Identification of Differentially Expressed Atlantic Salmon Mirnas Responding to Salmonid Alphavirus Infection; Genome Analysis and Target Gene Predictions Suggest Many DE MiRNAs Participate in Negative Feedback Networks in the Innate Immune System

MicroRNAs (miRNAs) control multiple biological processes including the innate immune responses by negative post-transcriptional regulation of gene expression. In this study we aimed to identify miRNAs responding to salmonid alphavirus (SAV) infection. Furthermore, the genome sequences of the identified miRNAs were analysed to reveal putative cis-regulatory elements, and their putative target genes were predicted.

Illumina small RNA sequencing and DESeq2 was used in the initial identification of differentially expressed miRNAs (DE miRNAs). RT-qPCR assays were applied to reveal expression of the individual DE miRNAs at different time points post infection with SAV isolates associated with different mortality (cardiac tissue samples, n=89). Viral load was measured by use of RT-qPCR. RNA hybrid was applied to predict target genes.

Twenty DE miRNAs were identified. The expression of the majority of these increased post infection with maximum levels reached after the viral load were stabilized or decreased. Sixteen of the DE miRNAs were predicted to target 21 innate immune network genes (e.g. IRF3, IRF7, viperine, interferone γ). The upstream sequences of the miRNA genes revealed a high density of cis-regulatory sequences known as targets for transcription factors involved in immune responses. Our findings suggest that many DE miRNAs are participants in negative feedback networks and may prohibit excess inflammatory reactions.

This is a first step in exploring miRNAs important in viral-host interaction in Atlantic salmon. Their predicted functions need to be validated and further studied in functional assays to fully understand their roles in immune homeostasis.