Pathogen infection alters the gene expression landscape of transposable elements inDrosophila melanogaster: A meta-analysis

ABSTRACT Transposable elements (TEs) are remnants of ancient viral infections and make up substantial proportions of eukaryotic genomes. Current research has begun to highlight the role TEs can play in the immune system response to infections. However, most of our knowledge about TE expression during infection is limited by the specific host and pathogen factors from each study, making it difficult to compare studies and develop broader patterns regarding the role of TEs during infection. Here, we use the tools and resources available in the model, Drosophila melanogaster , to analyze multiple RNAseq datasets of flies subject to bacterial, fungal, and viral infections. We analyzed differences in pathogen species, host genotype, host tissue, and sex to understand how these factors impact TE expression during infection. Our results highlight both shared and unique TE expression patterns between pathogens and suggest a larger effect of pathogen factors over host factors for influencing TE expression. AUTHOR SUMMARY Transposable elements (TEs) are short, repetitive genetic elements that make up substantial proportions of the genomes of all eukaryotic species. These TEs can become expressed during infections, either as a by-product of the infection itself or as a part of the defense mechanism of the immune system. Many studies have investigated TE activity during infection, often focusing on a single pathogen species, one specific host species and genotype, or even a small number of specific TEs. Though these studies provide important detail on these particular cases, less is known about broader patterns of TE activity during infections. Is TE expression the same across different types of infections, and how does the host affect these expression patterns? Here, we analyzed multiple gene expression datasets from infected flies to uncover these broader patterns in TE expression. We found that the type of infection, whether bacterial, fungal, or viral, has a large effect on TE expression. We also found that host factors, like sex, tissue, or genotype, have a much smaller effect on TE expression during infection compared to infection type. Our results offer a broader perspective on how TEs are activated during infections in flies.