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

Abstract

Smoltification (parr-smolt transformation) is a complex developmental process consisting of developmental changes that lead to remodeling of the Atlantic salmon gill. Here, the expression changes of miRNAs and mRNAs were studied by small-RNA sequencing and microarray analysis, respectively, to identify miRNAs and their predicted targets associated with smoltification and subsequent sea water adaptation (SWA). In total, 18 guide miRNAs were identified as differentially expressed (gDE miRNAs). Hierarchical clustering analysis of expression changes divided these into one cluster of 13 gDE miRNAs with decreasing expression during smoltification and SWA that included the miRNA-146, miRNA-30 and miRNA-7132 families. Another smaller cluster that showed increasing expression consisted of miR-101a-3p, miR-193b-5p, miR-499a-5p, miR-727a-3p and miR-8159-5p. The gDE miRNAs were predicted to target 747 of the genes (DE mRNAs), showing expression changes in the microarray analysis. The predicted targets included genes encoding NKA-subunits, aquaporin-subunits, cystic fibrosis transmembrane conductance regulator and the solute carrier family. Furthermore, the predicted target genes were enriched in biological processes associated with smoltification and SWA (e.g., immune system, reactive oxygen species, stress response and extracellular matrix organization). Collectively, the results indicate that remodeling of the gill involves the post-transcriptional regulation of gene expression by the characterized gDE miRNAs.

Identification and Characterization of Immune-Associated MicroRNAs in Silver Carp (Hypophthalmichthys molitrix) Responding to Aeromonas veronii and LPS Stimulation

“…Changes in the immune response of the miR-30 family during environmental stress and development have been recorded. Alice et al proposed that the miRNA-30 family is an important post-transcriptional regulator of parr-smolt transformation and seawater adaptation, and their enrichment analysis of target mRNAs showed that several biological processes are associated with the immune system [47]. In this work, it was speculated that miR-30b-5p's high expression had a regulatory function in the silver carp's antibacterial response.…”

Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

“…Moreover, seven genes involved in transmembrane transporter activity ( slc4a1b , slc39a10 , slc15a4 , slc20a1a , slc25a25b , slc45a2 , and slc16a5a ) and three genes involved in calcium homeostasis ( cabp1 , camk2a , and cacna1bb ) were also described. Genome epigenetic modifications and non-coding RNAs play a significant role in the rapid adaptation to changes in the salinity of the environment in fish [ 15 , 54 , 55 , 56 , 57 ]. Table S2 represents several such genes, including piwil1 ( piwi-like1 RNA-mediated gene ).…”

Poly (I:C)-Induced microRNA-30b-5p Negatively Regulates the JAK/STAT Signaling Pathway to Mediate the Antiviral Immune Response in Silver Carp (Hypophthalmichthys molitrix) via Targeting CRFB5

“…Previous research has shown that the miR-30 family can regulate oxidative stress, apoptosis, autophagy, inflammation, and tumor progression in mammals [ 23 , 24 , 25 ]. With the development of the research, the changes in the miR-30 family’s immune response during environmental stress and the development of teleost fish have been reported [ 26 ]. Additionally, miR-30b-5p plays a broad regulatory role in Gram-negative bacterial infections in silver carp according to our earlier studies [ 27 ].…”