A novel method for genome-wide profiling of dynamic host-pathogen interactions using 3′ end enriched RNA-seq

Marek’s disease is a contagious lymphoproliferative disease of chickens and typical model of viral oncogenesis. Mapping changes or different states over the course of infection for both host and pathogen would provide important insights into dynamic host-pathogen interactions. Here we introduced 3′ end enriched RNA-seq as a novel method to study host-pathogen interactions in chicken embryo fibroblasts cells challenged with Marek’s disease virus. The method allowed accurate profiling of gene expression and alternative polyadenylation sites for host and pathogen simultaneously. We totally identified 476 differentially expressed genes and 437 APA switching genes in host, including switching in tandem 3′ UTRs and switching between coding region and 3′ UTR. Most of these genes were related to innate immunity, apoptosis and metabolism, but two sets of genes overlapped a little, suggesting two complementary mechanisms in gene regulation during MDV infection. In summary, our results provided a relatively comprehensive insight into dynamic host-pathogen interactions in regulation of gene transcription during infection of Marek’s disease virus and suggested that 3′ end enriched RNA-seq was a promising method to investigate global host-pathogen interactions.