Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development

Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory...

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Autores principales:	Tao Zhang, Can Chen, Shushu Han, Lan Chen, Hao Ding, Yueyue Lin, Genxi Zhang, Kaizhou Xie, Jinyu Wang, Guojun Dai
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	pigeon skeletal muscle development lncRNA ceRNA network miRNA Genetics QH426-470
Acceso en línea:	https://doaj.org/article/b0a78df7bb5243c588627fd44a27dadc
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spelling	oai:doaj.org-article:b0a78df7bb5243c588627fd44a27dadc2021-11-25T17:41:58ZIntegrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development10.3390/genes121117872073-4425https://doaj.org/article/b0a78df7bb5243c588627fd44a27dadc2021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1787https://doaj.org/toc/2073-4425Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory mechanisms of lncRNA, we first analyzed the expression profiles of lncRNA, microRNA (miRNA), and mRNA during the development of pigeon skeletal muscle using high-throughput sequencing. We then constructed a lncRNA–miRNA–mRNA ceRNA network based on differentially expressed (DE) lncRNAs, miRNAs, and mRNAs according to the ceRNA hypothesis. Functional enrichment and short time-series expression miner (STEM) analysis were performed to explore the function of the ceRNA network. Hub lncRNA–miRNA–mRNA interactions were identified by connectivity degree and validated using dual-luciferase activity assay. The results showed that a total of 1625 DE lncRNAs, 11,311 DE mRNAs, and 573 DE miRNAs were identified. A ceRNA network containing 9120 lncRNA–miRNA–mRNA interactions was constructed. STEM analysis indicated that the function of the lncRNA-associated ceRNA network might be developmental specific. Functional enrichment analysis identified potential pathways regulating pigeon skeletal muscle development, such as cell cycle and MAPK signaling. Based on the connectivity degree, lncRNAs <i>TCONS_00066712</i>, <i>TCONS_00026594</i>, <i>TCONS_00001557</i>, <i>TCONS_00001553</i>, and <i>TCONS_00003307</i> were identified as hub genes in the ceRNA network. lncRNA <i>TCONS_00026594</i> might regulate the FSHD region gene 1 (<i>FRG1</i>)/ SRC proto-oncogene, non-receptor tyrosine kinase (<i>SRC</i>) by sponge adsorption of cli-miR-1a-3p to affect the development of pigeon skeletal muscle. Our findings provide a data basis for in-depth elucidation of the lncRNA-associated ceRNA mechanism underlying pigeon skeletal muscle development.Tao ZhangCan ChenShushu HanLan ChenHao DingYueyue LinGenxi ZhangKaizhou XieJinyu WangGuojun DaiMDPI AGarticlepigeonskeletal muscle developmentlncRNAceRNA networkmiRNAGeneticsQH426-470ENGenes, Vol 12, Iss 1787, p 1787 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	pigeon skeletal muscle development lncRNA ceRNA network miRNA Genetics QH426-470
spellingShingle	pigeon skeletal muscle development lncRNA ceRNA network miRNA Genetics QH426-470 Tao Zhang Can Chen Shushu Han Lan Chen Hao Ding Yueyue Lin Genxi Zhang Kaizhou Xie Jinyu Wang Guojun Dai Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development
description	Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory mechanisms of lncRNA, we first analyzed the expression profiles of lncRNA, microRNA (miRNA), and mRNA during the development of pigeon skeletal muscle using high-throughput sequencing. We then constructed a lncRNA–miRNA–mRNA ceRNA network based on differentially expressed (DE) lncRNAs, miRNAs, and mRNAs according to the ceRNA hypothesis. Functional enrichment and short time-series expression miner (STEM) analysis were performed to explore the function of the ceRNA network. Hub lncRNA–miRNA–mRNA interactions were identified by connectivity degree and validated using dual-luciferase activity assay. The results showed that a total of 1625 DE lncRNAs, 11,311 DE mRNAs, and 573 DE miRNAs were identified. A ceRNA network containing 9120 lncRNA–miRNA–mRNA interactions was constructed. STEM analysis indicated that the function of the lncRNA-associated ceRNA network might be developmental specific. Functional enrichment analysis identified potential pathways regulating pigeon skeletal muscle development, such as cell cycle and MAPK signaling. Based on the connectivity degree, lncRNAs <i>TCONS_00066712</i>, <i>TCONS_00026594</i>, <i>TCONS_00001557</i>, <i>TCONS_00001553</i>, and <i>TCONS_00003307</i> were identified as hub genes in the ceRNA network. lncRNA <i>TCONS_00026594</i> might regulate the FSHD region gene 1 (<i>FRG1</i>)/ SRC proto-oncogene, non-receptor tyrosine kinase (<i>SRC</i>) by sponge adsorption of cli-miR-1a-3p to affect the development of pigeon skeletal muscle. Our findings provide a data basis for in-depth elucidation of the lncRNA-associated ceRNA mechanism underlying pigeon skeletal muscle development.
format	article
author	Tao Zhang Can Chen Shushu Han Lan Chen Hao Ding Yueyue Lin Genxi Zhang Kaizhou Xie Jinyu Wang Guojun Dai
author_facet	Tao Zhang Can Chen Shushu Han Lan Chen Hao Ding Yueyue Lin Genxi Zhang Kaizhou Xie Jinyu Wang Guojun Dai
author_sort	Tao Zhang
title	Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development
title_short	Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development
title_full	Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development
title_fullStr	Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development
title_full_unstemmed	Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development
title_sort	integrated analysis reveals a lncrna–mirna–mrna network associated with pigeon skeletal muscle development
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/b0a78df7bb5243c588627fd44a27dadc
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Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development

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