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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MDPI AG
2021-11-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/11/1787 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T05:28:48Z |
| format | Article |
| id | doaj.art-b0a78df7bb5243c588627fd44a27dadc |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T05:28:48Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-b0a78df7bb5243c588627fd44a27dadc2023-11-22T23:28:47ZengMDPI AGGenes2073-44252021-11-011211178710.3390/genes12111787Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle DevelopmentTao Zhang0Can Chen1Shushu Han2Lan Chen3Hao Ding4Yueyue Lin5Genxi Zhang6Kaizhou Xie7Jinyu Wang8Guojun Dai9College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaShandong Chengwu County Animal Husbandry Service Center, Department of Agriculture and Rural Affairs of Heze City, Heze 274200, ChinaJoint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaJoint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCollege of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaGrowing 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.https://www.mdpi.com/2073-4425/12/11/1787pigeonskeletal muscle developmentlncRNAceRNA networkmiRNA |
| spellingShingle | 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 Genes pigeon skeletal muscle development lncRNA ceRNA network miRNA |
| title | 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_short | 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 |
| topic | pigeon skeletal muscle development lncRNA ceRNA network miRNA |
| url | https://www.mdpi.com/2073-4425/12/11/1787 |
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