title: TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes.
abstract: Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. Nevertheless, due to their repetitive nature it is considerably hard to integrate TE analysis into genome-wide studies. Here, we developed a specific tool for the analysis of TE expression: TEtools. This tool takes into account the TE sequence diversity of the genome, it can be applied to unannotated or unassembled genomes and is freely available under the GPL3 (https://github.com/l-modolo/TEtools). TEtools performs the mapping of RNA-seq data obtained from classical mRNAs or small RNAs onto a list of TE sequences and performs differential expression analyses with statistical relevance. Using this tool, we analyzed TE expression from five Drosophila wild-type strains. Our data show for the first time that the activity of TEs is strictly linked to the activity of the genes implicated in the piwi-interacting RNA biogenesis and therefore fits an arms race scenario between TE sequences and host control genes.
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Lerat
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Fablet
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Modolo
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Lopez-Maestre
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France.
authors.forename: Cristina
authors.initials: C
authors.lastname: Vieira
mesh_terms: D000067636:Drosophila simulans / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D020071:Interspersed Repetitive Sequences; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D012984:Software
chemical_list: D034741:RNA, Small Interfering