Altered histone modifications in Aedes aegypti following Rift Valley fever virus exposure

When arthropod-borne viruses (arboviruses) are delivered to vector mosquitoes in an infectious bloodmeal, viral components interact with host proteins to hijack cells and initiate replication. The extent to which arbovirus infection alters mosquito host transcriptional and genomic regulatory processes is currently unknown. We hypothesized that histone modifications would be altered in mosquitoes exposed to Rift Valley fever virus (RVFV MP12, Phlebovirus riftense, family Phleboviridae). We interrogated transcriptome and chromatin landscapes in Aedes aegypti midguts by performing Cleavage Under Targets and Release Using Nuclease (CUT&RUN), using H3K27ac and H3K9me3 marks. Altered H3K27ac marks were identified following RVFV MP12 exposure, as well as upon bloodfeeding alone. It took several days for differential H3K27ac marks to be associated with differentially expressed genes (DEGs) in RVFV-exposed midguts. H3K27ac peaks showed progressive depletion as infection progressed. Gene set enrichment analysis revealed that immune response transcripts were enriched at 1 and 3 dpf (days post-feeding) but depleted by 7 dpf. Hedgehog/Gli (glioma-associated oncogene homolog) signaling pathway transcripts were depleted, indicating possible viral manipulation of cellular polarization. Moreover, at 7 dpf, 7 of 102 DEGs were proximal to differentially acetylated sites in a pattern expected to favor viral propagation. However, one transcript coding for an antiviral effector (LysM-TLDc domain protein) showed significant depletion of both H3K9me3 and H3K27ac marks. Analysis of midguts after a non-infectious bloodmeal versus sugar-fed controls revealed global changes to H3K27ac and H3K9me3 marks during and following the period of bloodmeal digestion. Differential H3K27ac marks were proximal to one quarter of all DEGs at 1 dpf, consistent with an important role of H3K27ac in bloodmeal digestion. These results demonstrate that H3K27ac and H3K9me3 patterns are altered upon virus exposure in a complex interplay that favors viral replication but is also countered by host responses to limit replication. Author SummaryMosquito-borne viruses produce a high disease burden across the globe. Though transgenic mosquitoes are being developed to help mitigate disease transmission, little is known of the ways in which arbovirus infection alters chromatin structure in mosquitoes. Arboviruses typically replicate and assemble on cytoplasmic membranes and have not been traditionally expected to alter processes in the nucleus. Some histone post-translational modifications, such as, e.g. histone 3 lysine 27 acetylation (H3K27ac), are associated with accessible chromatin regions, whereas others, e.g, histone 3 lysine 9 triple-methylation (H3K9me3), are associated with inaccessible chromatin. This work explores these chromatin modifications and the ways in which they are tied to gene expression changes. Multiple lines of evidence presented here support the hypothesis that H3K27ac levels change in RVFV-exposed mosquitoes and are associated with altered gene expression in a manner consistent with viral hijacking of gene expression in the nucleus. In addition, bloodfeeding alone also altered H3K27ac levels at 1-day post-feeding, and over one quarter of differentially expressed genes had changes to H3K27ac marks near transcription start sites, which is consistent with the idea that broad metabolic changes occur to support digestion and egg development.