Expression Analysis in Atlantic Salmon Liver Reveals miRNAs Associated with Smoltification and Seawater Adaptation

Abstract

Optimal smoltification is crucial for normal development, growth, and health of farmed Atlantic salmon in seawater. Here, we characterize miRNA expression in liver to reveal whether miRNAs regulate gene expression during this developmental transition. Expression changes of miRNAs and mRNAs was studied by small-RNA sequencing and microarray analysis, respectively. This revealed 62 differentially expressed guide miRNAs (gDE-miRNAs) that could be divided into three groups with characteristic dynamic expression patterns. Three of miRNA families are known as highly expressed in liver. A rare arm shift was observed during smoltification in the Atlantic salmon-specific novel-ssa-miR-16. The gDE-miRNAs were predicted to target 2804 of the genes revealing expression changes in the microarray analysis. Enrichment analysis revealed that targets were significantly enriched in smoltification-associated biological process groups. These included lipid and cholesterol synthesis, carbohydrate metabolism, protein metabolism and protein transport, immune system genes, circadian rhythm and stress response. The results indicate that gDE-miRNAs may regulate many of the changes associated with this developmental transition in liver. The results pave the way for validation of the predicted target genes and further study of gDE-miRNA and their targets by functional assays.

Differential Expression of miRNAs and Their Predicted Target Genes Indicates That Gene Expression in Atlantic Salmon Gill Is Post-Transcriptionally Regulated by miRNAs in the Parr-Smolt Transformation and Adaptation to Sea Water

“…Seven of the gDE miRNAs revealed in this study were also reported to respond to smoltification and SWA in the liver [ 50 ]. Three of these, as well as ssa-miR-194b-5p, responded to smoltification and SWA in the head kidney (HK) [ 49 ] ( Table 5 ).…”

“…In contrast, ssa-miR-146a-5p and ssa-miR-146b-5p showed a decreasing expression pattern in the gill but an increasing one in the HK [ 49 ] and liver [ 50 ]. This could indicate that they have different regulatory functions in the gill than in the HK and liver.…”

“…A total of 70 Atlantic salmon from the Salmon Breed Model SB-Optimal were used for this study. The experimental fish selected here were the same fish as previously described by Shwe et al [ 49 , 50 ]. The fish were housed in a one tank supplied with running water and they were fed commercial dry feed (Skretting, Norway).…”

“…In addition, miRNAs have been reported to change their expression in the gills of Atlantic salmon in response to salinity challenges [ 48 ]. Our recent studies conducted in the head kidney [ 49 ] and liver [ 50 ] of Atlantic salmon identified a subset of miRNAs that were differentially expressed (DE) in response to smoltification and SW adaptation. The following enrichment analysis of the predicted targets of these DE miRNAs indicated that they were enriched in the biological processes associated with smoltification and SW adaptation in each of these organs [ 49 , 50 ].…”

Transcriptome and Genome Analyses Applied to Aquaculture Research

“…Nevertheless, how non-coding RNAs can contribute to these complex physiological alterations remained practically unexplored. Whereas Valenzuela-Muñoz et al [ 15 ] analyzed the mRNA and miRNA profiles in gills, intestine, and head kidney from Atlantic salmon ( Salmo salar ) exposed to a gradual salinity change or to a salinity shock, Shwe et al [ 16 ] studied their modulation in the liver during smoltification. The results revealed a set of miRNAs associated with smoltification and allowed us to predict their highly confident target genes [ 15 , 16 ].…”