Trend analysis of the role of circular RNA in goat skeletal muscle development
Abstract Background Circular RNA (circRNA) is produced during the splicing of mRNA (in addition to linear splicing) and is part of the gene regulatory network. The temporal expression patterns the different developmental stages were inseparable from these molecules’ function. Results Skeletal muscle...
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| Format: | Article |
| Language: | English |
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BMC
2020-03-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-6649-2 |
| _version_ | 1819014045696524288 |
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| author | Yinghui Ling Qi Zheng Lu Zhu Lina Xu Menghua Sui Yunhai Zhang Ya Liu Fugui Fang Mingxing Chu Yuehui Ma Xiaorong Zhang |
| author_facet | Yinghui Ling Qi Zheng Lu Zhu Lina Xu Menghua Sui Yunhai Zhang Ya Liu Fugui Fang Mingxing Chu Yuehui Ma Xiaorong Zhang |
| author_sort | Yinghui Ling |
| collection | DOAJ |
| description | Abstract Background Circular RNA (circRNA) is produced during the splicing of mRNA (in addition to linear splicing) and is part of the gene regulatory network. The temporal expression patterns the different developmental stages were inseparable from these molecules’ function. Results Skeletal muscles of Anhui white goat (AWG) across seven fetal to postnatal development stages were sequenced and 21 RNA sequencing libraries were constructed. We thereby identified 9090 circRNAs and analyzed their molecular properties, temporal expression patterns, and potential functions at the different stages. CircRNAs showed complexities and diversity of formation as the same host gene produces multiple isoforms of these nucleic acids with different expression profiles. The differential expression of 2881 circRNAs (DECs, P < 0.05) was identified and four were randomly selected and validated by qPCR. Moreover, 1118 DECs under strict selected (SDECs, |log2FC| > 2 and P-adj value < 0.01) showed 4 expression trends (Clusters 0, 19, 16 and 18). Cluster 0 molecules had increasing expression at all stages with effects on muscle through metabolism, regulation of enzyme activity, and biosynthesis. Cluster 16 circRNAs had high expression in the early and late stages and are involved in “Wnt signaling pathway”, “AMPK signaling pathway” and others. Cluster 18 molecules were mainly expressed at F120 and participate in “cytoskeletal protein binding”, “Notch signaling pathway” and so on. Cluster 19 circRNAs were down-regulated at all stages and related to muscle structure and development. Lastly, the SDECs divided the period of skeletal muscle development into three transitional stages: stage 1 (F45 to F90), which related to muscle satellite cell proliferation and muscle fiber structure; stage 2 (F90 to B1), in which the attachment of the cytoplasmic surface to the actin cytoskeleton initiates; and stage 3, which involved the “cGMP-PKG signaling pathway”. Moreover, the paraffin sections messages also validated that there are three transitional stages of skeletal muscle development. Conclusion Our current study provides a catalog of goat muscle-related circRNAs that can stratify skeletal muscle development fetus 45 days to newborn 90 days into three developmental stages. These findings better our understanding of functional transitions during mammalian muscle development. |
| first_indexed | 2024-12-21T02:09:36Z |
| format | Article |
| id | doaj.art-6da5b2cf1928495e989fc3307304076a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T02:09:36Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6da5b2cf1928495e989fc3307304076a2022-12-21T19:19:24ZengBMCBMC Genomics1471-21642020-03-0121111210.1186/s12864-020-6649-2Trend analysis of the role of circular RNA in goat skeletal muscle developmentYinghui Ling0Qi Zheng1Lu Zhu2Lina Xu3Menghua Sui4Yunhai Zhang5Ya Liu6Fugui Fang7Mingxing Chu8Yuehui Ma9Xiaorong Zhang10College of Animal Science and Technology, Anhui Agricultural UniversityCollege of Animal Science and Technology, Anhui Agricultural UniversityCollege of Animal Science and Technology, Anhui Agricultural UniversitySchool of Natural and Environmental Sciences, Newcastle UniversityCollege of Animal Science and Technology, Anhui Agricultural UniversityCollege of Animal Science and Technology, Anhui Agricultural UniversityCollege of Animal Science and Technology, Anhui Agricultural UniversityCollege of Animal Science and Technology, Anhui Agricultural UniversityKey Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese academy of agricultural sciencesKey Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese academy of agricultural sciencesCollege of Animal Science and Technology, Anhui Agricultural UniversityAbstract Background Circular RNA (circRNA) is produced during the splicing of mRNA (in addition to linear splicing) and is part of the gene regulatory network. The temporal expression patterns the different developmental stages were inseparable from these molecules’ function. Results Skeletal muscles of Anhui white goat (AWG) across seven fetal to postnatal development stages were sequenced and 21 RNA sequencing libraries were constructed. We thereby identified 9090 circRNAs and analyzed their molecular properties, temporal expression patterns, and potential functions at the different stages. CircRNAs showed complexities and diversity of formation as the same host gene produces multiple isoforms of these nucleic acids with different expression profiles. The differential expression of 2881 circRNAs (DECs, P < 0.05) was identified and four were randomly selected and validated by qPCR. Moreover, 1118 DECs under strict selected (SDECs, |log2FC| > 2 and P-adj value < 0.01) showed 4 expression trends (Clusters 0, 19, 16 and 18). Cluster 0 molecules had increasing expression at all stages with effects on muscle through metabolism, regulation of enzyme activity, and biosynthesis. Cluster 16 circRNAs had high expression in the early and late stages and are involved in “Wnt signaling pathway”, “AMPK signaling pathway” and others. Cluster 18 molecules were mainly expressed at F120 and participate in “cytoskeletal protein binding”, “Notch signaling pathway” and so on. Cluster 19 circRNAs were down-regulated at all stages and related to muscle structure and development. Lastly, the SDECs divided the period of skeletal muscle development into three transitional stages: stage 1 (F45 to F90), which related to muscle satellite cell proliferation and muscle fiber structure; stage 2 (F90 to B1), in which the attachment of the cytoplasmic surface to the actin cytoskeleton initiates; and stage 3, which involved the “cGMP-PKG signaling pathway”. Moreover, the paraffin sections messages also validated that there are three transitional stages of skeletal muscle development. Conclusion Our current study provides a catalog of goat muscle-related circRNAs that can stratify skeletal muscle development fetus 45 days to newborn 90 days into three developmental stages. These findings better our understanding of functional transitions during mammalian muscle development.http://link.springer.com/article/10.1186/s12864-020-6649-2circRNASkeletal muscleDevelopmentRNA-seq |
| spellingShingle | Yinghui Ling Qi Zheng Lu Zhu Lina Xu Menghua Sui Yunhai Zhang Ya Liu Fugui Fang Mingxing Chu Yuehui Ma Xiaorong Zhang Trend analysis of the role of circular RNA in goat skeletal muscle development BMC Genomics circRNA Skeletal muscle Development RNA-seq |
| title | Trend analysis of the role of circular RNA in goat skeletal muscle development |
| title_full | Trend analysis of the role of circular RNA in goat skeletal muscle development |
| title_fullStr | Trend analysis of the role of circular RNA in goat skeletal muscle development |
| title_full_unstemmed | Trend analysis of the role of circular RNA in goat skeletal muscle development |
| title_short | Trend analysis of the role of circular RNA in goat skeletal muscle development |
| title_sort | trend analysis of the role of circular rna in goat skeletal muscle development |
| topic | circRNA Skeletal muscle Development RNA-seq |
| url | http://link.springer.com/article/10.1186/s12864-020-6649-2 |
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