Infectious pancreatic necrosis virus (IPNV) is a critical pathogen that causes high mortality in salmonids worldwide. To date, molecular studies focus primarily on IPNV infection in classic immune tissues . However, its effects in non-classical immune tissues such as skeletal muscle have not been evaluated. On the other hand, epigenetic changes (e.g., DNA methylation) are induced by environmental factors, including pathogen infection. However, whether viral infection is capable of inducing epigenetic changes in fishes is unclear. We performed an in vivo assay in which juvenile rainbow trout were intraperitoneally injected with vehicle or IPNV for 15 and 30 days . After each treatment, biometric analysis was performed, and skeletal muscle was obtained from each fish. Both RNA and DNA were isolated from this tissue to generate sixteen cDNA and sixteen bisulfite- converted libraries and sequenced by Illumina technology to perform integrated bioinformatic analysis. We found that the condition factor (K) increased after 30 days in vehicle-administered fish but decreased after 30 days in IPNV-administered fish. This reveals that IPNV induces lower growth of infected fish compared to the vehicle. Regarding to RNA-seq analysis, a total of 647 and 361 differentially expressed transcripts (DETs ) were identified after 15- and 30- days post-infection . Biological processes such as t ranslation, protein deubiquitination, and r egulation of DNA-template transcription were found upregulated after 15 days; while p rotein phosphorylation, c ell adhesion and a ctin cytoskeleton organization were downregulated. On the other hand, d ephosphorylation and regulation of translation were found upregulated after 30 days; while r egulation of DNA-template transcription, protein phosphorylation, and chromatin remodeling were downregulated. Regarding to Methyl-seq analysis, a total of 731 and 1067 differentially methylated regions (DMRs) were identified after 15- and 30- days post-infection. Biological processes such as regulation of cytokines production and regulation of immune system process were found up-methylated after 15 days; while microtubule cytoskeleton organization, anatomical structure morphogenesis, and chloride transmembrane transport were found down-methylated. On the other hand, protein phosphorylation, intracellular signal transduction, extracellular matrix organization, and positive regulation of proteasome ubiquitin-dependent protein catabolic process were found up- methylated after 30 days; while DNA recombination, DNA integration, and regulation of membrane potential were found down-methylated. Overall, c orrelation analysis between RNA-seq and genome-wide DNA methylation suggests that IPNV regulates transcriptomic responses in the skeletal muscle through epigenetic mechanisms. This study contributes to the understanding of the molecular basis underlying IPNV infection in salmonids.
Acknowledgments: ANID Ph.D. scholarship 21220218 ; FONDECYT 1230794; FONDAP 1522A0004; FONDAP 1523A0007.