Dynamic host-pathogen interactions in pathogen-challenged chicken embryo fibroblasts cells with Marek’s Disease Virus using 3’ end enriched RNA-seq

Marek’s disease is a contagious lymphoproliferative disease of chickens and is a unique model of viral oncogenesis. Mapping changes or states over the course of infection for both host and pathogen would have the potential to generate 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 Marek’s disease virus challenged chicken embryo fibroblasts cells, which 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 for regulating gene expression during infection. In summary, our results gave a relatively comprehensive insight into dynamic host-pathogen interactions in gene transcription regulation during Marek’s disease virus infection and suggested that 3’ end enriched RNA-seq was a promising method to investigate global host-pathogen interactions. Overall design: Samples was collected at each time point after virus challenge. Thus, in total ten IVT-SAPAS libraries were constructed and sequenced with Illumina GA IIx.