Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs.
BACKGROUND:Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biologica...
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ftdoajarticles:oai:doaj.org/article:b86f944ee802400b81dbab1ba5554f8b 2023-05-15T15:26:54+02:00 Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. Rune Andreassen Fredrik Rangnes Maria Sivertsen Michelle Chiang Michelle Tran Merete Molton Worren 2016-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0153324 https://doaj.org/article/b86f944ee802400b81dbab1ba5554f8b EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC4851352?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0153324 https://doaj.org/article/b86f944ee802400b81dbab1ba5554f8b PLoS ONE, Vol 11, Iss 4, p e0153324 (2016) Medicine R Science Q article 2016 ftdoajarticles https://doi.org/10.1371/journal.pone.0153324 2022-12-31T12:29:55Z BACKGROUND:Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biological processes at the post-transcriptional level. Detailed knowledge about a species miRNA repertoire is necessary to study how the miRNA transcriptome modulate gene expression. We have therefore discovered and characterized mature miRNAs and their corresponding miRNA genes in Atlantic cod. We have also performed a validation study to identify suitable reference genes for RT-qPCR analysis of miRNA expression in Atlantic cod. Finally, we utilized the newly characterized miRNA repertoire and the dedicated RT-qPCR method to reveal miRNAs that are highly expressed in certain organs. RESULTS:The discovery analysis revealed 490 mature miRNAs (401 unique sequences) along with precursor sequences and genomic location of the miRNA genes. Twenty six of these were novel miRNA genes. Validation studies ranked gmo-miR-17-1-5p or the two-gene combination gmo-miR25-3p and gmo-miR210-5p as most suitable qPCR reference genes. Analysis by RT-qPCR revealed 45 miRNAs with significantly higher expression in tissues from one or a few organs. Comparisons to other vertebrates indicate that some of these miRNAs may regulate processes like growth, lipid metabolism, immune response to microbial infections and scar damage repair. Three teleost-specific and three novel Atlantic cod miRNAs were among the differentially expressed miRNAs. CONCLUSIONS:The number of known mature miRNAs was considerably increased by our identification of miRNAs and miRNA genes in Atlantic cod. This will benefit further functional studies of miRNA expression using deep sequencing methods. The validation study showed that stable miRNAs are suitable reference genes for RT-qPCR analysis of miRNA expression. Applying RT-qPCR we have identified several miRNAs likely to have ... Article in Journal/Newspaper atlantic cod Gadus morhua Directory of Open Access Journals: DOAJ Articles PLOS ONE 11 4 e0153324 |
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Medicine R Science Q |
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Medicine R Science Q Rune Andreassen Fredrik Rangnes Maria Sivertsen Michelle Chiang Michelle Tran Merete Molton Worren Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. |
topic_facet |
Medicine R Science Q |
description |
BACKGROUND:Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biological processes at the post-transcriptional level. Detailed knowledge about a species miRNA repertoire is necessary to study how the miRNA transcriptome modulate gene expression. We have therefore discovered and characterized mature miRNAs and their corresponding miRNA genes in Atlantic cod. We have also performed a validation study to identify suitable reference genes for RT-qPCR analysis of miRNA expression in Atlantic cod. Finally, we utilized the newly characterized miRNA repertoire and the dedicated RT-qPCR method to reveal miRNAs that are highly expressed in certain organs. RESULTS:The discovery analysis revealed 490 mature miRNAs (401 unique sequences) along with precursor sequences and genomic location of the miRNA genes. Twenty six of these were novel miRNA genes. Validation studies ranked gmo-miR-17-1-5p or the two-gene combination gmo-miR25-3p and gmo-miR210-5p as most suitable qPCR reference genes. Analysis by RT-qPCR revealed 45 miRNAs with significantly higher expression in tissues from one or a few organs. Comparisons to other vertebrates indicate that some of these miRNAs may regulate processes like growth, lipid metabolism, immune response to microbial infections and scar damage repair. Three teleost-specific and three novel Atlantic cod miRNAs were among the differentially expressed miRNAs. CONCLUSIONS:The number of known mature miRNAs was considerably increased by our identification of miRNAs and miRNA genes in Atlantic cod. This will benefit further functional studies of miRNA expression using deep sequencing methods. The validation study showed that stable miRNAs are suitable reference genes for RT-qPCR analysis of miRNA expression. Applying RT-qPCR we have identified several miRNAs likely to have ... |
format |
Article in Journal/Newspaper |
author |
Rune Andreassen Fredrik Rangnes Maria Sivertsen Michelle Chiang Michelle Tran Merete Molton Worren |
author_facet |
Rune Andreassen Fredrik Rangnes Maria Sivertsen Michelle Chiang Michelle Tran Merete Molton Worren |
author_sort |
Rune Andreassen |
title |
Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. |
title_short |
Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. |
title_full |
Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. |
title_fullStr |
Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. |
title_full_unstemmed |
Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. |
title_sort |
discovery of mirnas and their corresponding mirna genes in atlantic cod (gadus morhua): use of stable mirnas as reference genes reveals subgroups of mirnas that are highly expressed in particular organs. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2016 |
url |
https://doi.org/10.1371/journal.pone.0153324 https://doaj.org/article/b86f944ee802400b81dbab1ba5554f8b |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_source |
PLoS ONE, Vol 11, Iss 4, p e0153324 (2016) |
op_relation |
http://europepmc.org/articles/PMC4851352?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0153324 https://doaj.org/article/b86f944ee802400b81dbab1ba5554f8b |
op_doi |
https://doi.org/10.1371/journal.pone.0153324 |
container_title |
PLOS ONE |
container_volume |
11 |
container_issue |
4 |
container_start_page |
e0153324 |
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1766357380298178560 |