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Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle

There is growing evidence that non-coding RNAs are emerging as critical regulators of skeletal muscle development. In order to reveal their functional roles and regulatory mechanisms, we constructed a lncRNA–miRNA–mRNA network according to the ceRNA (competitive endogenous RNA) theory, using our hig...

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Autores principales: Yue, Binglin, Li, Hui, Liu, Mei, Wu, Jiyao, Li, Mingxun, Lei, Chuzhao, Huang, Bizhi, Chen, Hong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391848/
https://www.ncbi.nlm.nih.gov/pubmed/30842787
http://dx.doi.org/10.3389/fgene.2019.00091
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author Yue, Binglin
Li, Hui
Liu, Mei
Wu, Jiyao
Li, Mingxun
Lei, Chuzhao
Huang, Bizhi
Chen, Hong
author_facet Yue, Binglin
Li, Hui
Liu, Mei
Wu, Jiyao
Li, Mingxun
Lei, Chuzhao
Huang, Bizhi
Chen, Hong
author_sort Yue, Binglin
collection PubMed
description There is growing evidence that non-coding RNAs are emerging as critical regulators of skeletal muscle development. In order to reveal their functional roles and regulatory mechanisms, we constructed a lncRNA–miRNA–mRNA network according to the ceRNA (competitive endogenous RNA) theory, using our high-throughput sequencing data. Subsequently, the network analysis, GO (Gene Ontology) analysis, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed for functional annotation and exploration of lncRNA ceRNAs. The results uncovered a scale-free characteristics network which exhibited high functional specificity for bovine skeletal muscle development: co-expression lncRNAs were significantly enriched in muscle development related biological processes and the Wnt signaling pathway. Furthermore, GSEA (Gene Set Enrichment Analysis) indicated that the risk score has a tendency to associate with myogenesis, and differentially expressed RNAs were validated by qPCR, further confirming the credibility of our network. In summary, this study provides insights into lncRNA-mediated ceRNA function and mechanisms in bovine skeletal muscle development and will expand our understanding of lncRNA biology in mammals.
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spelling pubmed-63918482019-03-06 Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle Yue, Binglin Li, Hui Liu, Mei Wu, Jiyao Li, Mingxun Lei, Chuzhao Huang, Bizhi Chen, Hong Front Genet Genetics There is growing evidence that non-coding RNAs are emerging as critical regulators of skeletal muscle development. In order to reveal their functional roles and regulatory mechanisms, we constructed a lncRNA–miRNA–mRNA network according to the ceRNA (competitive endogenous RNA) theory, using our high-throughput sequencing data. Subsequently, the network analysis, GO (Gene Ontology) analysis, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed for functional annotation and exploration of lncRNA ceRNAs. The results uncovered a scale-free characteristics network which exhibited high functional specificity for bovine skeletal muscle development: co-expression lncRNAs were significantly enriched in muscle development related biological processes and the Wnt signaling pathway. Furthermore, GSEA (Gene Set Enrichment Analysis) indicated that the risk score has a tendency to associate with myogenesis, and differentially expressed RNAs were validated by qPCR, further confirming the credibility of our network. In summary, this study provides insights into lncRNA-mediated ceRNA function and mechanisms in bovine skeletal muscle development and will expand our understanding of lncRNA biology in mammals. Frontiers Media S.A. 2019-02-20 /pmc/articles/PMC6391848/ /pubmed/30842787 http://dx.doi.org/10.3389/fgene.2019.00091 Text en Copyright © 2019 Yue, Li, Liu, Wu, Li, Lei, Huang and Chen. 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 Genetics
Yue, Binglin
Li, Hui
Liu, Mei
Wu, Jiyao
Li, Mingxun
Lei, Chuzhao
Huang, Bizhi
Chen, Hong
Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle
title Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle
title_full Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle
title_fullStr Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle
title_full_unstemmed Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle
title_short Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle
title_sort characterization of lncrna–mirna–mrna network to reveal potential functional cernas in bovine skeletal muscle
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391848/
https://www.ncbi.nlm.nih.gov/pubmed/30842787
http://dx.doi.org/10.3389/fgene.2019.00091
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