A quantitative, genome-wide analysis inDrosophilareveals transposable elements’ influence on gene expression is species-specific

Abstract

AbstractTransposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They are controlled by the host through the targeting of silencing epigenetic marks, which may affect the chromatin structure of neighboring sequences, including genes. In this study, we used transcriptomic and epigenomic high-throughput data produced from ovarian samples of severalDrosophila melanogasterandDrosophila simulanswild-type strains, in order to finely quantify the influence of TE insertions on gene RNA levels and histone marks (H3K9me3 and H3K4me3). Our results reveal a stronger epigenetic effect of TEs on ortholog genes inD. simulanscompared toD. melanogaster. At the same time, we uncover a larger contribution of TEs to gene H3K9me3 variance within genomes inD. melanogaster, which is evidenced by a stronger correlation of TE numbers around genes with the levels of this chromatin mark inD. melanogaster. Overall, this work contributes to the understanding of species-specific influence of TEs within genomes. It provides a new light on the considerable natural variability provided by TEs, which may be associated with contrasted adaptive and evolutionary potentials.