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Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios

Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding...

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Autores principales: Xu, Houguo, Cao, Lin, Sun, Bo, Wei, Yuliang, Liang, Mengqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454198/
https://www.ncbi.nlm.nih.gov/pubmed/31001132
http://dx.doi.org/10.3389/fphys.2019.00331
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author Xu, Houguo
Cao, Lin
Sun, Bo
Wei, Yuliang
Liang, Mengqing
author_facet Xu, Houguo
Cao, Lin
Sun, Bo
Wei, Yuliang
Liang, Mengqing
author_sort Xu, Houguo
collection PubMed
description Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding trial on a typical marine teleost tongue sole C. semilaevis followed by transcriptomic analysis, the present study investigated the possible involvement of lncRNA in hepatic mRNA expression in response to different levels of dietary DHA and EPA, which are two most important fatty acids for marine fish. An 80-day feeding trial was conducted in a flow-through seawater system, and in this trial three experimental diets differing basically in DHA/EPA ratio, i.e., 0.61 (D/E-0.61), 1.46 (D/E-1.46), and 2.75 (D/E-2.75), were randomly assigned to 9 tanks of experimental fish. A total of 124.04 G high quality genome-wide clean data about coding and non-coding transcripts was obtained in the analysis of hepatic transcriptome. Compared to diet D/E-0.61, D/E-1.46 up-regulated expression of 178 lncRNAs and 2629 mRNAs, and down-regulated that of 47 lncRNAs and 3059 mRNAs, while D/E-2.75 resulted in much less change in gene expression. The co-expression and co-localization analysis of differentially expressed (DE) lncRNA and mRNA among dietary groups were then conducted. The co-expressed DE lncRNA and mRNA were primarily enriched in GO terms such as Metabolic process, Intracellular organelle, Catalytic activity, and Oxidoreductase activity, as well as in KEGG pathways such as Ribosome and Oxidative phosphorylation. Overlap of co-expression and co-localization analysis, i.e., lncRNA–mRNA matches “XR_523541.1–solute carrier family 16, member 5 (slc16a5)” and “LNC_000285–bromodomain adjacent to zinc finger domain 2A (baz2a),” were observed in all inter-group comparisons, indicating that they might crucially mediate the effects of dietary DHA and EPA on hepatic gene expression in tongue sole. In conclusion, this was the first time in marine teleost to investigate the possible lncRNA–mRNA interactions in response to dietary fatty acids. The results provided novel knowledge of lncRNAs in non-model marine teleost, and will serve as important resources for future studies that further investigate the roles of lncRNAs in lipid metabolism of marine teleost.
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spelling pubmed-64541982019-04-18 Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios Xu, Houguo Cao, Lin Sun, Bo Wei, Yuliang Liang, Mengqing Front Physiol Physiology Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding trial on a typical marine teleost tongue sole C. semilaevis followed by transcriptomic analysis, the present study investigated the possible involvement of lncRNA in hepatic mRNA expression in response to different levels of dietary DHA and EPA, which are two most important fatty acids for marine fish. An 80-day feeding trial was conducted in a flow-through seawater system, and in this trial three experimental diets differing basically in DHA/EPA ratio, i.e., 0.61 (D/E-0.61), 1.46 (D/E-1.46), and 2.75 (D/E-2.75), were randomly assigned to 9 tanks of experimental fish. A total of 124.04 G high quality genome-wide clean data about coding and non-coding transcripts was obtained in the analysis of hepatic transcriptome. Compared to diet D/E-0.61, D/E-1.46 up-regulated expression of 178 lncRNAs and 2629 mRNAs, and down-regulated that of 47 lncRNAs and 3059 mRNAs, while D/E-2.75 resulted in much less change in gene expression. The co-expression and co-localization analysis of differentially expressed (DE) lncRNA and mRNA among dietary groups were then conducted. The co-expressed DE lncRNA and mRNA were primarily enriched in GO terms such as Metabolic process, Intracellular organelle, Catalytic activity, and Oxidoreductase activity, as well as in KEGG pathways such as Ribosome and Oxidative phosphorylation. Overlap of co-expression and co-localization analysis, i.e., lncRNA–mRNA matches “XR_523541.1–solute carrier family 16, member 5 (slc16a5)” and “LNC_000285–bromodomain adjacent to zinc finger domain 2A (baz2a),” were observed in all inter-group comparisons, indicating that they might crucially mediate the effects of dietary DHA and EPA on hepatic gene expression in tongue sole. In conclusion, this was the first time in marine teleost to investigate the possible lncRNA–mRNA interactions in response to dietary fatty acids. The results provided novel knowledge of lncRNAs in non-model marine teleost, and will serve as important resources for future studies that further investigate the roles of lncRNAs in lipid metabolism of marine teleost. Frontiers Media S.A. 2019-04-02 /pmc/articles/PMC6454198/ /pubmed/31001132 http://dx.doi.org/10.3389/fphys.2019.00331 Text en Copyright © 2019 Xu, Cao, Sun, Wei and Liang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Physiology
Xu, Houguo
Cao, Lin
Sun, Bo
Wei, Yuliang
Liang, Mengqing
Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios
title Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios
title_full Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios
title_fullStr Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios
title_full_unstemmed Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios
title_short Transcriptomic Analysis of Potential “lncRNA–mRNA” Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios
title_sort transcriptomic analysis of potential “lncrna–mrna” interactions in liver of the marine teleost cynoglossus semilaevis fed diets with different dha/epa ratios
topic Physiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454198/
https://www.ncbi.nlm.nih.gov/pubmed/31001132
http://dx.doi.org/10.3389/fphys.2019.00331
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