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Wang H, Liu M, Tang H, Zhang Z, Wen H, He F. Identification and functional analysis of circpdlim5a generated from pdlim5a gene splicing in the skeletal muscle of Japanese flounder (Paralichthys olivaceus). Gen Comp Endocrinol 2024; 352:114500. [PMID: 38508470 DOI: 10.1016/j.ygcen.2024.114500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Circular RNAs (circRNAs) are non-coding RNAs with endogenous regulatory functions, including regulating skeletal muscle development. However, its role in the development of skeletal muscle in Japanese flounder (Paralichthys olivaceus) is not clear. Therefore we screened a candidate circpdlim5a, which is derived from the gene pdlim5a, from the skeletal muscle transcriptome of Japanese flounder. We characterized circpdlim5a, which was more stable compared to the linear RNA pdlim5a. Distributional characterization of circpdlim5a showed that circpdlim5a was predominantly distributed in the nucleus and was highly expressed in the skeletal muscle of adult Japanese flounder (24 months). When we further studied the circpdlim5a function, we found that it inhibited the expression of proliferation and differentiation genes according to the over-expression experiment of circpdlim5a in myoblasts. We concluded that circpdlim5a may inhibit the proliferation and differentiation of myoblasts and thereby inhibit skeletal muscle development in Japanese flounder. This experiment provides information for the study of circRNAs by identifying circpdlim5a and exploring its function, and offers clues for molecular breeding from an epigenetic perspective.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Min Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Hengtai Tang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Zhirui Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Feng He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China.
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Zhang W, Liu J, Zhou Y, Liu S, Wu J, Jiang H, Xu J, Mao H, Liu S, Chen B. Signaling pathways and regulatory networks in quail skeletal muscle development: insights from whole transcriptome sequencing. Poult Sci 2024; 103:103603. [PMID: 38457990 PMCID: PMC11067775 DOI: 10.1016/j.psj.2024.103603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
Quail, as an advantageous avian model organism due to its compact size and short reproductive cycle, holds substantial potential for enhancing our understanding of skeletal muscle development. The quantity of skeletal muscle represents a vital economic trait in poultry production. Unraveling the molecular mechanisms governing quail skeletal muscle development is of paramount importance for optimizing meat and egg yield through selective breeding programs. However, a comprehensive characterization of the regulatory dynamics and molecular control underpinning quail skeletal muscle development remains elusive. In this study, through the application of HE staining on quail leg muscle sections, coupled with preceding fluorescence quantification PCR of markers indicative of skeletal muscle differentiation, we have delineated embryonic day 9 (E9) and embryonic day 14 (E14) as the start and ending points, respectively, of quail skeletal muscle differentiation. Then, we employed whole transcriptome sequencing to investigate the temporal expression profiles of leg muscles in quail embryos at the initiation of differentiation (E9) and upon completion of differentiation (E14). Our analysis revealed the expression patterns of 12,012 genes, 625 lncRNAs, 14,457 circRNAs, and 969 miRNAs in quail skeletal muscle samples. Differential expression analysis between the E14 and E9 groups uncovered 3,479 differentially expressed mRNAs, 124 lncRNAs, 292 circRNAs, and 154 miRNAs. Furthermore, enrichment analysis highlighted the heightened activity of signaling pathways related to skeletal muscle metabolism and intermuscular fat formation, such as the ECM-receptor interaction, focal adhesion, and PPAR signaling pathway during E14 skeletal muscle development. Conversely, the E9 stage exhibited a prevalence of pathways associated with myoblast proliferation, exemplified by cell cycle processes. Additionally, we constructed regulatory networks encompassing lncRNA‒mRNA, miRNA‒mRNA, lncRNA‒miRNA-mRNA, and circRNA-miRNA‒mRNA interactions, thus shedding light on their putative roles within quail skeletal muscle. Collectively, our findings illuminate the gene and non-coding RNA expression characteristics during quail skeletal muscle development, serving as a foundation for future investigations into the regulatory mechanisms governing non-coding RNA and quail skeletal muscle development in poultry production.
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Affiliation(s)
- Wentao Zhang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Jing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China
| | - Ya'nan Zhou
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Shuibing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Jintao Wu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Hongxia Jiang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Jiguo Xu
- Biotech Research Institute of Nanchang Normal University, Nanchang 330032, Jiangxi, P. R. China
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Sanfeng Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China
| | - Biao Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China; Poultry Institute, Jiangxi Agricultural University, Nanchang 330045, P. R. China.
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Pai B. Regulating the regulators: understanding miRNA biogenesis and decay in adult skeletal muscles. FEBS J 2023; 290:5689-5691. [PMID: 37876331 DOI: 10.1111/febs.16975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]
Abstract
Maintaining cellular homeostasis necessitates precise control of gene expression, a process that molds both the transcriptome and proteome to adapt to internal and external changes effectively. MicroRNAs (miRNAs) are small RNAs (~ 22nucleotides) belonging to a broad family of non-coding RNAs and are important regulators of gene expression. While numerous studies have advanced our understanding of the common processes underlying miRNA biogenesis and function, individual cell types in diverse organisms have evolved distinct mechanisms for regulating them. In this current issue, Satoshi Oikawa and colleagues delve into the molecular dynamics of miRNAs in adult skeletal muscles. Their research introduces intriguing new inquiries for further investigations to uncover alternative mechanisms of miRNA biogenesis in skeletal muscle.
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Affiliation(s)
- Balagopal Pai
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Koopmans PJ, Ismaeel A, Goljanek-Whysall K, Murach KA. The roles of miRNAs in adult skeletal muscle satellite cells. Free Radic Biol Med 2023; 209:228-238. [PMID: 37879420 PMCID: PMC10911817 DOI: 10.1016/j.freeradbiomed.2023.10.403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Satellite cells are bona fide muscle stem cells that are indispensable for successful post-natal muscle growth and regeneration after severe injury. These cells also participate in adult muscle adaptation in several capacities. MicroRNAs (miRNAs) are post-transcriptional regulators of mRNA that are implicated in several aspects of stem cell function. There is evidence to suggest that miRNAs affect satellite cell behavior in vivo during development and myogenic progenitor behavior in vitro, but the role of miRNAs in adult skeletal muscle satellite cells is less studied. In this review, we provide evidence for how miRNAs control satellite cell function with emphasis on satellite cells of adult skeletal muscle in vivo. We first outline how miRNAs are indispensable for satellite cell viability and control the phases of myogenesis. Next, we discuss the interplay between miRNAs and myogenic cell redox status, senescence, and communication to other muscle-resident cells during muscle adaptation. Results from recent satellite cell miRNA profiling studies are also summarized. In vitro experiments in primary myogenic cells and cell lines have been invaluable for exploring the influence of miRNAs, but we identify a need for novel genetic tools to further interrogate how miRNAs control satellite cell behavior in adult skeletal muscle in vivo.
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Affiliation(s)
- Pieter Jan Koopmans
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Ahmed Ismaeel
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, 40506, USA
| | - Katarzyna Goljanek-Whysall
- School of Medicine, College of Medicine, Nursing, and Health Sciences, University of Galway, Galway, Ireland
| | - Kevin A Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, 72701, USA; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA.
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