Transgenerational effects of heat stress in Drosophila melanogaster: investigating changes in transcription and chromatin accessibility in different populations

Two factors that may contribute to adaptation under changing environmental conditions are environmentally sensitive epigenome regulation and transposable element (TE) activity under stress. Recent molecular studies suggest interactions between the epigenome and TEs could influence genome evolution in the vinegar fly Drosophila melanogaster. We explored these potential interactions in flies derived from three populations sampled from fruit fields in Spain (Manzanares, Burgos, and Tudela), and one population sampled from fruit fields in Finland (Akaa). From each population 10 female D. melanogaster were collected and brought to the lab. An F1 population was established with an equal number of offspring from each wild-caught female.In the first part of the project, we tested whether chromatin accessibility was influenced by the presence of TEs in F2 flies from the four populations, using ATAC-seq to characterize chromatin accessibility and whole genome resequencing to characterize TEs. Then in the F3, using one of the Spanish populations (Manzanares) and the Finnish population, we carried out a heat shock experiment (flies were heated to 37 degrees C for 1 hour), and immediately characterized the transcriptional and chromatin response in the ovaries of directly affected flies versus controls. Finally, we investigated if transgenerational effects were detectable three generations later in the ovaries of the F6 (great-grand offspring) descendants of heat shocked and control flies. Transcriptional response was characterized using RNA-seq and chromatin-accessibility was characterized using ATAC-seq. TEs were also re-characterized in the F3 using whole genome resequencing data.All ATAC-seq and RNA-seq samples consisted of pooled ovary samples (24-30 individuals), while DNA for whole genome resequencing was collected from pooled samples of the bodies of the same flies used in ATAC-sequencing. All samples were triplicated. Phenotypic data on time to pupation, time-to-eclosion, and egg-to-adult viability were also collected in the F4 (offspring of heat shocked flies) and F7 (great-great-grand offspring of the heat shocked flies). These data will be available with the publication that will accompany this sequencing data.