEs, either trying to decipher their transposition mechanisms or determing the impact of TEs on genes and genomes.
This year, the congress gathers together nearly 80 participants. It has been mainly sponsored by the GDR 2157 “Transposable elements: from the genome to populations”, a network research structure from the CNRS, but also by different biotechnology companies (ThermoFisher, Macherey-Nagel, Dutscher and Roth) and by the laboratory “Biométrie and Biologie Evolutive.” The different presentations were presented in six sessions that will be summarized hereafter.
Transposition Mechanism of LINE-1
The fine transposition mechanism of TEs, even if better understood now, still presents shadowy parts. This is the case for the LINE-1 (L1) elements for which many steps of the retrotransposition mechanism remain unknown, in particular the cellular factors that are. In his talk, Nicolas Gilbert (IGH, Montpellier) showed the development of an engineered L1, allowing for the characterization of a retrotransposition complex composed of the two proteins ORF1p and ORF2p, associated with the RNA. This engineered L1 should help identify host cell factors interacting with it. During the retrotransposition mechanism, the intiation of the reverse transcription of L1 is of particular importance. Clément Monot (laboratory of Biology and Pathology of Genomes, Nice) showed that this initiation is made at T-rich sites, which adds a new layer for the choice of the target site specificity. To allow a L1 to move, the production of the ORF2p is essential. Aurélien Douchet (University of Michigan, USA) has been interested in the analysis of the translation mode of this protein, which seems unconventional likely due to the biscitronic nature of L1. His results suggest that the initation mode of the translation acts by backward scanning.
Evolution and Comparative Genomics
The impact of TEs on genome evolution is no more to be demonstrated. In this session, studies of various organisms (from vertebrates to plants but also in bacteria and arthropods) gave insight into the dynamics of TEs in the genomes. Gaël Cristofari (laboratory of Biology and Pathology of Genomes, Nice) described a very interesting approach using next-generation sequencing (NGS) in order to explore the impact of LINE-1 elements on human health by detecting new insertions in tumors. Using comparative approaches of genome sequences and data from NGS, Gregory Carrier (INRA-IFV, Montpellier) reported that the origin of the clonal diversity in vine is mainly due to differences in TE insertions. This clonal diversity is present inside a single plant showing the importance of new somatic insertions. The occurrence of recurrent horizontal transfers of TEs was also reported both in bacteria (by Nicolas Cerveau, laboratory “Écologie, Évolution, Symbiose”, Poitiers) and in arthropods (by Daphné Reiss, laboratory “Biométrie et Biologie Evolutive”, Lyon), giving insight into the complex dynamics of those TEs across species. The extended analyses of fish and lupin genomes presented respectively by Domitille Chalopin (IGFL-ENS Lyon) and Guillaume Martin (laboratory Ecobio, Rennes), allowed them to show how large the diversity of TE families is, but also their proportion inside these species, confirming the real importance of this compartment in genomes.
Epigenetics Mechanisms of Regulation of TEs
Transposable elements in genomes can have deleterious impacts on their host. Regulation mechanisms have evolved to control their transposition in order to prevent such effects. These mechanisms are mainly epigenetic in nature, like the RNA interference via small RNAs, the histone modifications and DNA methylation. In this session, very interesting results were presented in Drosophila and in plants concerning the regulation of elements in these organisms. In his talk, Thomas Grentzinger (IGH, Montpellier) presented a study of the epigenetic control of the LINE-like element I through the generations of Drosophila where the length of the generations has an influence on the I repression. This indicates that the quantity of piwi-RNAs produced is correlated with the capacity to repress the element and that it increases with the age. Still in Drosophila, Jérémy Dufourt (GreD, Clermont-Ferrand) presented the somatic regulation of a LTR retrotransposon, Idefix for which both post-transcriptional and transcriptional regulations occur. This silencing implies histone modifications but no small RNAs. Nicolas Maunoury (INRA, Versailles), by analyzing the LTR retrotransposon Tnt1 in tobacco, showed that there is a differential induction of the element expression according to the stress but not of the production of small RNAs. Moreover, two regulation pathways targeting different portions of the element seems to exist. In the plant Arabidopsis, TEs are the target of RNA mediated DNA methylation to be silenced. Marion Clavel (Laboratory “Génome et développement des plantes”, Perpignan) revealed that this mechanism implies the action of two double-stranded RNA binding proteins DRB2 and DRB4, which have an antagonistic impact on the production of small RNAs polymerase-IV dependent, with DRB2 decreasing the level of siRNA when DRB4 increases it. In her talk, Marie Mirouze (Laboratory of Plant Genetics, Geneva) showed that the LTR-retrotransposon évadé regulation depends on both DNA methylation and on small RNAs. The study of another LTR-retrotransposon, onsen, indicates that it is transcriptionally responding to heat shock but without any subsequent new insertions, unless the siRNA pathway is defected. These different results demonstrated how complex the control of TEs is in both plants and insects.
Genomics and Transcriptome
The presence of TE insertions in a genome can have an impact on the expression of neighboring genes. In her talk, Quynh Trang Bui (IJPB-INRA, Versailles) presented the existence of chimeric transcripts of TEs and genes in tobacco, mainly under stress conditions. TEs seem thus to act as intermediates of stress stimuli to redirect messages towards cellular functions in stress conditions. In Drosophila, the impact of TEs on transcription can also be highlighted. Matthias Zytnicki (URGI-INRA, Versailles), using high-throughput sequencing, demonstrated that part of TEs may have been domesticated to act as an alternative transcriptional start site.
Genomics and Mechanisms
TEs can be used as molecular markers in order to trace the phylogenetics relationships of their hosts. In the Coffea genus, Alexandre de Kochko (IRD, Montpellier) showed that the use of two LTR-retrotransposons, Nana and Divo, via SSAP, REMAP and RBIP approaches, allows the revealing of distinct insertional histories and can define the phylogenetical structure of some species from the Coffea genus. In Paramecium, different kind of repeats exist. Some very short and very numerous, the IES (Internal Eliminated Sequences), are completely excised from the germline genome (mic) to form a new somatic genome (MAC) via the action of a domesticated transposase. Mireille Bétermier (CGM, Gif/Yvette) showed a study where the inactivation of this transposase allows sequencing by Illumina that approaches thousand of IES. The investigations of these sequences demonstrated that their excision from the mic is due to a precise mechanism of “cute and close”, which involves the introduction of initiating double-strand cleavages at both ends of each IES, followed by DNA double-strand breaks repair via highly precise end joining. The integration of TEs in the genome is also an important step in the life cycle of a TE. In the yeast, Aurélie Tchalikian-Cosson (“Institut Universitaire d'Hématologie”, Paris) showed that this integration is not random and depends of the interaction of the integrase with a cellular protein corresponding to a sub-unit of the polymerase III.
Annotation and Detection of TEs in silico
The presence of TEs that can represent high proportion in genomes makes it particularly important to be able to identify them in genome sequences and to annotate them. During this session several approaches have been presented, which rely on different type of TEs and on different host organisms. Matthieu Piednoël (laboratory “Systematic, Adaptation, Evolution”, Paris—currently in postdoc at the University of Munich) presented an approach to detect DIRS1-like elements in eukaryotic genomes. These elements are particular retroelements with Terminal Inverted Repeat at their extremities and coding for a recombinase. By screening hundreds of genome sequences, he identified several thousand of such sequences and was able to show that these type of elements are more widely represented in eukaryotes than previously thought. In bacteria, only a few number programs dedicated to identify TEs are available. In order to fill this gap, Jonathan Filée (LEGS, Gif/Yvette) proposed two pipelines that use de novo methods for the identification of Insertions Sequences (IS) and MITEs. When tested on archeal genomes, these pipelines allowed the discovery of significantly more new copies than other more classic approaches. Pipelines of programs are likely to be the most powerful approaches to detect TEs in genomes. The use of the REPET package on different organisms has helped in the annotation and the analysis of TEs in different genomes as presented by Joelle Amselem (URGI-INRA, Versailles) in fungal genomes, Veronique Jamilloux (URGI-INRA, Versailles) in plants and insects and Florian Maumus (URGI-INRA, Versailles) in marine stramenopiles.
In conclusion, this congress presented the great dynamics of the French TE community in the different aspects underlined by the study of mobile DNA. It gave once more the opportunity for interactions between very different fields of biological research. Exceptionally, there won't be an edition next year because of the conduct of the second International Congress on Transposable Elements (http://icte2012.com/) that will be held in Saint-Malo (France), organized by the members of the French TE community. However, the 18th edition of the French congress on Transposable Elements will take place in 2013, likely hosted by the TE researchers of groups from Montpellier.
