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Liu S, Wu J, Zhang W, Jiang H, Zhou Y, Liu J, Mao H, Liu S, Chen B. Whole-Transcriptome RNA Sequencing Uncovers the Global Expression Changes and RNA Regulatory Networks in Duck Embryonic Myogenesis. Int J Mol Sci 2023; 24:16387. [PMID: 38003577 PMCID: PMC10671564 DOI: 10.3390/ijms242216387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Duck meat is pivotal in providing high-quality protein for human nutrition, underscoring the importance of studying duck myogenesis. The regulatory mechanisms governing duck myogenesis involve both coding and non-coding RNAs, yet their specific expression patterns and molecular mechanisms remain elusive. To address this knowledge gap, we performed expression profiling analyses of mRNAs, lncRNAs, circRNAs, and miRNAs involved in duck myogenesis using whole-transcriptome RNA-seq. Our analysis identified 1733 differentially expressed (DE)-mRNAs, 1116 DE-lncRNAs, 54 DE-circRNAs, and 174 DE-miRNAs when comparing myoblasts and myotubes. A GO analysis highlighted the enrichment of DE molecules in the extracellular region, protein binding, and exocyst. A KEGG analysis pinpointed pathways related to ferroptosis, PPAR signaling, nitrogen metabolism, cell cycle, cardiac muscle contraction, glycerolipid metabolism, and actin cytoskeleton. A total of 51 trans-acting lncRNAs, including ENSAPLT00020002101 and ENSAPLT00020012069, were predicted to participate in regulating myoblast proliferation and differentiation. Based on the ceRNAs, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks involving five miRNAs (miR-129-5p, miR-133a-5p, miR-22-3p, miR-27b-3p, and let-7b-5p) that are relevant to myogenesis. Furthermore, the GO and KEGG analyses of the DE-mRNAs within the ceRNA network underscored the significant enrichment of the glycerolipid metabolism pathway. We identified five different DE-mRNAs, specifically ENSAPLG00020001677, ENSAPLG00020002183, ENSAPLG00020005019, ENSAPLG00020010497, and ENSAPLG00020017682, as potential target genes that are crucial for myogenesis in the context of glycerolipid metabolism. These five mRNAs are integral to ceRNA networks, with miR-107_R-2 and miR-1260 emerging as key regulators. In summary, this study provides a valuable resource elucidating the intricate interplay of mRNA-lncRNA-circRNA-miRNA in duck myogenesis, shedding light on the molecular mechanisms that govern this critical biological process.
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Affiliation(s)
- Shuibing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jintao Wu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wentao Zhang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongxia Jiang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yanan Zhou
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Sanfeng Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Biao Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
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