Coexpression signatures identify novel regulators of transposon expression in Drosophila

Transposable elements (TEs) are selfish DNA sequences that can replicate themselves in their host's genome. Hosts have evolved specialized strategies for mitigating the deleterious consequences of TE activity. In Drosophila, the piRNA pathway is the primary transposable element (TE) control pathway. However, many TEs are only expressed in specific cell types, raising the possibility that transcription factors (TFs) also regulate TEs in a sequence-specific manner. Indeed, recent studies in mammals have identified TF families that regulate TE expression in parallel with small RNA pathways, but the contribution of such factors to TE expression regulation in Drosophila remains poorly understood. We leveraged natural expression variation across genetic backgrounds in wild populations of Drosophila to test the hypothesis that TE expression should correlate with the expression of such trans-acting factors. We analyzed coexpression relationships between individual host genes and TEs while controlling for factors that commonly influence TE expression estimates. Our analysis indicates that the expression of some TFs is predictive of TE expression. We find evidence that some of these factors act as regulators of known TE silencing genes, while others may act by binding TE-derived sequences distributed throughout the genome. These results provide a list of candidates for future examination of host/TE interplay, including studies of TF co-option or instances of TE-mediated expansion of host gene regulatory networks.