Transcriptome Sequencing Reveals That Intact Expression of the Chicken Endogenous Retrovirus chERV3 In Vitro Can Possibly Block the Key Innate Immune Pathway

SIMPLE SUMMARY: Endogenous retroviruses (ERVs) are ancient viral sequences that have integrated into the genomes of vertebrates. In order to evaluate the function of chERV3 on the host innate immune response, a full-length (10,218 bp) reverse cloning plasmid (puc57-chERV3) was constructed and transfected into primary chicken embryo fibroblasts (CEFs) for transcriptome sequencing. We then performed transcriptome sequencing to analyze the gene expression changes induced by chERV3. We found that chERV3 down-regulated many genes involved in immune-related processes, such as the inflammatory response, innate immune response, and the Toll-like receptor signaling pathway. These processes are involved in detecting and responding to viral infection. Our study systematically identified the effect of chERV3 prokaryotic expression on the innate immune response in chickens. ERVs are a rich source of genetic diversity and innovation in vertebrates, and understanding their roles and mechanisms may have implications for susceptibility to animal diseases. ABSTRACT: Endogenous retroviruses (ERVs) are viral sequences that have integrated into the genomes of vertebrates. Our preliminary transcriptome sequencing analysis revealed that chERV3 is active and is located on chromosome 1:32602284–32615631. We hypothesized that chERV3 may have a role in the host innate immune response to viral infection. In this study, using reverse genetics, we constructed the puc57-chERV3 full-length reverse cloning plasmid in vitro. We measured the p27 content in culture supernatant by enzyme-linked immunosorbent assay (ELISA). Finally, transcriptome analysis was performed to analyze the function of chERV3 in innate immunity. The results showed that chERV3 may generate p27 viral particles. We found that compared to the negative control (NC) group (transfected with pMD18T-EGFP), the chERV3 group exhibited 2538 up-regulated differentially expressed genes (DEGs) and 1828 down-regulated DEGs at 24 hours (h) and 1752 up-regulated DEGs and 1282 down-regulated DEGs at 48 h. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the down-regulated DEGs were enriched mainly in immune-related processes such as the inflammatory response, innate immune response, and Toll-like receptor signaling pathway. GSEA showed that the Toll-like receptor signaling pathway was suppressed by chERV3 at both time points. We hypothesized that chERV3 can influence the activation of the innate immune pathway by blocking the Toll-like receptor signaling pathway to achieve immune evasion.