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

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.

马立克氏病（Marek’s disease）是一种传染性鸡淋巴增生性疾病，同时也是病毒致癌作用的独特研究模型。对宿主与病原体在感染进程中的变化与状态进行图谱绘制，有望为动态宿主-病原体互作机制提供重要见解。本研究引入3'端富集RNA测序（3' end enriched RNA-seq）作为研究马立克氏病病毒（Marek’s disease virus）感染鸡胚成纤维细胞时宿主-病原体互作的全新方法，该技术可同时精准分析宿主与病原体的基因表达水平及可变多聚腺苷酸化（alternative polyadenylation, APA）位点。本研究共鉴定出宿主的476个差异表达基因与437个APA切换基因，涉及串联3'非翻译区的切换以及编码区与3'非翻译区之间的切换。上述基因大多与先天免疫、细胞凋亡及代谢通路相关，但两类基因的重叠度极低，提示感染过程中存在两种互补的基因表达调控机制。综上，本研究结果较为全面地解析了马立克氏病病毒感染期间基因转录调控层面的动态宿主-病原体互作机制，并表明3'端富集RNA-seq是一种极具应用前景的全局宿主-病原体互作研究方法。整体实验设计：于病毒攻毒后的各时间点采集样本，本研究共构建10个IVT-SAPAS文库，并通过Illumina GA IIx测序平台完成测序。