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
:1. Introduction
2. Results
2.1. Total RNA Extraction, Library Preparation and Small RNA Sequencing
2.2. miRNAs Differentially Expressed in Atlantic Salmon Gill during Smoltification and SW Adaptation
2.3. Identification of DE mRNAs Associated with Smoltification and SW Adaptation
2.4. Prediction of Target Genes of the gDE miRNAs
2.5. Enriched Biological Processes and Pathways Associated with Predicted Target Genes
3. Discussion
3.1. In Silico Analysis Revealed That Smoltification Biomarkers and Smoltification Key Genes Were among Predicted Targets of the gDE miRNAs
3.2. gDE miRNA Target Gene Enrichment Analysis
4. Materials and Methods
4.1. Animal Welfare Statement
4.2. Fish Holding and Sample Collection
4.3. Total RNA Extraction
4.4. High-Throughput Sequencing of Mature miRNAs
4.5. Processing of HTS Data and miRNA Expression Analysis
4.6. Microarray Analysis of mRNA Expression
4.7. DE-miRNA Target Prediction and Enrichment of Predicted Target Genes
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Mature miRNAs | T2 1 | T3 2 | T4 3 | T5 4 | T6 5 |
---|---|---|---|---|---|
ssa-let-7b-3p | −1.2 * | −0.1 | 0.2 | −1.0 * | −0.6 |
ssa-miR-30a-1-2-5p | −0.4 | −0.6 | −0.6 | −1.0 * | −0.9 |
ssa-miR-30a-3-4-5p | −0.4 | −0.6 | −0.6 | −1.0 * | −0.9 |
ssa-miR-30e-5p | −1.2 | −1.2 | −1.4 * | −1.9 * | −1.3 |
ssa-miR-124abcd-3p | 1.1 * | 0.4 | −0.1 | −1.2 * | −1.5 * |
ssa-miR-146a-5p | −0.5 | −0.7 | −0.9 | −1.1 * | −0.4 |
ssa-miR-146b-3p | −0.6 | − 1.4 * | −2.0 * | −2.4 * | −0.7 |
ssa-miR-146b-5p | −0.1 | − 1.1 * | −1.6 * | −1.7 * | −0.4 |
ssa-miR-190b-5p | −1.2 * | − 1.4 * | −1.1 * | −1.7 * | −1.5 * |
ssa-miR-194b-5p | −1.1 * | −1.6 * | −1.3 * | −1.1 * | −0.7 |
ssa-miR-1778-3p | −1.0 * | −1.6 * | −1.0 * | −0.7 | −0.4 |
ssa-miR-7132b-5p | 0.0 | −0.6 | −1.0 * | −0.9 | −0.7 |
ssa-miR-7132a-5p | 0.0 | −0.6 | −1.0 * | −0.9 | −0.7 |
Mature miRNAs | T2 1 | T3 2 | T4 3 | T5 4 | T6 5 |
---|---|---|---|---|---|
ssa-miR-101a-3p | 1.1 * | 0.6 | 0.7 | 0.7 | 0.4 |
ssa-miR-193b-5p | 0.2 | 0.5 | 0.7 | 1.1 * | 1.4 * |
ssa-miR-499a-5p | 0.7 | 0.7 | 1.0 * | 0.6 | 0.8 |
ssa-miR-727a-3p | 0.6 | 0.9 | 0.8 | 1.2 * | 0.9 |
ssa-miR-8159-5p | 0.4 | 0.7 | 0.6 | 0.8 | 1.0 * |
Gene | FL Isoforms /Paralog Transcript Accession | gDE miRNAs |
---|---|---|
nkaα1a | GIYK01009408; GIYK01019309; GIYK01009409 | ssa-miR-8159-5p |
GIYK01019303 | ssa-miR-499a-5p | |
nkaβ | GIYK01043074; GIYK01043155; GIYK01043071; GIYK01043154; GIYK01043075; GIYK01043153; GIYK01043151; GIYK01043150 | ssa-miR-146b-5p ssa-miR-146a-5p ssa-miR-1778-3p |
cyp1a1 | GIYK01057368; GIYK01027094; GIYK01057370; GIYK01027092; GIYK01027093; GIYK01057371; GIYK01057369 | ssa-miR-1778-3p |
Pathway Category | Reactome Pathways | FE 1 | FDR 2 |
---|---|---|---|
Extracellular matrix org. | Integrin cell surface interactions | 4.3 | 5.0E-03 |
Cytokine signaling | Interferon Signaling | 2.9 | 1.0E-02 |
Cytokine Signaling in Immune system | 2.3 | 2.0E-05 | |
Signaling by Interleukins | 2.4 | 4.5E-04 | |
Innate immune system | Neutrophil degranulation | 2.2 | 4.6E-03 |
Innate Immune System | 1.9 | 9.8E-05 | |
Adaptive immune system | Adaptive Immune System | 1.7 | 3.4E-02 |
Hemostasis | Cell surface interactions at the vascular wall | 2.7 | 2.4E-02 |
Platelet activation, signaling and aggregation | 2.7 | 4.1E-03 | |
Metabolism | Metabolism of vitamins and cofactors | 2.7 | 3.2E-02 |
Metabolism of lipids | 2.2 | 3.9E-05 | |
Signal transduction | Signaling by Receptor Tyrosine Kinases | 2.4 | 1.1E-04 |
Disease | Diseases of signal transduction by growth factor receptors and second messengers | 2.2 | 1.6E-02 |
gDE miRNAs in Gill | DE miRNAs in Liver 1 | DE miRNAs in Head Kidney 2 |
---|---|---|
ssa-let-7b-3p | Yes | Yes |
ssa-miR-146a-5p | Yes | Yes |
ssa-miR-146b-5p | Yes | Yes |
ssa-miR-30a-1-2-5p | Yes | No |
ssa-miR-30a-3-4-5p | Yes | No |
ssa-miR-30e-5p | Yes | No |
ssa-miR-101a-3p | Yes | No |
ssa-miR-194b-5p | No | Yes |
ssa-miR-124abcd-3p | No | No |
ssa-miR-146b-3p | No | No |
ssa-miR-190b-5p | No | No |
ssa-miR-193b-5p | No | No |
ssa-miR-499a-5p | No | No |
ssa-miR-727a-3p | No | No |
ssa-miR-1778-3p | No | No |
ssa-miR-7132a-5p | No | No |
ssa-miR-7132b-5p | No | No |
ssa-miR-8159-5p | No | No |
Experimental Days | Hours of Light per Day (h) | Water Temperature (°C) | Water Type |
---|---|---|---|
Day 0 | 24 | 8 | Fresh water |
Day 1–5 | 12 | 13 | Fresh water |
Day 6–47 | 12 | 12 | Fresh water |
Day 48–60 | 24 | 12 | Fresh water |
Day 61–81 | 24 | 8 | Fresh water |
Day 82–111 | 24 | 8 | seawater |
Group | Sample Collection Time Points | L 1 | T 2 | Weight 3 | Water Type | Samp 4 |
---|---|---|---|---|---|---|
T1 | Parr, one day prior to light treatment | 24 | 8 | 29.4 ± 5.6 | Fresh water | Day 0 |
T2 | Halfway into light treatment | 12 | 12 | 52.6 ± 5.9 | Fresh water | Day 47 |
T3 | Three quarters into light treatment | 24 | 8 | 63.9 ± 10.1 | Fresh water | Day 67 |
T4 | Smolt, one day prior to SWT | 24 | 8 | 72.4 ± 8.7 | Fresh water | Day 81 |
T5 | One week after SWT | 24 | 8 | 63.2 ± 8.5 | seawater | Day 88 |
T6 | One month after SWT | 24 | 8 | 98.4 ± 14.9 | seawater | Day 111 |
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Shwe, A.; Krasnov, A.; Visnovska, T.; Ramberg, S.; Østbye, T.-K.K.; Andreassen, R. 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. Int. J. Mol. Sci. 2022, 23, 8831. https://doi.org/10.3390/ijms23158831
Shwe A, Krasnov A, Visnovska T, Ramberg S, Østbye T-KK, Andreassen R. 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. International Journal of Molecular Sciences. 2022; 23(15):8831. https://doi.org/10.3390/ijms23158831
Chicago/Turabian StyleShwe, Alice, Aleksei Krasnov, Tina Visnovska, Sigmund Ramberg, Tone-Kari K. Østbye, and Rune Andreassen. 2022. "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" International Journal of Molecular Sciences 23, no. 15: 8831. https://doi.org/10.3390/ijms23158831