1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Luo W, Zhang H, Wan R, Cai Y, Liu Y, Wu Y, Yang Y, Chen J, Zhang D, Luo Z, Shang X. Biomaterials-Based Technologies in Skeletal Muscle Tissue Engineering. Adv Healthc Mater 2024:e2304196. [PMID: 38712598 DOI: 10.1002/adhm.202304196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/26/2024] [Indexed: 05/08/2024]
Abstract
For many clinically prevalent severe injuries, the inherent regenerative capacity of skeletal muscle remains inadequate. Skeletal muscle tissue engineering (SMTE) seeks to meet this clinical demand. With continuous progress in biomedicine and related technologies including micro/nanotechnology and 3D printing, numerous studies have uncovered various intrinsic mechanisms regulating skeletal muscle regeneration and developed tailored biomaterial systems based on these understandings. Here, the skeletal muscle structure and regeneration process are discussed and the diverse biomaterial systems derived from various technologies are explored in detail. Biomaterials serve not merely as local niches for cell growth, but also as scaffolds endowed with structural or physicochemical properties that provide tissue regenerative cues such as topographical, electrical, and mechanical signals. They can also act as delivery systems for stem cells and bioactive molecules that have been shown as key participants in endogenous repair cascades. To achieve bench-to-bedside translation, the typical effect enabled by biomaterial systems and the potential underlying molecular mechanisms are also summarized. Insights into the roles of biomaterials in SMTE from cellular and molecular perspectives are provided. Finally, perspectives on the advancement of SMTE are provided, for which gene therapy, exosomes, and hybrid biomaterials may hold promise to make important contributions.
Collapse
Affiliation(s)
- Wei Luo
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Hanli Zhang
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Renwen Wan
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Yuxi Cai
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Yinuo Liu
- The Second Clinical Medical College of Nanchang University, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Yang Wu
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Yimeng Yang
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Jiani Chen
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, Hong Kong
| | - Zhiwen Luo
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Xiliang Shang
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| |
Collapse
|
3
|
Biferali B, Mocciaro E, Runfola V, Gabellini D. Long non-coding RNAs and their role in muscle regeneration. Curr Top Dev Biol 2024; 158:433-465. [PMID: 38670715 DOI: 10.1016/bs.ctdb.2024.02.010] [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] [Indexed: 04/28/2024]
Abstract
In mammals, most of the genome is transcribed to generate a large and heterogeneous variety of non-protein coding RNAs, that are broadly grouped according to their size. Long noncoding RNAs include a very large and versatile group of molecules. Despite only a minority of them has been functionally characterized, there is emerging evidence indicating long noncoding RNAs as important regulators of expression at multiple levels. Several of them have been shown to be modulated during myogenic differentiation, playing important roles in the regulation of skeletal muscle development, differentiation and homeostasis, and contributing to neuromuscular diseases. In this chapter, we have summarized the current knowledge about long noncoding RNAs in skeletal muscle and discussed specific examples of long noncoding RNAs (lncRNAs and circRNAs) regulating muscle stem cell biology. We have also discussed selected long noncoding RNAs involved in the most common neuromuscular diseases.
Collapse
Affiliation(s)
- Beatrice Biferali
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Mocciaro
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Runfola
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Gabellini
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
4
|
Sun H, Yuan X, Zhang N, Luo Z, Zhang L, Li X. Screening of hair follicle telogen-associated circRNAs in sheep and construction of their ceRNA network. Genomics 2024; 116:110818. [PMID: 38431032 DOI: 10.1016/j.ygeno.2024.110818] [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: 09/21/2023] [Revised: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Sheep breeds with hair-shedding traits have many advantages over non-shedding sheep breeds, not only because of reduced shearing labor and feeding management costs but also because it reduces in vitro parasites and improves adaptability to summer heat stress. The wool of Dorper sheep naturally sheds in spring due to the periodic growth of hair follicles. CircRNAs primarily regulate the morphogenesis of hair follicles through the ceRNA mechanism. In this study, five 2-year-old Dorper ewes with extreme hair-shedding phenotype (S) and three Dorper ewes with non-shedding (N) phenotype were selected for subsequent analyses. For RNA extraction, skin tissues were collected on 27th September 2019 (S1, N1), 3rd January 2020 (S2, N2), and 17th March 2020 (S3, N3), which were then subjected to RNA-seq. RNA-seq technology revealed 20,185 novel circRNAs in the hair follicles of Dorper sheep. Among them, 1450 circRNAs were differentially expressed (DE). Clustering heatmap and expression pattern analyses were performed on DE circRNAs, which indicated 78 circRNAs with T pattern (Telogen, highly expressed in telogen), and the source genes for candidate circRNAs were further screened by functional enrichment analysis, which identified 13 crucial genes enriched in pathways associated with hair follicle development. Additionally, a ceRNA regulatory network comprising 4 circRNAs, 11 miRNAs, and 13 target genes was constructed. Overall, this study screened circRNAs that may be associated with the telogen phase of hair follicles in sheep, providing a relevant theoretical basis for wool shedding in sheep and for breeding Dorper sheep with automatic wool shedding.
Collapse
Affiliation(s)
- Haoran Sun
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Xiaochun Yuan
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Ningyue Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Zhongze Luo
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Liang Zhang
- Ningxia China Animal Husbandry Yilin Livestock Co., Ltd., Yinchuan 750021, Ningxia, China
| | - Xinhai Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China.
| |
Collapse
|
5
|
Ma X, Guo X, Yongfu L, Wang T, Bao P, Chu M, Wu X, Yan P, Liang C. Identification of circRNA-associated ceRNA networks in the longissimus dorsi of yak under different feeding systems. BMC Vet Res 2024; 20:67. [PMID: 38395831 PMCID: PMC10893644 DOI: 10.1186/s12917-024-03926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Yaks (Bos grunniens), prized for their ability to thrive in high-altitude environments, are indispensable livestock in the plateau region. Modifying their feeding systems holds significant promise for improving their growth and meat quality. Tenderness, a key determinant of yak meat quality and consumer appeal, is demonstrably influenced by dietary regimen. Indoor feeding regimes have been shown to enhance tenderness by lowering shear stress and optimizing pH values. CircRNAs, well-known modulators of circulatory function, also play a crucial role in skeletal muscle development across various animal species. However, their functional significance in yak skeletal muscle remains largely unexplored. RESULTS In this study, we identified a total of 5,534 circRNAs within the longissimus dorsi muscle, and we found 51 differentially expressed circRNAs (20 up-regulated and 31 down-regulated) between the two feeding groups. Constructing a comprehensive ceRNA network illuminated intricate regulatory mechanisms, with PGP and circRNA_0617 converging on bta-miR-2285q, mirrored by KLF15/circRNA_0345/bta-miR-20b and CTSF/circRNA_0348/bta-miR-146a. These findings shed light on the potential of circRNAs to influence yak muscle development and meat quality, offering valuable insights for future research. CONCLUSIONS This investigation unraveled a complex interaction network between circRNAs、mRNAs and miRNAs in yak skeletal muscle. We further elucidated the target genes regulated by these target genes within the network, offering valuable insights into the potential regulatory mechanisms governing muscle development and meat quality-related traits in yaks.
Collapse
Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - La Yongfu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tong Wang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Institute of Western Agriculture, the Chinese Academy of Agricultural sciences, Changji, China.
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China.
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| |
Collapse
|
6
|
Huang R, Chen J, Dong X, Zhang X, Luo W. Transcriptome Data Revealed the circRNA-miRNA-mRNA Regulatory Network during the Proliferation and Differentiation of Myoblasts in Shitou Goose. Animals (Basel) 2024; 14:576. [PMID: 38396545 PMCID: PMC10885906 DOI: 10.3390/ani14040576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
CircRNA, a recently characterized non-coding RNA (ncRNA) variant, functions as a molecular sponge, exerting regulatory control by binding to microRNA (miRNA) and modulating the expression of downstream proteins, either promoting or inhibiting their expression. Among poultry species, geese hold significant importance, prized by consumers for their delectable taste and rich nutritional content. Despite the prominence of geese, research on the growth and development of goose muscle, particularly the regulatory role of circRNAs in goose muscle formation, remains insufficiently explored. In this study, we constructed comprehensive expression profiles of circRNAs and messenger RNAs (mRNAs) within the myoblasts and myotubes of Shitou geese. We identified a total of 96 differentially expressed circRNAs (DEcircRNAs) and 880 differentially expressed mRNAs (DEmRNAs). Notably, the parental genes of DEcircRNAs and DEmRNAs exhibited enrichment in the Wnt signaling pathway, highlighting its potential impact on the proliferation and differentiation of goose myoblasts. Employing RNAhybrid and miRDB, we identified circRNA-miRNA pairs and mRNA-miRNA pairs that may play a role in regulating myogenic differentiation or muscle growth. Subsequently, utilizing Cytoscape, we constructed a circRNA-miRNA-mRNA interaction network aimed at unraveling the intricate regulatory mechanisms involved in goose muscle growth and development, which comprises 93 circRNAs, 351 miRNAs, and 305 mRNAs. Moreover, the identification of 10 hub genes (ACTB, ACTN1, BDNF, PDGFRA, MYL1, EFNA5, MYSM1, THBS1, ITGA8, and ELN) potentially linked to myogenesis, along with the exploration of their circRNA-miRNA-hub gene regulatory axis, was also conducted. These competitive endogenous RNA (ceRNA) regulatory networks elucidate the molecular regulatory mechanisms associated with muscle growth in Shitou geese, providing deeper insights into the reciprocal regulation of circRNA, miRNA, and mRNA in the context of goose muscle formation.
Collapse
Affiliation(s)
- Rongqin Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Jiahui Chen
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xu Dong
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Wen Luo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.H.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| |
Collapse
|
7
|
Yang H, Yue B, Yang S, Qi A, Yang Y, Tang J, Ren G, Jiang X, Lan X, Pan C, Chen H. circUBE3C modulates myoblast development by binding to miR-191 and upregulating the expression of p27. J Cell Physiol 2024; 239:e31159. [PMID: 38212939 DOI: 10.1002/jcp.31159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/16/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024]
Abstract
Noncoding RNAs, including miRNAs (microRNAs) and circRNAs (circular RNA), are crucial regulators of myoblast proliferation and differentiation during muscle development. However, the specific roles and molecular mechanisms of circRNAs in muscle development remain poorly understood. Based on the existing circRNA-miRNA-mRNA network, our study focuses on circUBE3C, exploring its differential expression in fetal and adult muscle tissue of the cattle and investigating its impact on myoblast proliferation, apoptosis, and differentiation. The functional analysis of overexpression plasmids and siRNAs (small interfering RNAs) targeting circUBE3C was comprehensively evaluated by employing an array of advanced assays, encompassing CCK-8 (cell counting kit-8), EdU (5-ethynyl-20-deoxyuridine), flow cytometry, western blot analysis, and RT-qPCR. In vivo investigations indicated that overexpression of circUBE3C impedes the process of skeletal muscle regeneration. Mechanistically, we demonstrated that circUBE3C interacts with miR-191 and alleviates the suppression of p27 through cytoplasmic separation, bioinformatics prediction, dual-luciferase reporter assay, and RIP (RNA immunoprecipitation). Our findings indicate that the novel circRNA circUBE3C competitively binds to miR-191, thereby inhibiting proliferation and promoting apoptosis in bovine primary myoblasts and unveiling a regulatory pathway in bovine skeletal muscle development. These findings expand our understanding of circRNA functions in mammals and provide a basis for further exploration of their role in myogenesis and muscle diseases.
Collapse
Affiliation(s)
- Haiyan Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Binglin Yue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Shuling Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ao Qi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jia Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Gang Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojun Jiang
- Agriculture and Animal Husbandry Fine Seed Breeding Farm of Shaanxi Province, Fufeng, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| |
Collapse
|
8
|
Huang K, Li Z, Zhong D, Yang Y, Yan X, Feng T, Wang X, Zhang L, Shen X, Chen M, Luo X, Cui K, Huang J, Rehman SU, Jiang Y, Shi D, Pauciullo A, Tang X, Liu Q, Li H. A Circular RNA Generated from Nebulin (NEB) Gene Splicing Promotes Skeletal Muscle Myogenesis in Cattle as Detected by a Multi-Omics Approach. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2300702. [PMID: 38036415 PMCID: PMC10797441 DOI: 10.1002/advs.202300702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/16/2023] [Indexed: 12/02/2023]
Abstract
Cattle and the draught force provided by its skeletal muscle have been integral to agro-ecosystems of agricultural civilization for millennia. However, relatively little is known about the cattle muscle functional genomics (including protein coding genes, non-coding RNA, etc.). Circular RNAs (circRNAs), as a new class of non-coding RNAs, can be effectively translated into detectable peptides, which enlightened us on the importance of circRNAs in cattle muscle physiology function. Here, RNA-seq, Ribosome profiling (Ribo-seq), and peptidome data are integrated from cattle skeletal muscle, and detected five encoded peptides from circRNAs. It is further identified and functionally characterize a 907-amino acids muscle-specific peptide that is named circNEB-peptide because derived by the splicing of Nebulin (NEB) gene. This peptide localizes to the nucleus and cytoplasm and directly interacts with SKP1 and TPM1, key factors regulating physiological activities of myoblasts, via ubiquitination and myoblast fusion, respectively. The circNEB-peptide is found to promote myoblasts proliferation and differentiation in vitro, and induce muscle regeneration in vivo. These findings suggest circNEB-peptide is an important regulator of skeletal muscle regeneration and underscore the possibility that more encoding polypeptides derived by RNAs currently annotated as non-coding exist.
Collapse
Affiliation(s)
- Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
- School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhou510641China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Dandan Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Yufeng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Liyin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xinyue Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xier Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliasco (TO)10095Italy
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition and Feeding,Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing100193China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| |
Collapse
|
9
|
Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, Zhao Z, Hu J, Wang J, Liu X, Li S, Zhao F. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int J Mol Sci 2023; 25:158. [PMID: 38203329 PMCID: PMC10779322 DOI: 10.3390/ijms25010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | | | | | | | | |
Collapse
|
10
|
Ma M, Chen M, Wu X, Sooranna SR, Liu Q, Shi D, Wang J, Li H. A newly identified lncRNA lnc000100 regulates proliferation and differentiation of cattle skeletal muscle cells. Epigenetics 2023; 18:2270864. [PMID: 37910666 PMCID: PMC10768731 DOI: 10.1080/15592294.2023.2270864] [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: 12/05/2022] [Accepted: 09/01/2023] [Indexed: 11/03/2023] Open
Abstract
Cattle skeletal muscle development is a complex and highly coordinated biological process mediated by a series of myogenic regulators, which plays a critical role in beef yield and quality. Long non-coding RNAs (lncRNAs) have been shown to regulate skeletal muscle development. However, the molecular mechanism by which lncRNAs regulate skeletal muscle development is largely unknown. We performed transcriptome analysis of muscle tissues of adult and embryo Angus cattle to investigate the mechanism by which lncRNA regulates skeletal muscle development between adult and embryo cattle. A total of 37,115 candidate lncRNAs were detected, and a total of 1,998 lncRNAs were differentially expressed between the muscle tissue libraries of adult and embryo cattle, including 1,229 up-regulated lncRNAs and 769 down-regulated lncRNAs (adult cattle were the control group). We verified the expression of 7 differentially expressed lncRNAs by quantitative real-time PCR (RT-qPCR), and analysed the tissue expression profile of lnc000100, which is down-regulated in the longest dorsal muscle during foetal life and which is highly specifically expressed in muscle tissue. We found that the interference of lnc000100 significantly inhibited cell proliferation and promoted cell differentiation. Lnc000100 was located in the nucleus by RNA-FISH. Our research provides certain resources for the analysis of lncRNA regulating cattle skeletal muscle development, and may also provide new insights for improving beef production and breed selection.
Collapse
Affiliation(s)
- Mengke Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Suren R. Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Jian Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| |
Collapse
|
11
|
Zhu W, Huang Y, Yu C. The emerging role of circRNAs on skeletal muscle development in economical animals. Anim Biotechnol 2023; 34:2778-2792. [PMID: 36052979 DOI: 10.1080/10495398.2022.2118130] [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] [Indexed: 11/01/2022]
Abstract
CircRNAs are a novel type of closed circular molecules formed through a covalent bond lacking a 5'cap and 3' end tail, which mainly arise from mRNA precursor. They are widely distributed in plants and animals and are characterized by stable structure, high conservativeness in cells or tissues, and showed the expression specificity at different stages of development in different tissues. CircRNAs have been gradually attracted wide attention with the development of RNA sequencing, which become a new research hotspot in the field of RNA. CircRNAs play an important role in gene expression regulation. Presently, the related circRNAs research in the regulation of animal muscle development is still at the initial stage. In this review, the formation, properties, biological functions of circRNAs were summarized. The recent research progresses of circRNAs in skeletal muscle growth and development from economic animals including livestock, poultry and fishes were introduced. Finally, we proposed a prospective for further studies of circRNAs in muscle development, and we hope our research could provide new ideas, some theoretical supports and helps for new molecular genetic markers exploitation and animal genetic breeding in future.
Collapse
Affiliation(s)
- Wenwen Zhu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Chuan Yu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
| |
Collapse
|
12
|
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] [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.
Collapse
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
| |
Collapse
|
13
|
Yang Y, Wu J, Liu W, Zhao Y, Chen H. The Function and Regulation Mechanism of Non-Coding RNAs in Muscle Development. Int J Mol Sci 2023; 24:14534. [PMID: 37833983 PMCID: PMC10572267 DOI: 10.3390/ijms241914534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023] Open
Abstract
Animal skeletal muscle growth is regulated by a complex molecular network including some non-coding RNAs (ncRNAs). In this paper, we review the non-coding RNAs related to the growth and development of common animal skeletal muscles, aiming to provide a reference for the in-depth study of the role of ncRNAs in the development of animal skeletal muscles, and to provide new ideas for the improvement of animal production performance.
Collapse
Affiliation(s)
- Yaling Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
| | - Jian Wu
- Key Laboratory of Beef Cattle Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Academy of Agricultural Sciences of Jilin Province, Changchun 136100, China;
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
| | - Yumin Zhao
- Key Laboratory of Beef Cattle Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Academy of Agricultural Sciences of Jilin Province, Changchun 136100, China;
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
| |
Collapse
|
14
|
Yu Z, Xu X, Ai N, Wang K, Zhang P, Li X, LiuFu S, Liu X, Jiang J, Gu J, Gao N, Ma H. Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig. Front Cell Dev Biol 2023; 11:1185823. [PMID: 37465009 PMCID: PMC10350537 DOI: 10.3389/fcell.2023.1185823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction: The development of skeletal muscle is regulated by regulatory factors of genes and non-coding RNAs (ncRNAs). Methods: The objective of this study was to understand the transformation of muscle fiber type in the longissimus dorsi muscle of male Ningxiang pigs at four different growth stages (30, 90, 150, and 210 days after birth, n = 3) by histological analysis and whole transcriptome sequencing. Additionally, the study investigated the expression patterns of various RNAs involved in muscle fiber transformation and constructed a regulatory network for competing endogenous RNA (ceRNA) that includes circular RNA (circRNA)/long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA). Results: Histomorphology analysis showed that the diameter of muscle fiber reached its maximum at 150 days after birth. The slow muscle fiber transformation showed a pattern of initial decrease followed by an increase. 29,963 circRNAs, 2,683 lncRNAs, 986 miRNAs and 22,411 mRNAs with expression level ≥0 were identified by whole transcriptome sequencing. Furthermore, 642 differentially expressed circRNAs (DEc), 505 differentially expressed lncRNAs (DEl), 316 differentially expressed miRNAs (DEmi) and 6,090 differentially expressed mRNAs (DEm) were identified by differential expression analysis. Functions of differentially expressed mRNA were identified by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). GO enrichment analysis indicates that 40 known genes and 6 new genes are associated with skeletal muscle development. Additionally, KEGG analysis shows that these genes regulate skeletal muscle development via MAPK, FoxO, Hedgehog, PI3K-Akt, Notch, VEGF and other signaling pathways. Through protein-protein interaction (PPI) and transcription factor prediction (TFP), the action mode of skeletal muscle-related genes was explored. PPI analysis showed that there were stable interactions among 19 proteins, meanwhile, TFP analysis predicted 22 transcription factors such as HMG20B, MYF6, MYOD1 and MYOG, and 12 of the 19 interacting proteins were transcription factors. The regulatory network of ceRNA related to skeletal muscle development was constructed based on the correlation of various RNA expression levels and the targeted binding characteristics with miRNA. The regulatory network included 31 DEms, 59 miRNAs, 667 circRNAs and 224 lncRNAs. conclusion: Overall, the study revealed the role of ceRNA regulatory network in the transformation of skeletal muscle fiber types in Ningxiang pigs, which contributes to the understanding of ceRNA regulatory network in Ningxiang pigs during the skeletal muscle development period.
Collapse
Affiliation(s)
- Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Kaiming Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiwen Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Sui LiuFu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jingjing Gu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
15
|
Zhong D, Huang K, Zhang L, Cai Y, Li H, Liu Q, Shi D, Li H, Jiang Y. Circ2388 regulates myogenesis and muscle regeneration. Cell Tissue Res 2023; 393:149-161. [PMID: 37221302 DOI: 10.1007/s00441-023-03787-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/11/2023] [Indexed: 05/25/2023]
Abstract
The formation of skeletal muscle is a complex process that is coordinated by many regulatory factors, such as myogenic factors and noncoding RNAs. Numerous studies have proved that circRNA is an indispensable part of muscle development. However, little is known about circRNAs in bovine myogenesis. In this study, we discovered a novel circRNA, circ2388, formed by reverse splicing of the fourth and fifth exons of the MYL1 gene. The expression of circ2388 was different between fetal and adult cattle muscle. This circRNA is 99% homologous between cattle and buffalo and is localized in the cytoplasm. Thoroughly, we proved that circ2388 had no effect on cattle and buffalo myoblast proliferation but promotes myoblast differentiation and myotube fusion. Furthermore, circ2388 in vivo stimulated skeletal muscle regeneration in mouse muscle injury model. Taken together, our findings suggest that circ2388 promotes myoblast differentiation and promotes the recovery and regeneration of damaged muscles.
Collapse
Affiliation(s)
- Dandan Zhong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Liyin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China
| | - Huiren Li
- Animal Husbandry Station of Chongzuo City, 532200, Chongzuo, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225, Foshan, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources , College of Animal Science and Technology, Guangxi University, 530004, Nanning, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100, Xianyang, Yangling, Shaanxi, China
| |
Collapse
|
16
|
Ai N, Yu Z, Xu X, Liufu S, Wang K, Huang S, Li X, Liu X, Chen B, Ma H, Yin Y. Circular Intronic RNA circTTN Inhibits Host Gene Transcription and Myogenesis by Recruiting PURB Proteins to form Heterotypic Complexes. Int J Mol Sci 2023; 24:9859. [PMID: 37373006 DOI: 10.3390/ijms24129859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Muscle cell growth plays an important role in skeletal muscle development. Circular RNAs (circRNAs) have been proven to be involved in the regulation of skeletal muscle growth and development. In this study, we explored the effect of circTTN on myoblast growth and its possible molecular mechanism. Using C2C12 cells as a functional model, the authenticity of circTTN was confirmed by RNase R digestion and Sanger sequencing. Previous functional studies have showed that the overexpression of circTTN inhibits myoblast proliferation and differentiation. Mechanistically, circTTN recruits the PURB protein on the Titin (TTN) promoter to inhibit the expression of the TTN gene. Moreover, PURB inhibits myoblast proliferation and differentiation, which is consistent with circTTN function. In summary, our results indicate that circTTN inhibits the transcription and myogenesis of the host gene TTN by recruiting PURB proteins to form heterotypic complexes. This work may act as a reference for further research on the role of circRNA in skeletal muscle growth and development.
Collapse
Affiliation(s)
- Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Sui Liufu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Kaiming Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shengqiang Huang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bohe Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| |
Collapse
|
17
|
Chen R, Yang T, Jin B, Xu W, Yan Y, Wood N, Lehmann HI, Wang S, Zhu X, Yuan W, Chen H, Liu Z, Li G, Bowen TS, Li J, Xiao J. CircTmeff1 Promotes Muscle Atrophy by Interacting with TDP-43 and Encoding A Novel TMEFF1-339aa Protein. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206732. [PMID: 37088818 PMCID: PMC10265041 DOI: 10.1002/advs.202206732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/04/2023] [Indexed: 05/03/2023]
Abstract
Skeletal muscle atrophy is a common clinical feature of many acute and chronic conditions. Circular RNAs (circRNAs) are covalently closed RNA transcripts that are involved in various physiological and pathological processes, but their role in muscle atrophy remains unknown. Global circRNA expression profiling indicated that circRNAs are involved in the pathophysiological processes of muscle atrophy. circTmeff1 is identified as a potential circRNA candidate that influences muscle atrophy. It is further identified that circTmeff1 is highly expressed in multiple types of muscle atrophy in vivo and in vitro. Moreover, the overexpression of circTmeff1 triggers muscle atrophy in vitro and in vivo, while the knockdown of circTmeff1 expression rescues muscle atrophy in vitro and in vivo. In particular, the knockdown of circTmeff1 expression partially rescues muscle mass in mice during established atrophic settings. Mechanistically, circTmeff1 directly interacts with TAR DNA-binding protein 43 (TDP-43) and promotes aggregation of TDP-43 in mitochondria, which triggers the release of mitochondrial DNA (mtDNA) into cytosol and activation of the cyclic GMP-AMP synthase (cGAS)/ stimulator of interferon genes (STING) pathway. Unexpectedly, TMEFF1-339aa is identified as a novel protein encoded by circTmeff1 that mediates its pro-atrophic effects. Collectively, the inhibition of circTmeff1 represents a novel therapeutic approach for multiple types of skeletal muscle atrophy.
Collapse
Affiliation(s)
- Rui Chen
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Tingting Yang
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Bing Jin
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Wanru Xu
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Yuwei Yan
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Nathanael Wood
- School of Biomedical SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - H. Immo Lehmann
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Siqi Wang
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Xiaolan Zhu
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Weilin Yuan
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Hongjian Chen
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Zhengyu Liu
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - T. Scott Bowen
- School of Biomedical SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Jin Li
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University)Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong)School of MedicineShanghai UniversityNantong226011China
- Cardiac Regeneration and Ageing LabInstitute of Cardiovascular SciencesShanghai Engineering Research Center of Organ RepairSchool of Life SciencesShanghai UniversityShanghai200444China
| |
Collapse
|
18
|
Zhang C, Huang Y, Gao X, Ren H, Gao S, Zhu W. Biological functions of circRNAs and their advance on skeletal muscle development in bovine. 3 Biotech 2023; 13:133. [PMID: 37096117 PMCID: PMC10121973 DOI: 10.1007/s13205-023-03558-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 01/10/2023] [Indexed: 04/26/2023] Open
Abstract
The development of skeletal muscle in animals is a complex biological process, which are strictly and precisely regulated by many genes and non-coding RNAs. Circular RNA (circRNA) was found as a novel class of functional non-coding RNA with ring structure in recent years, which appears in the process of transcription and is formed by covalent binding of single-stranded RNA molecules. With the development of sequencing and bioinformatics analysis technology, the functions and regulation mechanisms of circRNAs have attracted great attention due to its high stability characteristics. The role of circRNAs in skeletal muscle development have been gradually revealed, where circRNAs were involved in various biological processes, such as proliferation, differentiation, and apoptosis of skeletal muscle cells. In this review, we summarized the current studies advance of circRNAs involved in skeletal muscle development in bovine, and hope to gain a deeper understanding of the functional roles of the circRNAs in muscle growth. Our results will provide some theoretical supports and great helps for the genetic breeding of this species, and aiming at improving bovine growth and development and preventing muscle diseases.
Collapse
Affiliation(s)
- Cai Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Xiaochan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Hongtao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Shiyang Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Wenwen Zhu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, 471023 China
| |
Collapse
|
19
|
Zhong D, Yao C, Zhang L, Wang J, Liu Q, Shi D, Jiang M, Li H. Comprehensive analysis of long non-coding RNA expression profiles of GC-1spg cells with m6A methylation knockdown. Gene 2023; 871:147430. [PMID: 37062454 DOI: 10.1016/j.gene.2023.147430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/18/2023]
Abstract
Spermatogenesis is a complex process that requires many regulatory mechanisms to form healthy sperm. Numerous studies have also proved that m6A methylation modification and lncRNA are essential for normal spermatogenesis. However, the mutual regulation of m6A methylation and lncRNA in spermatogenesis is still unclear. In this study, we knocked down METTL3 in GC-1spg cells and found that a reduction in METTL3 increased cell proliferation. Further, we examined the lncRNA expression profiles of normal spermatogonia and spermatogonia with knocked down METTL3. We detected 30,924 lncRNAs, of which 34 were up-regulated and 77 down-regulated. The results of the MeRIP-qPCR experiment showed that ENSMUST00000186472, MSTRG.8019.3 and ENSMUST00000202148 had m6A methylation sites and were regulated by METTL3. We constructed ceRNA networks for these 3 lncRNAs. And we identified that these 3 lncRNAs might act as miRNA sponges to regulate some genes related to spermatogenesis. This study focuses on exploring the regulatory mechanisms of m6A methylation on lncRNAs in spermatogonia and provides some epigenetic theories for subsequent studies on the expression mechanisms of lncRNAs.
Collapse
Affiliation(s)
- Dandan Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Chengxuan Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Liyin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jian Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Mingsheng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| |
Collapse
|
20
|
Dong X, Xing J, Liu Q, Ye M, Zhou Z, Li Y, Huang R, Li Z, Nie Q. CircPLXNA2 Affects the Proliferation and Apoptosis of Myoblast through circPLXNA2/gga-miR-12207-5P/MDM4 Axis. Int J Mol Sci 2023; 24:ijms24065459. [PMID: 36982536 PMCID: PMC10049439 DOI: 10.3390/ijms24065459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
CircRNAs are newly identified special endogenous RNA molecules that covalently close a loop by back-splicing with pre-mRNA. In the cytoplasm, circRNAs would act as molecular sponges to bind with specific miRNA to promote the expression of target genes. However, knowledge of circRNA functional alternation in skeletal myogenesis is still in its infancy. In this study, we identified a circRNA–miRNA–mRNA interaction network in which the axis may be implicated in the progression of chicken primary myoblasts’ (CPMs) myogenesis by multi-omics (i.e., circRNA-seq and ribo-seq). In total, 314 circRNA–miRNA–mRNA regulatory axes containing 66 circRNAs, 70 miRNAs, and 24 mRNAs that may be relevant to myogenesis were collected. With these, the circPLXNA2-gga-miR-12207-5P-MDM4 axis aroused our research interest. The circPLXNA2 is highly differentially expressed during differentiation versus proliferation. It was demonstrated that circPLXNA2 inhibited the process of apoptosis while at the same time stimulating cell proliferation. Furthermore, we demonstrated that circPLXNA2 could inhibit the repression of gga-miR-12207-5p to MDM4 by directing binding to gga-miR-12207-5p, thereby restoring MDM4 expression. In conclusion, circPLXNA2 could function as a competing endogenous RNA (ceRNA) to recover the function of MDM4 by directing binding to gga-miR-12207-5p, thereby regulating the myogenesis.
Collapse
Affiliation(s)
- Xu Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Jiabao Xing
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Qingchun Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Mao Ye
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Zhen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Yantao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Rongqin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Zhenhui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- Correspondence:
| | - Qinghua Nie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| |
Collapse
|
21
|
Rbbani G, Nedoluzhko A, Siriyappagouder P, Sharko F, Galindo-Villegas J, Raeymaekers JAM, Joshi R, Fernandes JMO. The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia. Genomics 2023; 115:110598. [PMID: 36906188 PMCID: PMC7614353 DOI: 10.1016/j.ygeno.2023.110598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023]
Abstract
Muscle growth in teleosts is a complex biological process orchestrated by numerous protein-coding genes and non-coding RNAs. A few recent studies suggest that circRNAs are involved in teleost myogenesis, but the molecular networks involved remain poorly understood. In this study, an integrative omics approach was used to determine myogenic circRNAs in Nile tilapia by quantifying and comparing the expression profile of mRNAs, miRNAs, and circRNAs in fast muscle from full-sib fish with distinct growth rates. There were 1947 mRNAs, 9 miRNAs, and 4 circRNAs differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. Our data indicate that circMef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, thus providing novel insights into the role of circRNAs in the regulation of muscle growth in teleosts.
Collapse
Affiliation(s)
- Golam Rbbani
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Artem Nedoluzhko
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Paleogenomics laboratory, European University at Saint Petersburg, 191187 Saint-Petersburg, Russia
| | | | | | - Jorge Galindo-Villegas
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Joost A M Raeymaekers
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | | | - Jorge M O Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
| |
Collapse
|
22
|
Shen L, Liao T, Chen Q, Lei Y, Wang L, Gu H, Qiu Y, Zheng T, Yang Y, Wei C, Chen L, Zhao Y, Niu L, Zhang S, Zhu Y, Li M, Wang J, Li X, Gan M, Zhu L. tRNA-derived small RNA, 5'tiRNA-Gly-CCC, promotes skeletal muscle regeneration through the inflammatory response. J Cachexia Sarcopenia Muscle 2023; 14:1033-1045. [PMID: 36755335 PMCID: PMC10067481 DOI: 10.1002/jcsm.13187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/07/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Increasing evidence shows that tRNA-derived small RNAs (tsRNAs) are not only by-products of transfer RNAs, but they participate in numerous cellular metabolic processes. However, the role of tsRNAs in skeletal muscle regeneration remains unknown. METHODS Small RNA sequencing revealed the relationship between tsRNAs and skeletal muscle injury. The dynamic expression level of 5'tiRNA-Gly after muscle injury was confirmed by real-time quantitative PCR (q-PCR). In addition, q-PCR, flow cytometry, the 5-ethynyl-2'-deoxyuridine (Edu), cell counting kit-8, western blotting and immunofluorescence were used to explore the biological function of 5'tiRNA-Gly. Bioinformatics analysis and dual-luciferase reporter assay were used to further explore the mechanism of action under the biological function of 5'tiRNA-Gly. RESULTS Transcriptome analysis revealed that tsRNAs were significantly enriched during inflammatory response immediately after muscle injury. Interestingly, we found that 5'tiRNA-Gly was significantly up-regulated after muscle injury (P < 0.0001) and had a strong positive correlation with inflammation in vivo. In vitro experiments showed that 5'tiRNA-Gly promoted the mRNA expression of proinflammatory cytokines (IL-1β, P = 0.0468; IL-6, P = 0.0369) and the macrophages of M1 markers (TNF-α, P = 0.0102; CD80, P = 0.0056; MCP-1, P = 0.0002). On the contrary, 5'tiRNA-Gly inhibited the mRNA expression of anti-inflammatory cytokines (IL-4, P = 0.0009; IL-10, P = 0.0007; IL-13, P = 0.0008) and the mRNA expression of M2 markers (TGF-β1, P = 0.0016; ARG1, P = 0.0083). Flow cytometry showed that 5'tiRNA-Gly promoted the percentage of CD86+ macrophages (16%, P = 0.011) but inhibited that of CD206+ macrophages (10.5%, P = 0.012). Immunofluorescence showed that knockdown of 5'tiRNA-Gly increased the infiltration of M2 macrophages to the skeletal muscles (13.9%, P = 0.0023) and inhibited the expression of Pax7 (P = 0.0089) in vivo. 5'tiRNA-Gly promoted myoblast the expression of myogenic differentiation marker genes (MyoD, P = 0.0002; MyoG, P = 0.0037) and myotube formation (21.3%, P = 0.0016) but inhibited the positive rate of Edu (27.7%, P = 0.0001), cell viability (22.6%, P = 0.003) and the number of myoblasts in the G2 phase (26.3%, P = 0.0016) in vitro. Mechanistically, we found that the Tgfbr1 gene is a direct target of 5'tiRNA-Gly mediated by AGO1 and AGO3. 5'tiRNA-Gly dysregulated the expression of downstream genes related to inflammatory response, activation of satellite cells and differentiation of myoblasts through the TGF-β signalling pathway by targeting Tgfbr1. CONCLUSIONS These results reveal that 5'tiRNA-Gly potentially regulated skeletal muscle regeneration by inducing inflammation via the TGF-β signalling pathway. The findings of this study uncover a new potential target for skeletal muscle regeneration treatment.
Collapse
Affiliation(s)
- Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Tianci Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Qiuyang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yuhang Lei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Linghui Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Hao Gu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yanhao Qiu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Ting Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yiting Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Chenggang Wei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yan Zhu
- College of Life Science, China West Normal University, Nanchong, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Mailin Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
23
|
Yan S, Pei Y, Li J, Tang Z, Yang Y. Recent Progress on Circular RNAs in the Development of Skeletal Muscle and Adipose Tissues of Farm Animals. Biomolecules 2023; 13:biom13020314. [PMID: 36830683 PMCID: PMC9953704 DOI: 10.3390/biom13020314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/15/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Circular RNAs (circRNAs) are a highly conserved and specifically expressed novel class of covalently closed non-coding RNAs. CircRNAs can function as miRNA sponges, protein scaffolds, and regulatory factors, and play various roles in development and other biological processes in mammals. With the rapid development of high-throughput sequencing technology, thousands of circRNAs have been discovered in farm animals; some reportedly play vital roles in skeletal muscle and adipose development. These are critical factors affecting meat yield and quality. In this review, we have highlighted the recent advances in circRNA-related studies of skeletal muscle and adipose in farm animals. We have also described the biogenesis, properties, and biological functions of circRNAs. Furthermore, we have comprehensively summarized the functions and regulatory mechanisms of circRNAs in skeletal muscle and adipose development in farm animals and their effects on economic traits such as meat yield and quality. Finally, we propose that circRNAs are putative novel targets to improve meat yield and quality traits during animal breeding.
Collapse
Affiliation(s)
- Shanying Yan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Jiju Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
- Correspondence: (Z.T.); (Y.Y.)
| | - Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
- Correspondence: (Z.T.); (Y.Y.)
| |
Collapse
|
24
|
Fan Y, Zhang Z, Deng K, Kang Z, Guo J, Zhang G, Zhang Y, Wang F. CircUBE3A promotes myoblasts proliferation and differentiation by sponging miR-28-5p to enhance expression. Int J Biol Macromol 2023; 226:730-745. [PMID: 36526061 DOI: 10.1016/j.ijbiomac.2022.12.064] [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: 06/20/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
circRNAs have been found to be involved in the regulatory network of skeletal muscle development in studies. However, their precise functions and regulatory mechanisms remain unknown. The expression patterns and alterations of circRNAs in the longissimus dorsi muscle of two major developmental stages of goats (D75 fetus and D1 kid) were studied using high-throughput sequencing technology and bioinformatics tools in this study. In kid skeletal muscles, 831 differently expressed circRNAs were found, comprising 486 up-regulated circRNAs and 345 down-regulated circRNAs. In skeletal muscle, we focused on the highly expressed and variably expressed circUBE3A. CircUBE3A levels were discovered to be much higher in kid skeletal muscle and differentiated myoblasts. Knocking down circUBE3A resulted in a significant increase in cell proliferation and differentiation in goat myoblasts. CircUBE3A specifically binds to and inhibits miR-28-5p, boosting the expression of Hydroxyacyl Coenzyme A Dehydrogenase Beta (HADHB) and contributing to goat myoblast proliferation and differentiation, according to the mechanistic investigation. The above results indicated that circUBE3A could regulate HADHB expression by targeting miR-28-5p, consequently increasing goat myoblast proliferation and differentiation. Our findings offer fresh perspectives on goat breeding and growth regulation, as well as substantial theoretical basis.
Collapse
Affiliation(s)
- Yixuan Fan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaiping Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziqi Kang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinjing Guo
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guomin Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
25
|
Sun P, Chen M, Sooranna SR, Shi D, Liu Q, Li H. The emerging roles of circRNAs in traits associated with livestock breeding. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1775. [PMID: 36631071 DOI: 10.1002/wrna.1775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Many indicators can be used to evaluate the productivity and quality of livestock, such as meat and milk production as well as fat deposition. Meat and milk production are measures of livestock performance, while fat deposition affects the taste and flavor of the meat. The circRNAs, are non-coding RNAs, that are involved in the regulation of all these three traits. We review the functions and mechanisms of circRNAs in muscle and fat development as well as lactation to provide a theoretical basis for circRNA research in animal husbandry. Various phenotypic changes presented in livestock may be produced by different circRNAs. Our current concern is how to use the roles played by circRNAs to our advantage to produce the best possible livestock. Hence, we describe the advantages and disadvantages of knockout techniques for circRNAs. In addition, we also put forward our thoughts regarding the mechanism and network of circRNAs to provide researchers with novel ideas of how molecular biology can help us advance our goals in animal farming. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
Collapse
Affiliation(s)
- Ping Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Suren R Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| |
Collapse
|
26
|
Haplotypes within the regulatory region of MYL4 are associated with pig muscle fiber size. Gene 2023; 850:146934. [DOI: 10.1016/j.gene.2022.146934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
|
27
|
Chen M, Liu Q, Song M, Liu X, Huang K, Zhong D, Chen Y, Jiang M, Sun J, Ouyang Y, Sooranna SR, Shi D, Li H. CircCLTH promotes skeletal muscle development and regeneration. Epigenetics 2022; 17:2296-2317. [PMID: 36043316 PMCID: PMC9665157 DOI: 10.1080/15592294.2022.2117115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/04/2022] [Accepted: 08/18/2022] [Indexed: 11/03/2022] Open
Abstract
Buffalo holds an excellent potential for beef production, and circRNA plays an important role in regulating myogenesis. However, the regulatory mechanism of circRNAs during buffalo skeletal muscle development has not been fully explored. In this study, circRNA expression profiles during the proliferation and differentiation stages of buffalo myoblasts were analysed by RNA-seq. Here, a total of 3,142 circRNAs candidates were identified, and 110 of them were found to be differentially expressed in the proliferation and differentiation stages of buffalo myoblast libraries. We focused on a 347 nt circRNA subsequently named circCLTH. It consists of three exons and is expressed specifically in muscle tissues. It is a highly conserved non-coding RNA with about 95% homology to both the human and the mouse circRNAs. The results of cell experiments and RNA pull-down assays indicated that circCLTH may capture PLEC protein, promote the proliferation and differentiation of myoblasts as well as inhibit apoptosis. Overexpression of circCLTH in vivo suggests that circCLTH is involved in the stimulation of skeletal muscle regeneration. In conclusion, we identified a novel noncoding regulator, circCLTH, that promotes proliferation and differentiation of myoblasts and skeletal muscles.
Collapse
Affiliation(s)
- Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- College of Life Science and Engineering, Foshan University, Foshan, China
| | - Mingming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xingyu Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Dandan Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yaling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Mingsheng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Junming Sun
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Yiqiang Ouyang
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Suren R Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| |
Collapse
|
28
|
Wang J, Chen JF, Ma Q, Mo DL, Sun JJ, Ren QL, Zhang JQ, Lu QX, Xing BS. Identification and characterization of circRNAs related to meat quality during embryonic development of the longissimus dorsi muscle in two pig breeds. Front Genet 2022; 13:1019687. [PMID: 36457752 PMCID: PMC9705349 DOI: 10.3389/fgene.2022.1019687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/27/2022] [Indexed: 11/26/2023] Open
Abstract
Meat quality, an important economic trait, is regulated by many factors, especially by genetic factors, including coding genes, miRNAs, and lncRNAs. Recent studies have elucidated that circRNAs also play a key role in muscle development and lipid deposition. However, the functions and regulatory mechanisms of circRNAs in meat quality remain mostly unknown. The circRNA expression profiles between Huainan pigs (Chinese indigenous pigs, fat-type, Huainan HN) and Large White pigs (Western commercial pigs, lean-type, LW) in the longissimus dorsi (LD) muscle at 38, 58, and 78 days post conception (dpc) were compared by sequencing. In total, 39,887 circRNAs were identified in 18 samples, and 60, 78, and 86 differentially expressed circRNAs (DECs) were found at the three stages mentioned above between these two breeds. The parent genes of DECs were enriched in myogenesis, proliferation, adipogenesis and muscle fiber-type transition. The circRNA-miRNA interaction networks included 38 DECs and 47 miRNAs, and these miRNAs were involved in muscle development and lipid metabolism. Two shared DECs (circ_0030593 and circ_0032760) of these three stages were selected, their head-to-tail junction sites were validated by Sanger sequencing, and RT‒qPCR results suggested that these two DECs might be involved in intramuscular fat deposition. These findings provide a basis for understanding the role of circRNAs in meat quality.
Collapse
Affiliation(s)
- Jing Wang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jun-Feng Chen
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qiang Ma
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - De-Lin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jia-Jie Sun
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Guangdong Laboratory for Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qiao-Ling Ren
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jia-Qing Zhang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qing-Xia Lu
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bao-Song Xing
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| |
Collapse
|
29
|
Sun X, Kang Y, Li M, Li Y, Song J. The emerging regulatory mechanisms and biological function of circular RNAs in skeletal muscle development. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194888. [DOI: 10.1016/j.bbagrm.2022.194888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/07/2022]
|
30
|
Yuan P, Zhao Y, Li H, Li S, Fan S, Zhai B, Li Y, Han R, Liu X, Tian Y, Kang X, Zhang Y, Li G. CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken. Genes (Basel) 2022; 13:1974. [PMID: 36360215 PMCID: PMC9689937 DOI: 10.3390/genes13111974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/26/2023] Open
Abstract
Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1-9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.
Collapse
Affiliation(s)
- Pengtao Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yinli Zhao
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hongtai Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Shuaihao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Shengxin Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Yanhua Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| |
Collapse
|
31
|
Cui R, Kang X, Liu Y, Liu X, Chan S, Wang Y, Li Z, Ling Y, Feng D, Li M, Lv F, Fang M. Integrated analysis of the whole transcriptome of skeletal muscle reveals the ceRNA regulatory network related to the formation of muscle fibers in Tan sheep. Front Genet 2022; 13:991606. [PMID: 36330447 PMCID: PMC9624228 DOI: 10.3389/fgene.2022.991606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 11/15/2022] Open
Abstract
Meat quality is highly influenced by the kind of muscle fiber, and it can be significantly improved by increasing the percentage of slow-twitch fibers. It is still not known which genes control the formation of muscle fibers or how those genes control the process of forming in sheep until now. In this study, we used high-throughput RNA sequencing to assess the expression profiles of coding and noncoding RNAs in muscle tissue of Tan sheep and Dorper sheep. To investigate the molecular processes involved in the formation of muscle fibers, we collected two different muscle tissues, longissimus dorsi and biceps femoris, from Tan sheep and Dorper sheep. The longissimus dorsi of Tan sheep and Dorper sheep displayed significantly differential expression levels for 214 lncRNAs, 25 mRNAs, 4 miRNAs, and 91 circRNAs. Similarly, 172 lncRNAs, 35 mRNAs, 12 miRNAs, and 95 circRNAs were differentially expressed in the biceps femoris of Tan sheep and Dorper sheep according to the expression profiling. GO and KEGG annotation revealed that these differentially expressed genes and noncoding RNAs were related to pathways of the formation of muscle fiber, such as the Ca2+, FoxO, and AMPK signaling pathways. Several key genes are involved in the formation of muscle fibers, including ACACB, ATP6V0A1, ASAH1, EFHB, MYL3, C1QTNF7, SFSWAP, and FBXL5. RT-qPCR verified that the expression patterns of randomly selected differentially expressed transcripts were highly consistent with those obtained by RNA sequencing. A total of 10 lncRNAs, 12 miRNAs, 20 circRNAs, and 19 genes formed lncRNA/circRNA-miRNA-gene networks, indicating that the formation of muscle fiber in Tan sheep is controlled by intricate regulatory networks of coding and noncoding genes. Our findings suggested that specific ceRNA subnetworks, such as circ_0017336-miR-23a-FBXL5, may be critical in the regulation of the development of muscle fibers, offering a valuable resource for future study of the development of muscle fibers in this animal species. The findings increase our understanding of the variety in how muscle fibers originate in various domestic animals and lay the groundwork for future research into new systems that regulate the development of muscle.
Collapse
Affiliation(s)
- Ran Cui
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaolong Kang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ximing Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuheng Chan
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yubei Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Ling
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dengzhen Feng
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Menghua Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fenghua Lv
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Fenghua Lv, ; Meiying Fang,
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Fenghua Lv, ; Meiying Fang,
| |
Collapse
|
32
|
Yang X, Ma X, Mei C, Zan L. A genome-wide landscape of mRNAs, lncRNAs, circRNAs and miRNAs during intramuscular adipogenesis in cattle. BMC Genomics 2022; 23:691. [PMID: 36203142 PMCID: PMC9535873 DOI: 10.1186/s12864-022-08911-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
Abstract
Background Intramuscular preadipocyte differentiation plays a critical role in bovine intramuscular fat (IMF) deposition. However, the roles of different RNAs, including mRNAs, circRNAs, lncRNAs and miRNAs, in regulating the adipogenic differentiation of intramuscular preadipocytes remain largely unclear. Results In the present study, a whole transcriptome sequencing and analysis, including the analysis of mRNAs, circRNAs, lncRNAs and miRNAs, during different differentiation stages (0, 3, 6, and 9 d) of intramuscular preadipocytes from Qinchuan cattle was performed. All samples were prepared with 3 biological replicates. Here, a total of 27,153 mRNAs, 14,070 circRNAs, 7035 lncRNAs, and 427 miRNAs were annotated. Among them, we identified 4848 differentially expressed mRNAs (DEMs), 181 DE circRNAs (DECs), 501 DE lncRNAs (DELs) and 77 DE miRNAs (DEmiRs) between 0 d and other differentiation days (3, 6, and 9 d). GO and KEGG functional enrichment analyses showed that these differentially expressed genes were mainly enriched in cell differentiation, fat metabolism and adipogenesis-related pathways. Furthermore, weighted gene coexpression network analysis (WGCNA) and co-expression network analysis screened out multiple important mRNAs, circRNAs and lncRNAs related to intramuscular adipogenesis. Based on the competing endogenous RNA (ceRNA) regulatory mechanism, we finally identified 24 potential ceRNA networks and 31 potential key genes, including FOXO1/miR-330/circRNA2018/MSTRG.20301, GPAM/miR-27b/ciRNA489 and SESN3/miR-433/circRNA2627MSTRG.20342. Conclusions This study provides new insights into the differential expression patterns of different transcript types (i.e., mRNAs, circRNAs, lncRNAs and miRNAs) in intramuscular preadipocyte differentiation. Our findings provide data support for studying the molecular mechanism of key mRNAs and noncoding RNAs in IMF deposition, and provide new candidate markers for the molecular breeding of beef cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08911-z.
Collapse
Affiliation(s)
- Xinran Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinhao Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China. .,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
33
|
Pan Z, Yang C, Zhao R, Jiang X, Yu C, Li Z. Characterization of lncRNA/circRNA-miRNA-mRNA network to reveal potential functional ceRNAs in the skeletal muscle of chicken. Front Physiol 2022; 13:969854. [PMID: 36246144 PMCID: PMC9558166 DOI: 10.3389/fphys.2022.969854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Skeletal muscle, comprising approximately 40% of body mass, is a highly complex and heterogeneous tissue serving a multitude of functions in the organism. Non-coding RNAs (ncRNAs) are known to participate in skeletal muscle development as critical regulators. However, the regulatory mechanisms of ncRNAs on chicken muscle traits are not well understood. In the present study, we collected the leg muscle from male embryos of Tibetan chicken at embryonic (E) 10 and E18 for RNA sequencing. A total of 6,583 differentially expressed mRNAs (DEMs) including 3,055 down-regulated and 3,528 up-regulated were identified in E18. We identified 695 differentially expressed lncRNAs (DELs) (187 down-regulated and 508 up-regulated) and 1,906 differentially expressed circRNAs (DECs) (1,224 down-regulated and 682 up-regulated) in E18. Among the 130 differentially expressed miRNAs (DEMIs), 59 were up-regulated and 71 were down-regulated in E18. Numerous DEMs and target genes for miRNAs/lncRNAs were significantly enriched in the muscle system process and cell cycle. We constructed a miRNA-gene-pathway network by considering target relationships between genes related to skeletal muscle development and miRNAs. A competing endogenous RNA (ceRNA) network was also constructed by integrating competing relationships between DEMs, DELs, and DECs. Several DELs and DECs were predicted to regulate the ADRA1B, ATP2A2, ATP2B1, CACNA1S, CACNB4, MYLK2, and ROCK2 genes. We discovered the crosstalk between the ncRNAs and their competing mRNAs, which provides insights into ceRNA function and mechanisms in the skeletal muscle development of chicken.
Collapse
Affiliation(s)
- Zegun Pan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of EducationSouthwest Minzu University, Chengdu, Sichuan, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Ruipeng Zhao
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of EducationSouthwest Minzu University, Chengdu, Sichuan, China
| | - Xiaosong Jiang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Chunli Yu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Zhixiong Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of EducationSouthwest Minzu University, Chengdu, Sichuan, China
- *Correspondence: Zhixiong Li,
| |
Collapse
|
34
|
Gao Y, Wang S, Ma Y, Lei Z, Ma Y. Circular RNA regulation of fat deposition and muscle development in cattle. Vet Med Sci 2022; 8:2104-2113. [PMID: 35689831 PMCID: PMC9514475 DOI: 10.1002/vms3.857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are important transcriptional regulatory RNA molecule that can regulate the transcription of downstream genes by competitive binding of miRNAs or coding proteins or by blocking mRNAs translation. Numerous studies have shown that circRNAs are extensively involved in cell proliferation, differentiation and apoptosis, gene transcription and signal transduction. Fat deposition and muscle development have important effects on beef traits. CircRNAs are involved in regulating bovine fat and muscle cells and are differentially expressed in the tissues composed of these cells, suggesting that circRNAs play an important role in regulating bovine fat formation and muscle development. This review describes differential expression of circRNAs in bovine fat and muscle tissues, research progress in understanding how circRNAs regulate the proliferation and differentiation of bovine fat and muscle cells through competing endogenous RNAs networks, and provide a reference for the subsequent research on the molecular mechanism of circRNAs in regulating fat deposition and muscle development in cattle.
Collapse
Affiliation(s)
- Yuhong Gao
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, School of Agriculture Ningxia University Yinchuan China
| | - Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, School of Agriculture Ningxia University Yinchuan China
| | - Yanfen Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, School of Agriculture Ningxia University Yinchuan China
| | - Zhaoxiong Lei
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, School of Agriculture Ningxia University Yinchuan China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, School of Agriculture Ningxia University Yinchuan China
| |
Collapse
|
35
|
Huang J, Guo D, Zhu R, Feng Y, Li R, Yang X, Shi D. FATP1 Exerts Variable Effects on Adipogenic Differentiation and Proliferation in Cells Derived From Muscle and Adipose Tissue. Front Vet Sci 2022; 9:904879. [PMID: 35898540 PMCID: PMC9310014 DOI: 10.3389/fvets.2022.904879] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
In livestock, intramuscular adipose tissue is highly valued whereas adipose tissue in other depots is considered as waste. Thus, genetic factors that favor fat deposition in intramuscular compartments over that in other adipose depots are highly desirable in meat-producing animals. Fatty acid transport 1 (FATP1) has been demonstrated to promote cellular fatty acid uptake and metabolism; however, whether it also influences cellular lipid accumulation remains unclear. In the present study, we investigated the effects of FATP1 on the differentiation and proliferation of adipocytes in five types of cells derived from muscle and adipose tissue and estimated the effects of FATP1 on intramuscular fat (IMF) deposition. We showed that FATP1 is mainly expressed in heart and muscle tissue in buffaloes as well as cells undergoing adipogenic differentiation. Importantly, we found that FATP1 promoted the adipogenic differentiation of muscle-derived cells (buffalo myocytes and intramuscular preadipocytes and mouse C2C12 cells) but did not affect, or even inhibited, that of adipose-derived cells (buffalo subcutaneous preadipocytes and mouse 3T3-L1 cells, respectively). Correspondingly, our results further indicated that FATP1 promotes IMF deposition in mice in vivo. Meanwhile, FATP1 was found to enhance the proliferative activity of all the assessed cells, except murine 3T3-L1 cells. These results provide new insights into the potential effects of FATP1 on IMF deposition, especially regarding its positive effects on meat quality in buffaloes and other livestock.
Collapse
|
36
|
NEAT1 variant 1 weakens the genome-wide effect of miR-3122 on blocking H3K79me3 in bladder cancer. Aging (Albany NY) 2022; 14:4819-4826. [PMID: 35687898 PMCID: PMC9217706 DOI: 10.18632/aging.204113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
Abstract
Nuclear-enriched abundant transcript 1 (NEAT1) is one of the most well-studied long non-coding RNAs (lncRNAs) in multiple human carcinoma. Two distinct variants of NEAT1, however, are never illuminated their specific functions and mechanisms underlying carcinogenesis. In this study, biotin-labelled NEAT1 variants were generated to incubate with cell lysate of bladder cancer cell T24 cells, and fished a batch of RNA substances. Here, we observed that NEAT1.1 (the short transcript) could capture 122 microRNAs (miRNAs), 36 small nucleolar RNAs (snoRNAs), 55 lncRNAs and 38 mRNAs while NEAT1.2 (the long transcript) could obtain 142 miRNAs, 51 snoRNAs, 72 lncRNAs and 41 mRNAs. Furthermore, we also found that the distinctions of RNA binding substances between these two variants were mainly expressed in nucleus rather than cytoplasm. GO analysis indicated that these non-coding RNAs governed histone modification, nucleosome assembly and chromosome organization. We picked up miRNA miR-3122, which substantially interacted with NEAT1.1, and found that histone H3K79me3 was reduced in bladder cancer T24, BIU-87 and EJ-1 cells after miR-3122 overexpression, and rescued by NEAT1.1 additional compensation. Nonetheless, we failed to find that miR-3122 could interfere with expression of H3K79 methyltransferase disruptor of telomeric silencing-1 like (DOT1L). Interestingly, we harvested histone 3 fished by biotin-labelled miR-3122, and validated this intercrossing using RNA immunoprecipitation. Taken together, we demonstrated that NEAT1.1 weakened the effect of miR-3122 on H3K79me3 suppression in bladder cancer.
Collapse
|
37
|
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that widely exist in eukaryotes. As a new focus in the field of molecular regulation, circRNAs have attracted much attention in recent years. Previous studies have confirmed that circRNAs are associated with many physiological and pathological processes. CircRNAs also participate in the regulation of stem cells. Stem cells have the properties of self-renewal and differentiation, which make stem cell therapy popular. CircRNAs may serve as new targets in stem cell therapy due to their regulation in stem cells. However, the underlying relationships between circRNAs and stem cells are still being explored. In this review, we briefly summarize the effects of circRNAs on stem cells, in the context of biological activities, aging and apoptosis, and aberrant changes. Moreover, we also examine the biological roles of stem cell-derived exosomal circRNAs. We believe our review will provide insights into the effects of circRNAs on stem cells.
Collapse
|
38
|
Wang J, Wu X, Kang Y, Zhang L, Niu H, Qu J, Wang Y, Ji D, Li Y. Integrative analysis of circRNAs from Yangtze River Delta white goat neck skin tissue by high-throughput sequencing (circRNA-seq). Anim Genet 2022; 53:405-415. [PMID: 35383992 DOI: 10.1111/age.13198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/16/2022] [Accepted: 03/22/2022] [Indexed: 01/22/2023]
Abstract
The Yangtze River Delta white goat is a unique goat species that can produce superior-quality brush hair. The formation of this brush hair is controlled by a series of critical genes and related signaling pathways. Circular RNAs (circRNAs), are ubiquitous endogenous non-coding RNAs that regulate many biological and physiological processes in mammals. However, little is known about the potential regulatory role of circRNAs on superior-quality brush hair formation in Yangtze River Delta white goat. In this study, high-throughput sequencing technology was used to only detect circRNAs in the neck skin tissue of normal-quality goats (NHQs) and superior-quality goats (HQs). A total of 61 803 circRNAs were identified and 32 of them were differentially expressed in the NHQ group vs. the HQ group. Functional enrichment analysis showed that the source gene of differentially expressed circRNAs (DE-circRNAs) was enriched mostly in platelet activation and the focal adhesion signal pathway. Action mechanism analysis revealed that DE-circRNAs could sponge to many identified miRNAs, including miR-31, miR-125b, miR-let-7a and miR-149-5p, which have important roles in goat hair follicle stem cell growth, hair follicle development and morphogenesis. Altogether, our findings provide a valuable basis for studying circRNAs involved in superior-quality brush hair traits and meanwhile advance our understanding of circRNA complex regulation mechanisms in Yangtze River Delta white goat skin hair follicle development.
Collapse
Affiliation(s)
- Jian Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xi Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yan Kang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Liuming Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Haoyuan Niu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingwen Qu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yanhu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Dejun Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yongjun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| |
Collapse
|
39
|
Wang J, Wu X, Sun X, Zhang L, Wang Q, Qu J, Wang Y, Li Y. The Circular RNA CircCOL1A1 Functions as a miR-149-5p Sponge to Regulate the Formation of Superior-Quality Brush Hair via the CMTM3/AR Axis. Front Cell Dev Biol 2022; 10:760466. [PMID: 35186916 PMCID: PMC8847694 DOI: 10.3389/fcell.2022.760466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 12/18/2022] Open
Abstract
Superior-quality brush hair, also called Type III hair, can be obtained only from the cervical spine region of skin tissues of Yangtze River Delta white goats. The formation of superior-quality brush hair is controlled by a series of critical genes and related signaling pathways. Circular RNAs (circRNAs) are ubiquitous endogenous noncoding RNAs that regulate many biological and physiological processes in mammals. However, little is known about the potential regulatory role of circRNAs in superior-quality brush hair formation. Here, we analyzed circRNA sequencing data from cervical spine region skin tissues of normal-quality brush hair goats and superior-quality brush hair goats and then selected and identified the differentially expressed circRNA circCOL1A1. To investigate the regulatory role and mechanism of action of circCOL1A1, goat hair follicle stem cells (gHFSCs) were cultured and treated with a circCOL1A1 overexpression plasmid and small-interfering RNAs (siRNAs). Functional assays showed that circCOL1A1 knockdown promoted the proliferation and differentiation of gHFSCs cultured in vitro but inhibited stem cell apoptosis, whereas overexpression of circCOL1A1 suppressed stem cell proliferation and differentiation and induced apoptosis. Bioinformatics analysis combined with dual-luciferase reporter assays and RNA binding protein immunoprecipitation (RIP) verified that, mechanistically, circCOL1A1 could bind miR-149-5p directly and then relieve its inhibitory effect on CMTM3 to further control the CMTM3/AR axis. Collectively, our results reveal a novel regulatory pathway for the formation of superior-quality brush hair and indicate that circCOL1A1 plays a role in gHFSC growth and superior-quality brush hair formation by targeting the miR-149-5p/CMTM3/AR axis.
Collapse
Affiliation(s)
- Jian Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xi Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaomei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Liuming Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qiang Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingwen Qu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yanhu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yongjun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| |
Collapse
|
40
|
Xu G, Hu Y, Yu D, Chen X, Li X, Duan S, Zhang N, Xu G, Hu J, Yang G, Sun S, Liu Y. Discovery of Differentially Expressed MicroRNAs in Porcine Ovaries With Smaller and Larger Litter Size. Front Genet 2022; 13:762124. [PMID: 35222529 PMCID: PMC8864311 DOI: 10.3389/fgene.2022.762124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/03/2022] [Indexed: 12/14/2022] Open
Abstract
The number of live births in a litter is an important reproductive trait, and is one of the main indicators which reflect the production level and economic benefit of a pig farm. The ovary is an important reproductive organ of the sow, and it undergoes a series of biological processes during each estrous cycle. A complex transcriptional network containing coding and non-coding RNAs in the ovary closely regulates the reproductive capability of sows. However, the molecular regulation mechanisms affecting sow litter size are still unclear. We investigated the expression profiles of microRNAs (miRNAs) in porcine ovaries from sows with smaller than average litter sizes (SLS) and those with larger litter sizes (LLS). In total, 411 miRNAs were identified, and of these 17 were significantly down-regulated and 16 miRNAs were up-regulated when comparing sows with LLS and SLS, respectively. We further characterized the role of miR-183 which was one of the most up-regulated miRNAs. CCK-8, EdU incorporation and western blotting assays demonstrated that miR-183 promoted the proliferation of granulosa cells (GCs) in pig ovaries. Moreover, miR-183 inhibited the synthesis of estradiol in GCs and promoted the synthesis of progesterone. These results will help in gaining understanding of the role of miRNAs in regulating porcine litter size.
Collapse
Affiliation(s)
- Gaoxiao Xu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Yamei Hu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Dongling Yu
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Xingfa Chen
- Nanning Dabeinong Feed Technology Co., Ltd., Nanning, China
| | - Xiao Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Saixing Duan
- Teaching and Research Section of Biotechnology, Nanning University, Nanning, China
| | - Ning Zhang
- Nanning Dabeinong Feed Technology Co., Ltd., Nanning, China
| | - Gaoyu Xu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
| | - Jianhong Hu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Gongshe Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Shiduo Sun
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Yong Liu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
- *Correspondence: Yong Liu,
| |
Collapse
|
41
|
Li K, Huang W, Wang Z, Chen Y, Cai D, Nie Q. circTAF8 Regulates Myoblast Development and Associated Carcass Traits in Chicken. Front Genet 2022; 12:743757. [PMID: 35058965 PMCID: PMC8764441 DOI: 10.3389/fgene.2021.743757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Recent studies have shown that circular RNAs (circRNAs) play important roles in skeletal muscle development. CircRNA biogenesis is dependent on the genetic context. Single-nucleotide polymorphisms in the introns flanking circRNAs may be intermediate-inducible factors between circRNA expression and phenotypic traits. Our previous study showed that circTAF8 is an abundantly and differentially expressed circRNA in leg muscle during chicken embryonic development. Here, we aimed to investigate circTAF8 function in muscle development and the association of the SNPs in the circTAF8 flanking introns with carcass traits. In this study, we observed that overexpression of circTAF8 could promote the proliferation of chicken primary myoblasts and inhibit their differentiation. In addition, the SNPs in the introns flanking the circTAF8 locus and those associated with chicken carcass traits were analyzed in 335 partridge chickens. A total of eight SNPs were found associated with carcass traits such as leg muscle weight, live weight, and half and full-bore weight. The association analysis results of haplotype combinations were consistent with the association analysis of a single SNP. These results suggest that circTAF8 plays a regulatory role in muscle development. These identified SNPs were found correlated with traits to muscle development and carcass muscle weight in chickens.
Collapse
Affiliation(s)
- Kan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Weichen Huang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Zhijun Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Yangfeng Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Danfeng Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| |
Collapse
|
42
|
Zhang Z, Fan Y, Deng K, Liang Y, Zhang G, Gao X, El-Samahy MA, Zhang Y, Deng M, Wang F. Circular RNA circUSP13 sponges miR-29c to promote differentiation and inhibit apoptosis of goat myoblasts by targeting IGF1. FASEB J 2021; 36:e22097. [PMID: 34935184 DOI: 10.1096/fj.202101317r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/10/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022]
Abstract
Circular RNAs (circRNAs) are an indispensable element of post-transcriptional gene regulation, influencing a variety of biological processes including myogenic differentiation; however, little is known about the function of circRNA in goat myogenic differentiation. Using RNA-sequencing data from our laboratory, we explored the influences of circUSP13, as a candidate circRNA, on myoblast differentiation since its expression is higher in myoblasts of lamb (first day of age) than that of the fetus (75th day of pregnancy). In in vitro experiments, circUSP13 significantly promoted differentiation and inhibited apoptosis in goat primary myoblasts. Mechanistically, circUSP13 localized with miR-29c in the cytoplasm of goat myoblasts to regulate IGF1 expression. We further demonstrated that circUSP13 sponges miR-29c, promoting IGF1 expression that upregulated the expression of MyoG and MyHC. Thus, our results identified circUSP13 as a molecular marker for breeding programs of mutton production, as well as the circUSP13-miR-29c-IGF1 axis as a potential therapeutic target for combating muscle wasting.
Collapse
Affiliation(s)
- Zhen Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yixuan Fan
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Kaiping Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yaxu Liang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Guomin Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiao Gao
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - M A El-Samahy
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Yanli Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Mingtian Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|