Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development
The precise role of lncRNAs in skeletal muscle development and atrophy remain elusive. We conducted a bioinformatic analysis of 26 GEO datasets from mouse studies, encompassing embryonic development, postnatal growth, regeneration, cell proliferation, and differentiation, using R and relevant packag...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2024.1494717/full |
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| author | Wang Wenlun Wang Wenlun Yu Chaohang Huang Yan Li Wenbin Zhou Nanqing Hu Qianmin Wu Shengcai Yuan Qing Yu Shirui Zhang Feng Zhu Lingyun |
| author_facet | Wang Wenlun Wang Wenlun Yu Chaohang Huang Yan Li Wenbin Zhou Nanqing Hu Qianmin Wu Shengcai Yuan Qing Yu Shirui Zhang Feng Zhu Lingyun |
| author_sort | Wang Wenlun |
| collection | DOAJ |
| description | The precise role of lncRNAs in skeletal muscle development and atrophy remain elusive. We conducted a bioinformatic analysis of 26 GEO datasets from mouse studies, encompassing embryonic development, postnatal growth, regeneration, cell proliferation, and differentiation, using R and relevant packages (limma et al.). LncRNA-miRNA relationships were predicted using miRcode and lncBaseV2, with miRNA-mRNA pairs identified via miRcode, miRDB, and Targetscan7. Based on the ceRNA theory, we constructed and visualized the lncRNA-miRNA-mRNA regulatory network using ggalluvial among other R packages. GO, Reactome, KEGG, and GSEA explored interactions in muscle development and regeneration. We identified five candidate lncRNAs (Xist, Gas5, Pvt1, Airn, and Meg3) as potential mediators in these processes and microgravity-induced muscle wasting. Additionally, we created a detailed lncRNA-miRNA-mRNA regulatory network, including interactions such as lncRNA Xist/miR-126/IRS1, lncRNA Xist/miR-486-5p/GAB2, lncRNA Pvt1/miR-148/RAB34, and lncRNA Gas5/miR-455-5p/SOCS3. Significant signaling pathway changes (PI3K/Akt, MAPK, NF-κB, cell cycle, AMPK, Hippo, and cAMP) were observed during muscle development, regeneration, and atrophy. Despite bioinformatics challenges, our research underscores the significant roles of lncRNAs in muscle protein synthesis, degradation, cell proliferation, differentiation, function, and metabolism under both normal and microgravity conditions. This study offers new insights into the molecular mechanisms governing skeletal muscle development and regeneration. |
| format | Article |
| id | doaj-art-61cae28e81214579a782c29692a0ad88 |
| institution | Kabale University |
| issn | 2673-7647 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj-art-61cae28e81214579a782c29692a0ad882025-01-15T06:10:30ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472025-01-01410.3389/fbinf.2024.14947171494717Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle developmentWang Wenlun0Wang Wenlun1Yu Chaohang2Huang Yan3Li Wenbin4Zhou Nanqing5Hu Qianmin6Wu Shengcai7Yuan Qing8Yu Shirui9Zhang Feng10Zhu Lingyun11Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, ChinaDepartment of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, Hunan, ChinaThe precise role of lncRNAs in skeletal muscle development and atrophy remain elusive. We conducted a bioinformatic analysis of 26 GEO datasets from mouse studies, encompassing embryonic development, postnatal growth, regeneration, cell proliferation, and differentiation, using R and relevant packages (limma et al.). LncRNA-miRNA relationships were predicted using miRcode and lncBaseV2, with miRNA-mRNA pairs identified via miRcode, miRDB, and Targetscan7. Based on the ceRNA theory, we constructed and visualized the lncRNA-miRNA-mRNA regulatory network using ggalluvial among other R packages. GO, Reactome, KEGG, and GSEA explored interactions in muscle development and regeneration. We identified five candidate lncRNAs (Xist, Gas5, Pvt1, Airn, and Meg3) as potential mediators in these processes and microgravity-induced muscle wasting. Additionally, we created a detailed lncRNA-miRNA-mRNA regulatory network, including interactions such as lncRNA Xist/miR-126/IRS1, lncRNA Xist/miR-486-5p/GAB2, lncRNA Pvt1/miR-148/RAB34, and lncRNA Gas5/miR-455-5p/SOCS3. Significant signaling pathway changes (PI3K/Akt, MAPK, NF-κB, cell cycle, AMPK, Hippo, and cAMP) were observed during muscle development, regeneration, and atrophy. Despite bioinformatics challenges, our research underscores the significant roles of lncRNAs in muscle protein synthesis, degradation, cell proliferation, differentiation, function, and metabolism under both normal and microgravity conditions. This study offers new insights into the molecular mechanisms governing skeletal muscle development and regeneration.https://www.frontiersin.org/articles/10.3389/fbinf.2024.1494717/fulllncRNAmuscle development and regenerationcell proliferation and differentiationmuscle atrophyceRNA networksignaling pathway |
| spellingShingle | Wang Wenlun Wang Wenlun Yu Chaohang Huang Yan Li Wenbin Zhou Nanqing Hu Qianmin Wu Shengcai Yuan Qing Yu Shirui Zhang Feng Zhu Lingyun Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development Frontiers in Bioinformatics lncRNA muscle development and regeneration cell proliferation and differentiation muscle atrophy ceRNA network signaling pathway |
| title | Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development |
| title_full | Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development |
| title_fullStr | Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development |
| title_full_unstemmed | Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development |
| title_short | Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development |
| title_sort | developing a cerna based lncrna mirna mrna regulatory network to uncover roles in skeletal muscle development |
| topic | lncRNA muscle development and regeneration cell proliferation and differentiation muscle atrophy ceRNA network signaling pathway |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2024.1494717/full |
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