Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon
Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of g...
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ftpubmed:oai:pubmedcentral.nih.gov:7565298 2023-05-15T15:31:25+02:00 Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon Shwe, Alice Østbye, Tone-Kari Knutsdatter Krasnov, Aleksei Ramberg, Sigmund Andreassen, Rune 2020-09-08 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565298/ http://www.ncbi.nlm.nih.gov/pubmed/32911670 https://doi.org/10.3390/genes11091059 en eng MDPI http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565298/ http://www.ncbi.nlm.nih.gov/pubmed/32911670 http://dx.doi.org/10.3390/genes11091059 © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). CC-BY Genes (Basel) Article Text 2020 ftpubmed https://doi.org/10.3390/genes11091059 2020-11-01T01:30:27Z Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies. Text Atlantic salmon PubMed Central (PMC) Genes 11 9 1059 |
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Article Shwe, Alice Østbye, Tone-Kari Knutsdatter Krasnov, Aleksei Ramberg, Sigmund Andreassen, Rune Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon |
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Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies. |
format |
Text |
author |
Shwe, Alice Østbye, Tone-Kari Knutsdatter Krasnov, Aleksei Ramberg, Sigmund Andreassen, Rune |
author_facet |
Shwe, Alice Østbye, Tone-Kari Knutsdatter Krasnov, Aleksei Ramberg, Sigmund Andreassen, Rune |
author_sort |
Shwe, Alice |
title |
Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon |
title_short |
Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon |
title_full |
Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon |
title_fullStr |
Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon |
title_full_unstemmed |
Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon |
title_sort |
characterization of differentially expressed mirnas and their predicted target transcripts during smoltification and adaptation to seawater in head kidney of atlantic salmon |
publisher |
MDPI |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565298/ http://www.ncbi.nlm.nih.gov/pubmed/32911670 https://doi.org/10.3390/genes11091059 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Genes (Basel) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565298/ http://www.ncbi.nlm.nih.gov/pubmed/32911670 http://dx.doi.org/10.3390/genes11091059 |
op_rights |
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
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CC-BY |
op_doi |
https://doi.org/10.3390/genes11091059 |
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Genes |
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