A Quantitative, Genome-Wide Analysis in Drosophila Reveals Transposable Elements' Influence on Gene Expression Is Species-Specific.

Transposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They can be 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 several Drosophila melanogaster and Drosophila simulans wild-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 in D. simulans compared with D. melanogaster. At the same time, we uncover a larger contribution of TEs to gene H3K9me3 variance within genomes in D. melanogaster, which is evidenced by a stronger correlation of TE numbers around genes with the levels of this chromatin mark in D. 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.

An attempt to select non-genetic variation in resistance to starvation and reduced chill coma recovery time in Drosophila melanogaster.

Phenotypic variance is attributed to genetic and non-genetic factors, and only the former are presumed to be inherited and thus suitable for the action of selection. Although increasing amounts of data suggest that non-genetic variability may be inherited, we have limited empirical data in animals. Here, we performed an artificial selection experiment using Drosophila melanogaster inbred lines. We quantified the response to selection for a decrease in chill coma recovery time and an increase in starvation resistance. We observed a weak response to selection in the inbred and outbred lines, with variability across lines. At the end of the selection process, differential expression was detected for some genes associated with epigenetics, the piRNA pathway and canalization functions. As the selection process can disturb the canalization process and increase the phenotypic variance of developmental traits, we also investigated possible effects of the selection process on the number of scutellar bristles, fluctuating asymmetry levels and fitness estimates. These results suggest that, contrary to what was shown in plants, selection of non-genetic variability is not straightforward in Drosophila and appears to be strongly genotype dependent.