Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Université de Lyon, Villeurbanne 69622, France.
Nucleic Acids Res. 2017 Feb 28;45(4):e17. doi: 10.1093/nar/gkw953.
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.
近几十年来，人们在理解宿主基因组与转座元件 (TEs) 之间的相互作用方面付出了巨大努力。TEs 对宿主基因调控的影响是众所周知的，TEs 可以作为调控序列的平台。然而，由于它们的重复性质，将 TEs 分析纳入全基因组研究相当困难。在这里，我们开发了一种专门用于 TE 表达分析的工具：TEtools。该工具考虑了基因组中转座元件序列的多样性，可应用于未注释或未组装的基因组，并在 GPL3 下免费提供（https://github.com/l-modolo/TEtools）。TEtools 将从经典 mRNAs 或小 RNAs 获得的 RNA-seq 数据映射到 TE 序列列表上，并进行具有统计相关性的差异表达分析。使用此工具，我们分析了来自五个野生型黑腹果蝇品系的 TE 表达情况。我们的数据首次表明，TE 的活性与涉及 piwi 相互作用 RNA 生物发生的基因的活性严格相关，因此符合 TE 序列和宿主控制基因之间的军备竞赛情景。
