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Mantica F, Iñiguez LP, Marquez Y, Permanyer J, Torres-Mendez A, Cruz J, Franch-Marro X, Tulenko F, Burguera D, Bertrand S, Doyle T, Nouzova M, Currie PD, Noriega FG, Escriva H, Arnone MI, Albertin CB, Wotton KR, Almudi I, Martin D, Irimia M. Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Nat Ecol Evol 2024; 8:1140-1153. [PMID: 38622362 DOI: 10.1038/s41559-024-02398-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/08/2024] [Indexed: 04/17/2024]
Abstract
Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution.
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Affiliation(s)
- Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Luis P Iñiguez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Marquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josefa Cruz
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Xavier Franch-Marro
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | - Toby Doyle
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Marcela Nouzova
- Institute of Parasitology, CAS, České Budějovice, Czech Republic
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia; Victorian Node, Monash University, Clayton, Victoria, Australia
| | - Fernando G Noriega
- Biology and BSI, Florida International University, Miami, FL, USA
- Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | | | - Caroline B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Karl R Wotton
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Isabel Almudi
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - David Martin
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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2
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Zhu K, He H, Guo H, Liu B, He X, Zhang N, Xian L, Zhang D. Identification of two MEF2s and their role in inhibiting the transcription of the mstn2a gene in the yellowfin seabream, Acanthopagrus latus (Hottuyn, 1782). Gene 2024; 909:148322. [PMID: 38423140 DOI: 10.1016/j.gene.2024.148322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Myocyte-specific enhancer binding factor 2 (MEF2), which belongs to the MADS superfamily, is a pivotal and conserved transcription factor that combines with the E-box motif to control the expression of muscle genes. Myostatin (mstn), a muscle growth inhibitor, is a vital member of the TGF-β superfamily. Currently, an understanding of the mechanisms of A. latus mstn (Almstn) transcriptional regulation mediated by MEF2 in fish muscle development is lacking. In the present study, two AlMEF2s (AlMEF2A and AlMEF2B) and Almstn2a were characterized from Acanthopagrus latus. AlMEF2A and AlMEF2B had 456 and 315 amino acid (aa) residues, respectively. Two typical regions, a MADS-box, MEF2, and transcriptionally activated (TAD) domains, are present in both AlMEF2s. The expression profiles of the two AlMEF2 genes were similar. The AlMEF2 genes were mainly expressed in the brain, white muscle, and liver, while Almstn2a expression was higher in the brain than in other tissues. Moreover, the expression trends of AlMEF2s and Almstn2a were significantly changed after starvation and refeeding in the five groups. Additionally, truncation experiments showed that -987 to +168 and -105 to +168 were core promoters of Almstn2a that responded to AlMEF2A and AlMEF2B, respectively. The point mutation experiment confirmed that Almstn2a transcription relies on the mutation binding sites 1 or 5 (M1/5) and mutation binding sites 4 or 5 (M4/5) for AlMEF2A and AlMEF2B regulation, respectively. The electrophoretic mobile shift assay (EMSA) further verified that M1 (-527 to -512) was a pivotal site where AlMEF2A acted on the Almstn2a gene. Furthermore, a siRNA interference gene expression experiment showed that reduced levels of AlMEF2A or AlMEF2B could prominently increase Almstn2a transcription. These results provide new information about the regulation of Almstn2a transcriptional activity by AlMEF2s and a theoretical basis for the regulatory mechanisms involved in muscle development in fish.
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Affiliation(s)
- Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Hongxi He
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Baosuo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Xin He
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Lin Xian
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China
| | - Dianchang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, Guangdong Province, PR China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, PR China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, PR China.
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3
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Chen W, Xiao Y, Yang F, Liufu S, Gong Y, Li Z, Zhang S, Tang S, Li B, Ma H. Integrated analysis of muscle transcriptome, miRNA, and proteome of Chinese indigenous breed Ningxiang pig in three developmental stages. Front Genet 2024; 15:1393834. [PMID: 38808333 PMCID: PMC11130441 DOI: 10.3389/fgene.2024.1393834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
The Ningxiang pig, a distinguished local breed in China, is recognized for its good meat quality traits. This study examines the proteomics of Ningxiang pigs at three developmental stages and delves into the upstream transcriptomics of these proteomics. Such an analysis facilitates a deeper understanding of the molecular interplay between proteins and transcriptomes in the Ningxiang pig muscle, influencing muscle growth and development. In this research, we analyzed the muscles of Ningxiang pigs at three developmental stages: 30 days in weaned piglets, 90 days in nursery pigs, and 210 days in late fattening pigs. There a total of 16 differentially co-expressed miRNAs (ssc-miRNA-1, ssc-miRNA-378, ssc-miRNA-143, ssc-miRNA-30e, etc.), 74 differentially co-expressed mRNA (PLIN3, CPT2, IGF2 and HSP90AB1, etc.) have been identified in the three stages. 572 differentially abundant proteins (DAPs) (APOC3, NDUFA2, HSPD1, ATP5E, PDHA1, etc.) were readily identified by comparing different time periods. According to the KEGG enrich pathway results that DAPs most enriched in growth and development pathways, immune mechanism pathways and maintaining functions of physical. Through short time-series expression miner (STEM) association analysis, a total of 571 negative miRNA-mRNA interaction pairs and 2 negative miRNA-mRNA-protein (Chr05_11955-Pig.17268.1-ATP5F1B, ssc-miR-194a-3p-Pig.15802.1-ACY1) interaction pairs were found. Our study provides a theoretical basis on molecular mechanism for the study of IMF deposition, muscle growth and immunity in Ningxiang pig breed.
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Affiliation(s)
- Wenwu Chen
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
| | - Yu Xiao
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
| | - Fang Yang
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
| | - Sui Liufu
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
| | - Yan Gong
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
| | - Zhi Li
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
| | - Shuo Zhang
- Yunnan Southwest Agriculture and Animal Husbandry Group Co., Ltd., Kunming, Yunnan, China
| | - Shengguo Tang
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
- Institute of Yunnan Circular Agricultural Industry, Puer, Yunnan, China
| | - Biao Li
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan, Agricultural University, Changsha, Hunan, China
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4
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Wang X, Shen H, Chen Y, Zhang Y, Wang J, Liu S, Xu B, Wang H, Frangou C, Zhang J. MEF2D Functions as a Tumor Suppressor in Breast Cancer. Int J Mol Sci 2024; 25:5207. [PMID: 38791246 PMCID: PMC11121549 DOI: 10.3390/ijms25105207] [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: 03/19/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The myocyte enhancer factor 2 (MEF2) gene family play fundamental roles in the genetic programs that control cell differentiation, morphogenesis, proliferation, and survival in a wide range of cell types. More recently, these genes have also been implicated as drivers of carcinogenesis, by acting as oncogenes or tumor suppressors depending on the biological context. Nonetheless, the molecular programs they regulate and their roles in tumor development and progression remain incompletely understood. The present study evaluated whether the MEF2D transcription factor functions as a tumor suppressor in breast cancer. The knockout of the MEF2D gene in mouse mammary epithelial cells resulted in phenotypic changes characteristic of neoplastic transformation. These changes included enhanced cell proliferation, a loss of contact inhibition, and anchorage-independent growth in soft agar, as well as the capacity for tumor development in mice. Mechanistically, the knockout of MEF2D induced the epithelial-to-mesenchymal transition (EMT) and activated several oncogenic signaling pathways, including AKT, ERK, and Hippo-YAP. Correspondingly, a reduced expression of MEF2D was observed in human triple-negative breast cancer cell lines, and a low MEF2D expression in tissue samples was found to be correlated with a worse overall survival and relapse-free survival in breast cancer patients. MEF2D may, thus, be a putative tumor suppressor, acting through selective gene regulatory programs that have clinical and therapeutic significance.
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Affiliation(s)
- Xiaoxia Wang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - He Shen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - Yanmin Chen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - Yali Zhang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Bo Xu
- Department of Pathology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Hai Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Costa Frangou
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Jianmin Zhang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
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5
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Yang G, Zhang J, Liu Y, Sun J, Ge L, Lu L, Long K, Li X, Xu D, Ma J. Acetate Alleviates Gut Microbiota Depletion-Induced Retardation of Skeletal Muscle Growth and Development in Young Mice. Int J Mol Sci 2024; 25:5129. [PMID: 38791168 PMCID: PMC11121558 DOI: 10.3390/ijms25105129] [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: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The normal growth and development of skeletal muscle is essential for the health of the body. The regulation of skeletal muscle by intestinal microorganisms and their metabolites has been continuously demonstrated. Acetate is the predominant short-chain fatty acids synthesized by gut microbiota through the fermentation of dietary fiber; however, the underlying molecular mechanisms governing the interaction between acetate and skeletal muscle during the rapid growth stage remains to be further elucidated. Herein, specific pathogen-free (SPF) mice, germ-free (GF) mice, and germ-free mice supplemented with sodium acetate (GS) were used to evaluate the effects of acetate on the skeletal muscle growth and development of young mice with gut microbiota deficiency. We found that the concentration of serum acetate, body mass gain, succinate dehydrogenase activity, and expression of the myogenesis maker gene of skeletal muscle in the GS group were higher than those in the GF group, following sodium acetate supplementation. Furthermore, the transcriptome analysis revealed that acetate activated the biological processes that regulate skeletal muscle growth and development in the GF group, which are otherwise inhibited due to a gut microbiota deficiency. The in vitro experiment showed that acetate up-regulated Gm16062 to promote skeletal muscle cell differentiation. Overall, our findings proved that acetate promotes skeletal muscle growth and development in young mice via increasing Gm16062 expression.
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Affiliation(s)
- Guitao Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.Y.); (Y.L.); (L.L.); (K.L.); (X.L.)
| | - Jinwei Zhang
- Chongqing Academy of Animal Science, Chongqing 402460, China; (J.Z.); (J.S.); (L.G.); (D.X.)
| | - Yan Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.Y.); (Y.L.); (L.L.); (K.L.); (X.L.)
| | - Jing Sun
- Chongqing Academy of Animal Science, Chongqing 402460, China; (J.Z.); (J.S.); (L.G.); (D.X.)
| | - Liangpeng Ge
- Chongqing Academy of Animal Science, Chongqing 402460, China; (J.Z.); (J.S.); (L.G.); (D.X.)
| | - Lu Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.Y.); (Y.L.); (L.L.); (K.L.); (X.L.)
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.Y.); (Y.L.); (L.L.); (K.L.); (X.L.)
| | - Xuewei Li
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.Y.); (Y.L.); (L.L.); (K.L.); (X.L.)
| | - Dengfeng Xu
- Chongqing Academy of Animal Science, Chongqing 402460, China; (J.Z.); (J.S.); (L.G.); (D.X.)
| | - Jideng Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.Y.); (Y.L.); (L.L.); (K.L.); (X.L.)
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6
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Steiman S, Miyake T, McDermott JC. FoxP1 Represses MEF2A in Striated Muscle. Mol Cell Biol 2024; 44:57-71. [PMID: 38483114 PMCID: PMC10950271 DOI: 10.1080/10985549.2024.2323959] [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: 09/06/2023] [Accepted: 01/23/2024] [Indexed: 03/19/2024] Open
Abstract
Myocyte enhancer factor 2 (MEF2) proteins are involved in multiple developmental, physiological, and pathological processes in vertebrates. Protein-protein interactions underlie the plethora of biological processes impacted by MEF2A, necessitating a detailed characterization of the MEF2A interactome. A nanobody based affinity-purification/mass spectrometry strategy was employed to achieve this goal. Specifically, the MEF2A protein complexes were captured from myogenic lysates using a GFP-tagged MEF2A protein immobilized with a GBP-nanobody followed by LC-MS/MS proteomic analysis to identify MEF2A interactors. After bioinformatic analysis, we further characterized the interaction of MEF2A with a transcriptional repressor, FOXP1. FOXP1 coprecipitated with MEF2A in proliferating myogenic cells which diminished upon differentiation (myotube formation). Ectopic expression of FOXP1 inhibited MEF2A driven myogenic reporter genes (derived from the creatine kinase muscle and myogenin genes) and delayed induction of endogenous myogenin during differentiation. Conversely, FOXP1 depletion enhanced MEF2A transactivation properties and myogenin expression. The FoxP1:MEF2A interaction is also preserved in cardiomyocytes and FoxP1 depletion enhanced cardiomyocyte hypertrophy. FOXP1 prevented MEF2A phosphorylation and activation by the p38MAPK pathway. Overall, these data implicate FOXP1 in restricting MEF2A function in order to avoid premature differentiation in myogenic progenitors and also to possibly prevent re-activation of embryonic gene expression in cardiomyocyte hypertrophy.
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Affiliation(s)
- Sydney Steiman
- Department of Biology, York University, Toronto, ON, Canada
- Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada
- Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
| | - Tetsuaki Miyake
- Department of Biology, York University, Toronto, ON, Canada
- Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada
- Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
| | - John C. McDermott
- Department of Biology, York University, Toronto, ON, Canada
- Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada
- Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
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7
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Keshri R, Detraux D, Phal A, McCurdy C, Jhajharia S, Chan TC, Mathieu J, Ruohola-Baker H. Next-generation direct reprogramming. Front Cell Dev Biol 2024; 12:1343106. [PMID: 38371924 PMCID: PMC10869521 DOI: 10.3389/fcell.2024.1343106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/12/2024] [Indexed: 02/20/2024] Open
Abstract
Tissue repair is significantly compromised in the aging human body resulting in critical disease conditions (such as myocardial infarction or Alzheimer's disease) and imposing a tremendous burden on global health. Reprogramming approaches (partial or direct reprogramming) are considered fruitful in addressing this unmet medical need. However, the efficacy, cellular maturity and specific targeting are still major challenges of direct reprogramming. Here we describe novel approaches in direct reprogramming that address these challenges. Extracellular signaling pathways (Receptor tyrosine kinases, RTK and Receptor Serine/Theronine Kinase, RSTK) and epigenetic marks remain central in rewiring the cellular program to determine the cell fate. We propose that modern protein design technologies (AI-designed minibinders regulating RTKs/RSTK, epigenetic enzymes, or pioneer factors) have potential to solve the aforementioned challenges. An efficient transdifferentiation/direct reprogramming may in the future provide molecular strategies to collectively reduce aging, fibrosis, and degenerative diseases.
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Affiliation(s)
- Riya Keshri
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Damien Detraux
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Ashish Phal
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Bioengineering, College of Engineering, University of Washington, Seattle, WA, United States
| | - Clara McCurdy
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Samriddhi Jhajharia
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Tung Ching Chan
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Hannele Ruohola-Baker
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Bioengineering, College of Engineering, University of Washington, Seattle, WA, United States
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8
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Anjum AA, Lin MJ, Jin L, Li GQ. Twist is required for muscle development of the adult legs in Henosepilachna vigintioctopunctata. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22063. [PMID: 37920138 DOI: 10.1002/arch.22063] [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: 08/31/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Although muscle development has been widely studied in Drosophila melanogaster, it was a great challenge to apply to developmental processes of other insect muscles. This study was focused on the functional characterization of a basic helix-loop-helix transcription factor gene twist in an herbivorous ladybird Henosepilachna vigintioctopunctata. Its transcript (Hvtwist) levels were detected in all developmental stages. RNA interference (RNAi)-aided knockdown of Hvtwist at the penultimate larval instar stage impaired pupation, and caused a deformed adult in the legs. The tarsi were malformed and did not support the bodies in an upright position. The climbing ability was impaired. Moreover, around 50% of the impaired adults had a malformed elytrum. In addition, they consumed less foliage and did not lay eggs. A hematoxylin-eosin staining of the leg demonstrated that the tibial extensor (TE) and the tibial flexor (TF) muscles were originated from the femurs while levator and depressor muscles of the tarsus (TL and TD) were located in the tibia in the control adults, in which tarsal segments were devoid of muscles. RNAi treatment specific to Hvtwist expression markedly impaired TE and TF muscles in the femurs, and prevented the development of TL and TD muscles in the tibia. Therefore, our findings demonstrate Twist plays a vital role in the myogenesis in H. vigintioctopunctata adult legs.
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Affiliation(s)
- Ahmad Ali Anjum
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Meng-Jiao Lin
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lin Jin
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Qing Li
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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9
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Guo D, Wei Y, Li X, Bai Y, Liu Z, Li J, Chen Z, Shi B, Zhang X, Zhao Z, Hu J, Han X, Wang J, Liu X, Li S, Zhao F. Comprehensive Analysis of miRNA and mRNA Expression Profiles during Muscle Development of the Longissimus Dorsi Muscle in Gannan Yaks and Jeryaks. Genes (Basel) 2023; 14:2220. [PMID: 38137042 PMCID: PMC10742600 DOI: 10.3390/genes14122220] [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: 11/17/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
A hybrid offspring of Gannan yak and Jersey cattle, the Jeryak exhibits apparent hybrid advantages over the Gannan yak in terms of production performance and other factors. The small non-coding RNAs known as miRNAs post-transcriptionally exert a significant regulatory influence on gene expression. However, the regulatory mechanism of miRNA associated with muscle development in Jeryak remains elusive. To elucidate the regulatory role of miRNAs in orchestrating skeletal muscle development in Jeryak, we selected longissimus dorsi muscle tissues from Gannan yak and Jeryak for transcriptome sequencing analysis. A total of 230 (DE) miRNAs were identified in the longissimus dorsi muscle of Gannan yak and Jeryak. The functional enrichment analysis revealed a significant enrichment of target genes from differentially expressed (DE)miRNAs in signaling pathways associated with muscle growth, such as the Ras signaling pathway and the MAPK signaling pathway. The network of interactions between miRNA and mRNA suggest that some (DE)miRNAs, including miR-2478-z, miR-339-x, novel-m0036-3p, and novel-m0037-3p, played a pivotal role in facilitating muscle development. These findings help us to deepen our understanding of the hybrid dominance of Jeryaks and provide a theoretical basis for further research on the regulatory mechanisms of miRNAs associated with Jeryak muscle growth and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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10
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Wu B, Gao X, Hu M, Hu J, Lan T, Xue T, Xu W, Zhu C, Yuan Y, Zheng J, Qin T, Xin P, Li Y, Gong L, Feng C, He S, Liu H, Li H, Wang Q, Ma Z, Qiu Q, Wang K. Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2629-2645. [PMID: 37273070 DOI: 10.1007/s11427-022-2312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 06/06/2023]
Abstract
Although most fishes are ectothermic, some, including tuna and billfish, achieve endothermy through specialized heat producing tissues that are modified muscles. How these heat producing tissues evolved, and whether they share convergent molecular mechanisms, remain unresolved. Here, we generated a high-quality genome from the mackerel tuna (Euthynnus affinis) and investigated the heat producing tissues of this fish by single-nucleus and bulk RNA sequencing. Compared with other teleosts, tuna-specific genetic variation is strongly associated with muscle differentiation. Single-nucleus RNA-seq revealed a high proportion of specific slow skeletal muscle cell subtypes in the heat producing tissues of tuna. Marker genes of this cell subtype are associated with the relative sliding of actin and myosin, suggesting that tuna endothermy is mainly based on shivering thermogenesis. In contrast, cross-species transcriptome analysis indicated that endothermy in billfish relies mainly on non-shivering thermogenesis. Nevertheless, the heat producing tissues of the different species do share some tissue-specific genes, including vascular-related and mitochondrial genes. Overall, although tunas and billfishes differ in their thermogenic strategies, they share similar expression patterns in some respects, highlighting the complexity of convergent evolution.
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Affiliation(s)
- Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xueli Gao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingling Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jing Hu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Tingfeng Xue
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jiangmin Zheng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tao Qin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Peidong Xin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ye Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
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11
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Yun Y, Wu R, He X, Qin X, Chen L, Sha L, Yun X, Nishiumi T, Borjigin G. Integrated Transcriptome Analysis of miRNAs and mRNAs in the Skeletal Muscle of Wuranke Sheep. Genes (Basel) 2023; 14:2034. [PMID: 38002977 PMCID: PMC10671749 DOI: 10.3390/genes14112034] [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: 10/08/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
MicroRNAs (miRNAs) are regarded as important regulators in skeletal muscle development. To reveal the regulatory roles of miRNAs and their target mRNAs underlying the skeletal muscle development of Wuranke sheep, we investigated the miRNA and mRNA expression profiles in the biceps femoris of these sheep at the fetal (3 months of gestation) and 3- and 15-month-old postnatal stages. Consequently, a total of 1195 miRNAs and 24,959 genes were identified. Furthermore, 474, 461, and 54 differentially expressed miRNAs (DEMs) and 6783, 7407, and 78 differentially expressed genes (DEGs) were detected among three comparative groups. Functional analysis demonstrated that the target mRNAs of the DEMs were enriched in multiple pathways related to muscle development. Moreover, the interactions among several predicted miRNA-mRNA pairs (oar-miR-133-HDAC1, oar-miR-1185-5p-MYH1/HADHA/OXCT1, and PC-5p-3703_578-INSR/ACTG1) that potentially affect skeletal muscle development were verified using dual-luciferase reporter assays. In this study, we identified the miRNA and mRNA differences in the skeletal muscle of Wuranke sheep at different developmental stages and revealed that a series of candidate miRNA-mRNA pairs may act as modulators of muscle development. These results will contribute to future studies on the function of miRNAs and their target mRNAs during skeletal muscle development in Wuranke sheep.
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Affiliation(s)
- Yueying Yun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Rihan Wu
- College of Biochemistry and Engineering, Hohhot Vocational College, Hohhot 010051, China;
| | - Xige He
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Xia Qin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Lu Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Lina Sha
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Xueyan Yun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
| | - Tadayuki Nishiumi
- Division of Life and Food Science, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Y.); (X.H.); (X.Q.); (L.C.); (L.S.); (X.Y.)
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12
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Smith GR, Zhao B, Lindholm ME, Raja A, Viggars M, Pincas H, Gay NR, Sun Y, Ge Y, Nair VD, Sanford JA, Amper MAS, Vasoya M, Smith KS, Montgomery S, Zaslavsky E, Bodine SC, Esser KA, Walsh MJ, Snyder MP. Multi-omic identification of key transcriptional regulatory programs during endurance exercise training. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523450. [PMID: 36711841 PMCID: PMC9882056 DOI: 10.1101/2023.01.10.523450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Transcription factors (TFs) play a key role in regulating gene expression and responses to stimuli. We conducted an integrated analysis of chromatin accessibility, DNA methylation, and RNA expression across eight rat tissues following endurance exercise training (EET) to map epigenomic changes to transcriptional changes and determine key TFs involved. We uncovered tissue-specific changes and TF motif enrichment across all omic layers, differentially accessible regions (DARs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs). We discovered distinct routes of EET-induced regulation through either epigenomic alterations providing better access for TFs to affect target genes, or via changes in TF expression or activity enabling target gene response. We identified TF motifs enriched among correlated epigenomic and transcriptomic alterations, DEGs correlated with exercise-related phenotypic changes, and EET-induced activity changes of TFs enriched for DEGs among their gene targets. This analysis elucidates the unique transcriptional regulatory mechanisms mediating diverse organ effects of EET.
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Affiliation(s)
- Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- These authors contributed equally
| | - Bingqing Zhao
- Department of Genetics, Stanford University, Stanford, CA 94305
- These authors contributed equally
| | - Malene E Lindholm
- Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305
| | - Archana Raja
- Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305
| | - Mark Viggars
- Department of Physiology and Aging, University of Florida, Gainesville, Florida 32610
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Nicole R Gay
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - James A Sanford
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Mary Anne S Amper
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Mital Vasoya
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kevin S Smith
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Stephen Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sue C Bodine
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Karyn A Esser
- Department of Physiology and Aging, University of Florida, Gainesville, Florida 32610
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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13
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Imbriano C, Moresi V, Belluti S, Renzini A, Cavioli G, Maretti E, Molinari S. Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives. Int J Mol Sci 2023; 24:15161. [PMID: 37894843 PMCID: PMC10606696 DOI: 10.3390/ijms242015161] [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: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which are N6-methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as a therapeutic approach. In this review, we aim to provide an overview of the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high-throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.
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Affiliation(s)
- Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy;
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Eleonora Maretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
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14
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Zhang Y, Li C, Zhou X, Jiang W, Wu P, Liu Y, Ren H, Zhang L, Mi H, Tang J, Zhang R, Feng L. Implications of vitamin D for flesh quality of grass carp (Ctenopharyngodon idella): antioxidant ability, nutritional value, sensory quality, and myofiber characteristics. J Anim Sci Biotechnol 2023; 14:134. [PMID: 37759314 PMCID: PMC10523690 DOI: 10.1186/s40104-023-00911-7] [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: 02/17/2023] [Accepted: 07/02/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Muscle represents a unique and complex system with many components and comprises the major edible part of animals. Vitamin D is a critical nutrient for animals and is known to enhance calcium absorption and immune response. In recent years, dietary vitamin D supplementation in livestock has received increased attention due to biological responses including improving shear force in mammalian meat. However, the vitamin D acquisition and myofiber development processes in fish differ from those in mammals, and the effect of vitamin D on fish flesh quality is poorly understood. Here, the influence of dietary vitamin D on fillet quality, antioxidant ability, and myofiber development was examined in grass carp (Ctenopharyngodon idella). METHODS A total of 540 healthy grass carp, with an initial average body weight of 257.24 ± 0.63 g, were allotted in 6 experimental groups with 3 replicates each, and respectively fed corresponding diets with 15.2, 364.3, 782.5, 1,167.9, 1,573.8, and 1,980.1 IU/kg vitamin D for 70 d. RESULTS Supplementation with 1,167.9 IU/kg vitamin D significantly improved nutritional value and sensory quality of fillets, enhancing crude protein, free amino acid, lipid, and collagen contents; maintaining an ideal pH; and reducing lactate content, shear force, and cooking loss relative to respective values in the control (15.2 IU/kg) group. Average myofiber diameter and the frequency of myofibers > 50 μm in diameter increased under supplementation with 782.5-1,167.9 IU/kg vitamin D. Levels of oxidative damage biomarkers decreased, and the expression of antioxidant enzymes and nuclear factor erythroid 2-related factor 2 signaling molecules was upregulated in the 1,167.9 IU/kg vitamin D treatment compared to respective values in the control group. Furthermore, vitamin D supplementation activated cell differentiation by enhancing the expression of myogenic regulatory factors and myocyte enhancer factors compared to that in the control group. In addition, supplementation with 1,167.9 IU/kg vitamin D improved protein deposition associated with protein synthesis molecule (target of rapamycin) signaling and vitamin D receptor paralogs, along with inhibition of protein degradation (forkhead box protein 1) signaling. CONCLUSIONS Overall, the results demonstrated that vitamin D strengthened antioxidant ability and myofiber development, thereby enhancing nutritional value and sensory quality of fish flesh. These findings suggest that dietary vitamin D supplementation is conducive to the production of nutrient-rich, high quality aquaculture products.
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Affiliation(s)
- Yao Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chaonan Li
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoqiu Zhou
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, 611130, China
| | - Weidan Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongmei Ren
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lu Zhang
- Healthy Aquaculture Key Laboratory of Sichuan Province, Tongwei Co., Ltd., Chengdu, 610041, Sichuan, China
| | - Haifeng Mi
- Healthy Aquaculture Key Laboratory of Sichuan Province, Tongwei Co., Ltd., Chengdu, 610041, Sichuan, China
| | - Jiayong Tang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ruinan Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lin Feng
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
- Key Laboratory for Animal Disease-Resistant Nutrition of China Ministry of Education, Sichuan Agricultural University, Chengdu, 611130, China.
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15
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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.
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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.)
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16
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Li Z, Wei H, Hu D, Li X, Guo Y, Ding X, Guo H, Zhang L. Research Progress on the Structural and Functional Roles of hnRNPs in Muscle Development. Biomolecules 2023; 13:1434. [PMID: 37892116 PMCID: PMC10604023 DOI: 10.3390/biom13101434] [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: 09/04/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a superfamily of RNA-binding proteins consisting of more than 20 members. These proteins play a crucial role in various biological processes by regulating RNA splicing, transcription, and translation through their binding to RNA. In the context of muscle development and regeneration, hnRNPs are involved in a wide range of regulatory mechanisms, including alternative splicing, transcription regulation, miRNA regulation, and mRNA stability regulation. Recent studies have also suggested a potential association between hnRNPs and muscle-related diseases. In this report, we provide an overview of our current understanding of how hnRNPs regulate RNA metabolism and emphasize the significance of the key members of the hnRNP family in muscle development. Furthermore, we explore the relationship between the hnRNP family and muscle-related diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Linlin Zhang
- Key Laboratory of Animal Breeding and Healthy Livestock Farming, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China; (Z.L.); (H.W.); (D.H.); (X.L.); (Y.G.); (X.D.); (H.G.)
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17
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Gu X, Wang S, Li D, Jin B, Qi Z, Deng J, Huang C, Yin X. MicroRNA-142a-3p regulates neurogenic skeletal muscle atrophy by targeting Mef2a. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:191-204. [PMID: 37483274 PMCID: PMC10362021 DOI: 10.1016/j.omtn.2023.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/31/2023] [Indexed: 07/25/2023]
Abstract
Peripheral nerve injury can lead to progressive muscle atrophy and poor motor function recovery, which is a difficult point of treatment, and the mechanism needs to be further explored. In previous studies, we found that miR-142a-3p was significantly upregulated and persistently highly expressed in denervated mouse skeletal muscle. Here, we show that overexpression of miR-142a-3p inhibited the growth and differentiation of C2C12 myoblast, while knockdown of miR-142a-3p had a promoting effect. In vitro, knockdown of miR-142a-3p in denervated mouse skeletal muscle effectively increased proliferating muscle satellite cells and ameliorated muscle atrophy. Mechanistically, the myoregulator Mef2a was proved to be an important downstream target of miR-142a-3p, and miR-142a-3p regulates skeletal muscle differentiation and regeneration by inhibiting the expression of Mef2a. The co-knockdown of Mef2a and miR-142a-3p effectively alleviated or offset the biological effects of miR-142a-3p knockdown. In conclusion, our data revealed that miR-142a-3p regulates neurogenic skeletal muscle atrophy by targeting Mef2a.
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Affiliation(s)
- Xinyi Gu
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Shen Wang
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Dongdong Li
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Bo Jin
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Zhidan Qi
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Jin Deng
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Chen Huang
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
| | - Xiaofeng Yin
- Department of Orthopedics and Traumatology, Peking University People’s Hospital, Beijing, China
- Key Laboratory of Trauma and Neural Regeneration (Peking University), Beijing, China
- Pizhou people’s Hospital, Pizhou, China
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18
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Shen X, Zhao X, He H, Zhao J, Wei Y, Chen Y, Han S, Zhu Y, Zhang Y, Zhu Q, Yin H. Evolutionary conserved circular MEF2A RNAs regulate myogenic differentiation and skeletal muscle development. PLoS Genet 2023; 19:e1010923. [PMID: 37676887 PMCID: PMC10508632 DOI: 10.1371/journal.pgen.1010923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/19/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Circular RNAs (circRNAs) have been recognized as critical regulators of skeletal muscle development. Myocyte enhancer factor 2A (MEF2A) is an evolutionarily conserved transcriptional factor that regulates myogenesis. However, it remains unclear whether MEF2A produces functional circRNAs. In this study, we identified two evolutionarily conserved circular MEF2A RNAs (circMEF2As), namely circMEF2A1 and circMEF2A2, in chicken and mouse muscle stem cells. Our findings revealed that circMEF2A1 promotes myogenesis by regulating the miR-30a-3p/PPP3CA/NFATC1 axis, whereas circMEF2A2 facilitates myogenic differentiation by targeting the miR-148a-5p/SLIT3/ROBO2/β-catenin signaling pathway. Furthermore, in vivo experiments demonstrated that circMEF2As both promote skeletal muscle growth. We also discovered that the linear MEF2A mRNA-derived MEF2A protein binds to its own promoter region, accelerating the transcription of MEF2A and upregulating the expression of both linear MEF2A and circMEF2As, forming a MEF2A autoregulated positive feedback loop. Moreover, circMEF2As positively regulate the expression of linear MEF2A by adsorbing miR-30a-3p and miR-148a-5p, which directly contribute to the MEF2A autoregulated feedback loop. Importantly, we found that mouse circMEF2As are essential for the myogenic differentiation of C2C12 cells. Collectively, our results demonstrated the evolution, function, and underlying mechanisms of circMEF2As in animal myogenesis, which may provide novel insight for both the farm animal meat industry and human medicine.
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Affiliation(s)
- Xiaoxu Shen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiyu Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haorong He
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuanhang Wei
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuqi Chen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shunshun Han
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yifeng Zhu
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yao Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Zhu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huadong Yin
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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19
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Padilla-Benavides T, Olea-Flores M, Sharma T, Syed SA, Witwicka H, Zuñiga-Eulogio MD, Zhang K, Navarro-Tito N, Imbalzano AN. Differential Contributions of mSWI/SNF Chromatin Remodeler Sub-Families to Myoblast Differentiation. Int J Mol Sci 2023; 24:11256. [PMID: 37511016 PMCID: PMC10378909 DOI: 10.3390/ijms241411256] [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: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Mammalian SWI/SNF (mSWI/SNF) complexes are ATP-dependent chromatin remodeling enzymes that are critical for normal cellular functions. mSWI/SNF enzymes are classified into three sub-families based on the presence of specific subunit proteins. The sub-families are Brm- or Brg1-associated factor (BAF), ncBAF (non-canonical BAF), and polybromo-associated BAF (PBAF). The biological roles for the different enzyme sub-families are poorly described. We knocked down the expression of genes encoding unique subunit proteins for each sub-family, Baf250A, Brd9, and Baf180, which mark the BAF, ncBAF, and PBAF sub-families, respectively, and examined the requirement for each in myoblast differentiation. We found that Baf250A and the BAF complex were required to drive lineage-specific gene expression. KD of Brd9 delayed differentiation. However, while the Baf250A-dependent gene expression profile included myogenic genes, the Brd9-dependent gene expression profile did not, suggesting Brd9 and the ncBAF complex indirectly contributed to differentiation. Baf180 was dispensable for myoblast differentiation. The results distinguish between the roles of the mSWI/SNF enzyme sub-families during myoblast differentiation.
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Affiliation(s)
- Teresita Padilla-Benavides
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Monserrat Olea-Flores
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Tapan Sharma
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Miriam D. Zuñiga-Eulogio
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Kexin Zhang
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Napoleon Navarro-Tito
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
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20
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White LJ, Russell AJ, Pizzey AR, Dasmahapatra KK, Pownall ME. The Presence of Two MyoD Genes in a Subset of Acanthopterygii Fish Is Associated with a Polyserine Insert in MyoD1. J Dev Biol 2023; 11:jdb11020019. [PMID: 37218813 DOI: 10.3390/jdb11020019] [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: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023] Open
Abstract
The MyoD gene was duplicated during the teleost whole genome duplication and, while a second MyoD gene (MyoD2) was subsequently lost from the genomes of some lineages (including zebrafish), many fish lineages (including Alcolapia species) have retained both MyoD paralogues. Here we reveal the expression patterns of the two MyoD genes in Oreochromis (Alcolapia) alcalica using in situ hybridisation. We report our analysis of MyoD1 and MyoD2 protein sequences from 54 teleost species, and show that O. alcalica, along with some other teleosts, include a polyserine repeat between the amino terminal transactivation domains (TAD) and the cysteine-histidine rich region (H/C) in MyoD1. The evolutionary history of MyoD1 and MyoD2 is compared to the presence of this polyserine region using phylogenetics, and its functional relevance is tested using overexpression in a heterologous system to investigate subcellular localisation, stability, and activity of MyoD proteins that include and do not include the polyserine region.
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Affiliation(s)
- Lewis J White
- Biology Department, University of York, York YO10 5DD, UK
| | | | | | | | - Mary E Pownall
- Biology Department, University of York, York YO10 5DD, UK
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21
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Sun Y, Zhan S, Zhao S, Zhong T, Wang L, Guo J, Dai D, Li D, Cao J, Li L, Zhang H. HuR Promotes the Differentiation of Goat Skeletal Muscle Satellite Cells by Regulating Myomaker mRNA Stability. Int J Mol Sci 2023; 24:ijms24086893. [PMID: 37108057 PMCID: PMC10138435 DOI: 10.3390/ijms24086893] [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: 02/17/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Human antigen R (HuR) is an RNA-binding protein that contributes to a wide variety of biological processes and diseases. HuR has been demonstrated to regulate muscle growth and development, but its regulatory mechanisms are not well understood, especially in goats. In this study, we found that HuR was highly expressed in the skeletal muscle of goats, and its expression levels changed during longissimus dorsi muscle development in goats. The effects of HuR on goat skeletal muscle development were explored using skeletal muscle satellite cells (MuSCs) as a model. The overexpression of HuR accelerated the expression of myogenic differentiation 1 (MyoD), Myogenin (MyoG), myosin heavy chain (MyHC), and the formation of myotubes, while the knockdown of HuR showed opposite effects in MuSCs. In addition, the inhibition of HuR expression significantly reduced the mRNA stability of MyoD and MyoG. To determine the downstream genes affected by HuR at the differentiation stage, we conducted RNA-Seq using MuSCs treated with small interfering RNA, targeting HuR. The RNA-Seq screened 31 upregulated and 113 downregulated differentially expressed genes (DEGs) in which 11 DEGs related to muscle differentiation were screened for quantitative real-time PCR (qRT-PCR) detection. Compared to the control group, the expression of three DEGs (Myomaker, CHRNA1, and CAPN6) was significantly reduced in the siRNA-HuR group (p < 0.01). In this mechanism, HuR bound to Myomaker and increased the mRNA stability of Myomaker. It then positively regulated the expression of Myomaker. Moreover, the rescue experiments indicated that the overexpression of HuR may reverse the inhibitory impact of Myomaker on myoblast differentiation. Together, our findings reveal a novel role for HuR in promoting muscle differentiation in goats by increasing the stability of Myomaker mRNA.
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Affiliation(s)
- Yanjin Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Sen Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dinghui Dai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
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22
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Nieto-Felipe J, Macias-Diaz A, Sanchez-Collado J, Berna-Erro A, Jardin I, Salido GM, Lopez JJ, Rosado JA. Role of Orai-family channels in the activation and regulation of transcriptional activity. J Cell Physiol 2023; 238:714-726. [PMID: 36952615 DOI: 10.1002/jcp.30971] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 03/25/2023]
Abstract
Store operated Ca2+ entry (SOCE) is a cornerstone for the maintenance of intracellular Ca2+ homeostasis and the regulation of a variety of cellular functions. SOCE is mediated by STIM and Orai proteins following the activation of inositol 1,4,5-trisphosphate receptors. Then, a reduction of the endoplasmic reticulum intraluminal Ca2+ concentration is sensed by STIM proteins, which undergo a conformational change and activate plasma membrane Ca2+ channels comprised by Orai proteins. STIM1/Orai-mediated Ca2+ signals are finely regulated and modulate the activity of different transcription factors, including certain isoforms of the nuclear factor of activated T-cells, the cAMP-response element binding protein, the nuclear factor κ-light chain-enhancer of activated B cells, c-fos, and c-myc. These transcription factors associate SOCE with a plethora of signaling events and cellular functions. Here we provide an overview of the current knowledge about the role of Orai channels in the regulation of transcription factors through Ca2+ -dependent signaling pathways.
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Affiliation(s)
- Joel Nieto-Felipe
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
| | - Alvaro Macias-Diaz
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
| | - Jose Sanchez-Collado
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
| | - Alejandro Berna-Erro
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
| | - Isaac Jardin
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
| | - Gines M Salido
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
| | - Jose J Lopez
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
| | - Juan A Rosado
- Departamento de Fisiología, Instituto Universitario de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, Caceres, Spain
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23
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Gene Structure, Expression and Function Analysis of MEF2 in the Pacific White Shrimp Litopenaeus vannamei. Int J Mol Sci 2023; 24:ijms24065832. [PMID: 36982906 PMCID: PMC10051702 DOI: 10.3390/ijms24065832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
The Pacific white shrimp Litopenaeus vannamei is the most economically important crustacean in the world. The growth and development of shrimp muscle has always been the focus of attention. Myocyte Enhancer Factor 2 (MEF2), a member of MADS transcription factor, has an essential influence on various growth and development programs, including myogenesis. In this study, based on the genome and transcriptome data of L. vannamei, the gene structure and expression profiles of MEF2 were characterized. We found that the LvMEF2 was widely expressed in various tissues, mainly in the Oka organ, brain, intestine, heart, and muscle. Moreover, LvMEF2 has a large number of splice variants, and the main forms are the mutually exclusive exon and alternative 5′ splice site. The expression profiles of the LvMEF2 splice variants varied under different conditions. Interestingly, some splice variants have tissue or developmental expression specificity. After RNA interference into LvMEF2, the increment in the body length and weight decreased significantly and even caused death, suggesting that LvMEF2 can affect the growth and survival of L. vannamei. Transcriptome analysis showed that after LvMEF2 was knocked down, the protein synthesis and immune-related pathways were affected, and the associated muscle protein synthesis decreased, indicating that LvMEF2 affected muscle formation and the immune system. The results provide an important basis for future studies of the MEF2 gene and the mechanism of muscle growth and development in shrimp.
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24
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Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis. Nat Commun 2023; 14:1329. [PMID: 36898987 PMCID: PMC10006080 DOI: 10.1038/s41467-023-37017-7] [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: 03/10/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
During muscle cell differentiation, the alternatively spliced, acidic β-domain potentiates transcription of Myocyte-specific Enhancer Factor 2 (Mef2D). Sequence analysis by the FuzDrop method indicates that the β-domain can serve as an interaction element for Mef2D higher-order assembly. In accord, we observed Mef2D mobile nuclear condensates in C2C12 cells, similar to those formed through liquid-liquid phase separation. In addition, we found Mef2D solid-like aggregates in the cytosol, the presence of which correlated with higher transcriptional activity. In parallel, we observed a progress in the early phase of myotube development, and higher MyoD and desmin expression. In accord with our predictions, the formation of aggregates was promoted by rigid β-domain variants, as well as by a disordered β-domain variant, capable of switching between liquid-like and solid-like higher-order states. Along these lines, NMR and molecular dynamics simulations corroborated that the β-domain can sample both ordered and disordered interactions leading to compact and extended conformations. These results suggest that β-domain fine-tunes Mef2D higher-order assembly to the cellular context, which provides a platform for myogenic regulatory factors and the transcriptional apparatus during the developmental process.
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25
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Zhelankin AV, Iulmetova LN, Ahmetov II, Generozov EV, Sharova EI. Diversity and Differential Expression of MicroRNAs in the Human Skeletal Muscle with Distinct Fiber Type Composition. Life (Basel) 2023; 13:659. [PMID: 36983815 PMCID: PMC10056610 DOI: 10.3390/life13030659] [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: 01/28/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
The ratio of fast- and slow-twitch fibers in human skeletal muscle is variable and largely determined by genetic factors. In this study, we investigated the contribution of microRNA (miRNA) in skeletal muscle fiber type composition. The study involved biopsy samples of the vastus lateralis muscle from 24 male participants with distinct fiber type ratios. The miRNA study included samples from five endurance athletes and five power athletes with the predominance of slow-twitch (61.6-72.8%) and fast-twitch (69.3-80.7%) fibers, respectively. Total and small RNA were extracted from tissue samples. Total RNA sequencing (N = 24) revealed 352 differentially expressed genes between the groups with the predominance of fast- and slow-twitch muscle fibers. Small RNA sequencing showed upregulation of miR-206, miR-501-3p and miR-185-5p, and downregulation of miR-499a-5p and miR-208-5p in the group of power athletes with fast-twitch fiber predominance. Two miRtronic miRNAs, miR-208b-3p and miR-499a-5p, had strong correlations in expression with their host genes (MYH7 and MYH7B, respectively). Correlations between the expression of miRNAs and their experimentally validated messenger RNA (mRNA) targets were calculated, and 11 miRNA-mRNA interactions with strong negative correlations were identified. Two of them belonged to miR-208b-3p and miR-499a-5p, indicating their regulatory links with the expression of CDKN1A and FOXO4, respectively.
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Affiliation(s)
- Andrey V. Zhelankin
- Department of Molecular Biology and Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Liliia N. Iulmetova
- Department of Molecular Biology and Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Ildus I. Ahmetov
- Department of Molecular Biology and Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 5AF, UK
| | - Eduard V. Generozov
- Department of Molecular Biology and Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Elena I. Sharova
- Department of Molecular Biology and Genetics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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The Role of MEF2 Transcription Factor Family in Neuronal Survival and Degeneration. Int J Mol Sci 2023; 24:ijms24043120. [PMID: 36834528 PMCID: PMC9963821 DOI: 10.3390/ijms24043120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
The family of myocyte enhancer factor 2 (MEF2) transcription factors comprises four highly conserved members that play an important role in the nervous system. They appear in precisely defined time frames in the developing brain to turn on and turn off genes affecting growth, pruning and survival of neurons. MEF2s are known to dictate neuronal development, synaptic plasticity and restrict the number of synapses in the hippocampus, thus affecting learning and memory formation. In primary neurons, negative regulation of MEF2 activity by external stimuli or stress conditions is known to induce apoptosis, albeit the pro or antiapoptotic action of MEF2 depends on the neuronal maturation stage. By contrast, enhancement of MEF2 transcriptional activity protects neurons from apoptotic death both in vitro and in preclinical models of neurodegenerative diseases. A growing body of evidence places this transcription factor in the center of many neuropathologies associated with age-dependent neuronal dysfunctions or gradual but irreversible neuron loss. In this work, we discuss how the altered function of MEF2s during development and in adulthood affecting neuronal survival may be linked to neuropsychiatric disorders.
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27
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Cuttini E, Goi C, Pellarin E, Vida R, Brancolini C. HDAC4 in cancer: A multitasking platform to drive not only epigenetic modifications. Front Mol Biosci 2023; 10:1116660. [PMID: 36762207 PMCID: PMC9902726 DOI: 10.3389/fmolb.2023.1116660] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Controlling access to genomic information and maintaining its stability are key aspects of cell life. Histone acetylation is a reversible epigenetic modification that allows access to DNA and the assembly of protein complexes that regulate mainly transcription but also other activities. Enzymes known as histone deacetylases (HDACs) are involved in the removal of the acetyl-group or in some cases of small hydrophobic moieties from histones but also from the non-histone substrate. The main achievement of HDACs on histones is to repress transcription and promote the formation of more compact chromatin. There are 18 different HDACs encoded in the human genome. Here we will discuss HDAC4, a member of the class IIa family, and its possible contribution to cancer development.
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Affiliation(s)
- Emma Cuttini
- Scuola Superiore Universitaria di Toppo Wassermann, Università degli Studi di Udine, Udine, Italy
| | - Camilla Goi
- Scuola Superiore Universitaria di Toppo Wassermann, Università degli Studi di Udine, Udine, Italy
| | - Ester Pellarin
- Scuola Superiore Universitaria di Toppo Wassermann, Università degli Studi di Udine, Udine, Italy
| | - Riccardo Vida
- Scuola Superiore Universitaria di Toppo Wassermann, Università degli Studi di Udine, Udine, Italy
| | - Claudio Brancolini
- Scuola Superiore Universitaria di Toppo Wassermann, Università degli Studi di Udine, Udine, Italy,Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, Udine, Italy,*Correspondence: Claudio Brancolini,
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28
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Gong S, Yin Y, Han M, Guo L, Duan Y, Guo Q, Yin J, Li F. Dietary leucine and fish oil cooperatively regulate skeletal myofiber type transformation via the CaMKII signaling pathway of pigs. Food Funct 2023; 14:133-147. [PMID: 36524418 DOI: 10.1039/d2fo03338k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The study investigated the effects of dietary leucine (Leu) and fish oil (FO) on skeletal myofiber type transformations in pigs and their potential interactions. The results showed that Leu increased the content of Leu, upregulated myocyte enhancer factor-2C (MEF2C) and activated the CaMKII-AMPK/SIRT1-PGC-1α pathway in the longissimus dorsi (LD) muscle. FO increased adiponectin and fatty acid beta-oxidation of LD muscle. Activation of the adiponectin signaling pathway by FO further enhanced the CaMKII pathway and upregulated the expression of MEF2C. Moreover, we found that Leu increased cyclic AMP and caffeine, and FO increased linoleic acid and glutamine in muscle metabolites, which may be the cause of myofiber conversion. In conclusion, this study demonstrated that dietary Leu and FO co-regulated the transformation from glycolytic to oxidative skeletal myofiber type. It is hypothesized that there is an interaction between amino acids and polyunsaturated fatty acids, possibly via the CaMKII signaling pathway to upregulate MEF2 and mitochondrial biogenesis.
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Affiliation(s)
- Saiming Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China. .,Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha 410125, China.
| | - Yunju Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China. .,Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha 410125, China.
| | - Mengmeng Han
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha 410125, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liu Guo
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha 410125, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yehui Duan
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha 410125, China.
| | - Qiuping Guo
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha 410125, China.
| | - Jie Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.
| | - Fengna Li
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha 410125, China. .,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Mao F, Shi YG. Targeting the LSD1/KDM1 Family of Lysine Demethylases in Cancer and Other Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:15-49. [PMID: 37751134 DOI: 10.1007/978-3-031-38176-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase discovered and the founding member of the flavin-dependent lysine demethylase family (KDM1). The human KDM1 family includes KDM1A and KDM1B, which primarily catalyze demethylation of histone H3K4me1/2. The KDM1 family is involved in epigenetic gene regulation and plays important roles in various biological and disease pathogenesis processes, including cell differentiation, embryonic development, hormone signaling, and carcinogenesis. Malfunction of many epigenetic regulators results in complex human diseases, including cancers. Regulators such as KDM1 have become potential therapeutic targets because of the reversibility of epigenetic control of genome function. Indeed, several classes of KDM1-selective small molecule inhibitors have been developed, some of which are currently in clinical trials to treat various cancers. In this chapter, we review the discovery, biochemical, and molecular mechanisms, atomic structure, genetics, biology, and pathology of the KDM1 family of lysine demethylases. Focusing on cancer, we also provide a comprehensive summary of recently developed KDM1 inhibitors and related preclinical and clinical studies to provide a better understanding of the mechanisms of action and applications of these KDM1-specific inhibitors in therapeutic treatment.
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Affiliation(s)
- Fei Mao
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yujiang Geno Shi
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China.
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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30
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Structural functionality of skeletal muscle mitochondria and its correlation with metabolic diseases. Clin Sci (Lond) 2022; 136:1851-1871. [PMID: 36545931 DOI: 10.1042/cs20220636] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
The skeletal muscle is one of the largest organs in the mammalian body. Its remarkable ability to swiftly shift its substrate selection allows other organs like the brain to choose their preferred substrate first. Healthy skeletal muscle has a high level of metabolic flexibility, which is reduced in several metabolic diseases, including obesity and Type 2 diabetes (T2D). Skeletal muscle health is highly dependent on optimally functioning mitochondria that exist in a highly integrated network with the sarcoplasmic reticulum and sarcolemma. The three major mitochondrial processes: biogenesis, dynamics, and mitophagy, taken together, determine the quality of the mitochondrial network in the muscle. Since muscle health is primarily dependent on mitochondrial status, the mitochondrial processes are very tightly regulated in the skeletal muscle via transcription factors like peroxisome proliferator-activated receptor-γ coactivator-1α, peroxisome proliferator-activated receptors, estrogen-related receptors, nuclear respiratory factor, and Transcription factor A, mitochondrial. Physiological stimuli that enhance muscle energy expenditure, like cold and exercise, also promote a healthy mitochondrial phenotype and muscle health. In contrast, conditions like metabolic disorders, muscle dystrophies, and aging impair the mitochondrial phenotype, which is associated with poor muscle health. Further, exercise training is known to improve muscle health in aged individuals or during the early stages of metabolic disorders. This might suggest that conditions enhancing mitochondrial health can promote muscle health. Therefore, in this review, we take a critical overview of current knowledge about skeletal muscle mitochondria and the regulation of their quality. Also, we have discussed the molecular derailments that happen during various pathophysiological conditions and whether it is an effect or a cause.
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31
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Catalani E, Zecchini S, Giovarelli M, Cherubini A, Del Quondam S, Brunetti K, Silvestri F, Roux-Biejat P, Napoli A, Casati SR, Ceci M, Romano N, Bongiorni S, Prantera G, Clementi E, Perrotta C, De Palma C, Cervia D. RACK1 is evolutionary conserved in satellite stem cell activation and adult skeletal muscle regeneration. Cell Death Dis 2022; 8:459. [PMID: 36396939 PMCID: PMC9672362 DOI: 10.1038/s41420-022-01250-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022]
Abstract
Skeletal muscle growth and regeneration involves the activity of resident adult stem cells, namely satellite cells (SC). Despite numerous mechanisms have been described, different signals are emerging as relevant in SC homeostasis. Here we demonstrated that the Receptor for Activated C-Kinase 1 (RACK1) is important in SC function. RACK1 was expressed transiently in the skeletal muscle of post-natal mice, being abundant in the early phase of muscle growth and almost disappearing in adult mature fibers. The presence of RACK1 in interstitial SC was also detected. After acute injury in muscle of both mouse and the fruit fly Drosophila melanogaster (used as alternative in vivo model) we found that RACK1 accumulated in regenerating fibers while it declined with the progression of repair process. To note, RACK1 also localized in the active SC that populate recovering tissue. The dynamics of RACK1 levels in isolated adult SC of mice, i.e., progressively high during differentiation and low compared to proliferating conditions, and RACK1 silencing indicated that RACK1 promotes both the formation of myotubes and the accretion of nascent myotubes. In Drosophila with depleted RACK1 in all muscle cells or, specifically, in SC lineage we observed a delayed recovery of skeletal muscle after physical damage as well as the low presence of active SC in the wound area. Our results also suggest the coupling of RACK1 to muscle unfolded protein response during SC activation. Collectively, we provided the first evidence that transient levels of the evolutionarily conserved factor RACK1 are critical for adult SC activation and proper skeletal muscle regeneration, favoring the efficient progression of SC from a committed to a fully differentiated state.
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32
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Zeng SQ, Liu CL, Huang CN, Si WJ, Liu CB, Ren LX, Zhang WY, He YM, Yuan Y, Zhang HY, Han YG, Na RS, E GX, Huang YF. Identification of the Differential Expression Profile of miRNAs in Longissimus dorsi Muscle of Dazu Black Goat. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542211014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Battistelli C, Garbo S, Maione R. MyoD-Induced Trans-Differentiation: A Paradigm for Dissecting the Molecular Mechanisms of Cell Commitment, Differentiation and Reprogramming. Cells 2022; 11:3435. [PMID: 36359831 PMCID: PMC9654159 DOI: 10.3390/cells11213435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 10/20/2023] Open
Abstract
The discovery of the skeletal muscle-specific transcription factor MyoD represents a milestone in the field of transcriptional regulation during differentiation and cell-fate reprogramming. MyoD was the first tissue-specific factor found capable of converting non-muscle somatic cells into skeletal muscle cells. A unique feature of MyoD, with respect to other lineage-specific factors able to drive trans-differentiation processes, is its ability to dramatically change the cell fate even when expressed alone. The present review will outline the molecular strategies by which MyoD reprograms the transcriptional regulation of the cell of origin during the myogenic conversion, focusing on the activation and coordination of a complex network of co-factors and epigenetic mechanisms. Some molecular roadblocks, found to restrain MyoD-dependent trans-differentiation, and the possible ways for overcoming these barriers, will also be discussed. Indeed, they are of critical importance not only to expand our knowledge of basic muscle biology but also to improve the generation skeletal muscle cells for translational research.
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Affiliation(s)
| | | | - Rossella Maione
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
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34
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The effect of fermented wheat protein hydrolysate on the exercise performance in mice. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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35
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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.
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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,
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Hildyard JC, Riddell DO, Harron RC, Rawson F, Foster EM, Massey C, Taylor-Brown F, Wells DJ, Piercy RJ. The skeletal muscle phenotype of the DE50-MD dog model of Duchenne muscular dystrophy. Wellcome Open Res 2022; 7:238. [PMID: 36865375 PMCID: PMC9971692 DOI: 10.12688/wellcomeopenres.18251.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Animal models of Duchenne muscular dystrophy (DMD) are essential to study disease progression and assess efficacy of therapeutic intervention, however dystrophic mice fail to display a clinically relevant phenotype, limiting translational utility. Dystrophin-deficient dogs exhibit disease similar to humans, making them increasingly important for late-stage preclinical evaluation of candidate therapeutics. The DE50-MD canine model of DMD carries a mutation within a human 'hotspot' region of the dystrophin gene, amenable to exon-skipping and gene editing strategies. As part of a large natural history study of disease progression, we have characterised the DE50-MD skeletal muscle phenotype to identify parameters that could serve as efficacy biomarkers in future preclinical trials. Methods: Vastus lateralis muscles were biopsied from a large cohort of DE50-MD dogs and healthy male littermates at 3-monthly intervals (3-18 months) for longitudinal analysis, with multiple muscles collected post-mortem to evaluate body-wide changes. Pathology was characterised quantitatively using histology and measurement of gene expression to determine statistical power and sample sizes appropriate for future work. Results: DE50-MD skeletal muscle exhibits widespread degeneration/regeneration, fibrosis, atrophy and inflammation. Degenerative/inflammatory changes peak during the first year of life, while fibrotic remodelling appears more gradual. Pathology is similar in most skeletal muscles, but in the diaphragm, fibrosis is more prominent, associated with fibre splitting and pathological hypertrophy. Picrosirius red and acid phosphatase staining represent useful quantitative histological biomarkers for fibrosis and inflammation respectively, while qPCR can be used to measure regeneration ( MYH3, MYH8), fibrosis ( COL1A1), inflammation ( SPP1), and stability of DE50-MD dp427 transcripts. Conclusion: The DE50-MD dog is a valuable model of DMD, with pathological features similar to young, ambulant human patients. Sample size and power calculations show that our panel of muscle biomarkers are of strong pre-clinical value, able to detect therapeutic improvements of even 25%, using trials with only six animals per group.
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Affiliation(s)
- John C.W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,
| | - Dominique O. Riddell
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Rachel C.M. Harron
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Faye Rawson
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,Langford Veterinary Services, University of Bristol, Langford, UK
| | - Emma M.A. Foster
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Claire Massey
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK
| | - Frances Taylor-Brown
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,Cave Veterinary Specialists, George's Farm, West Buckland, UK
| | - Dominic J. Wells
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, London, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, London, UK,
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Zhang J, Raza SHA, Wei D, Yaping S, Chao J, Jin W, Almohaimeed HM, A Batarfi M, Assiri R, Aggad WS, Ghalib SH, Ageeli AA. Roles of MEF2A and MyoG in the transcriptional regulation of bovine LATS2 gene. Res Vet Sci 2022; 152:417-426. [PMID: 36126508 DOI: 10.1016/j.rvsc.2022.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
As an important downstream effector gene in the hippo signaling pathway, large tumor suppressor gene 2 (LATS2) is involved in cell proliferation and differentiation, organ size and tissue regeneration, and plays an important role in regulating the growth and development of animal muscles. The purpose of this study is to explore the temporal expression of bovine LATS2 gene, and determine the key transcription factors for regulating bovine LATS2 gene. The result showed that bovine LATS2 gene was highly expressed in liver and longissimus dorsi, and was up-regulated in infancy muscle. In addition, it was highly expressed on the 2th day during the differentiation stage of myoblast. The upstream 1.7 Kb sequence of the 5 'translation region of bovine LATS2 gene was cloned, and 7 different deletion fragments were amplified by the upstream primers. These fragments were constructed into double luciferase reporter vectors and transfected into myoblasts and myotubes cells, respectively to detect the core promoter regions. In addition, the key transcription factors of the core promoter sequence of the bovine LATS2 gene were analyzed and predicted by online software. Combining with site-directed mutations, siRNA interference and chromatin immunoprecipitation technology, it was identified that MEF2A and MyoG combined in core promoter region (-248/-56) to regulate the transcription activity of bovine LATS2 gene. The results have laid a theoretical foundation for exploring the molecular regulation mechanism of LATS2 gene in the process of muscle growth.
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Affiliation(s)
- Jiupan Zhang
- Institute of Animal Sciences, Ningxia Academy of agricultural and Forestry Sciences, Yinchuan 750021, China
| | | | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan 750021, China.
| | - Song Yaping
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Jiang Chao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Wang Jin
- Institute of Animal Sciences, Ningxia Academy of agricultural and Forestry Sciences, Yinchuan 750021, China
| | - Hailah M Almohaimeed
- Department of Basic Science, College of Medicine, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Munirah A Batarfi
- Department of Anatomy, Basic medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Rasha Assiri
- Department of Basic Medical Sciences, College of Medicine, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Waheeb S Aggad
- Department of Anatomy, College of Medicine, University of Jeddah, P.O. Box 8304, Jeddah 23234, Saudi Arabia
| | - Samirah H Ghalib
- Chemistry department, Collage of Science (female section), Jazan University, Jazan 82621, Saudi Arabia
| | - Abeer A Ageeli
- Chemistry department, Collage of Science (female section), Jazan University, Jazan 82621, Saudi Arabia
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Du K, Zhao X, Li Y, Wu Z, Sun W, Wang J, Jia X, Chen S, Lai S. Genome-Wide Identification and Characterization of Circular RNAs during Skeletal Muscle Development in Meat Rabbits. Animals (Basel) 2022; 12:ani12172208. [PMID: 36077928 PMCID: PMC9454498 DOI: 10.3390/ani12172208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/14/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Our knowledge of circRNAs regulating skeletal muscle development remains largely unknown in meat rabbits. Therefore, we collected the leg muscle tissues of ZIKA rabbits at three key growth stages. A combination of circRNA assembly from a circRNA-seq library and the whole-transcriptome sequencing data identified credible circRNAs in our samples. We found these circRNAs were more conserved between rabbits and humans than between rabbits and mice. A prediction of circRNA–microRNA–mRNAs networks revealed that circRNAs might be the regulators that mainly functioned in rabbits’ muscle neuron development and metabolic processes. Our work provides a catalog of circRNAs regulating skeletal muscle development at key growth stages in rabbits and might give a new insight into rabbit breeding. Abstract Skeletal muscle development plays a vital role in muscle quality and yield in meat rabbits. Circular RNAs (circRNAs) are a new type of single-stranded endogenous non-coding RNAs involved in different biological processes. However, our knowledge of circRNAs regulating skeletal muscle development remains largely unknown in meat rabbits. In this study, we collected the leg muscle tissues of ZIKA rabbits at three key growth stages. By performing whole-transcriptome sequencing, we found the sequential expression of day 0- (D0-), D35-, and D70-selective mRNAs mainly functioned in muscle development, nervous development, and immune response during skeletal muscle development, respectively. Then, a combination of circRNA assembly from a circRNA-seq library and the whole-transcriptome sequencing data identified 6845 credible circRNAs in our samples. Most circRNAs were transcribed from exons of known genes, contained few exons, and showed short length, and these circRNAs were more conserved between rabbits and humans than between rabbits and mice. The upregulated circRNAs, which were synchronously changed with host genes, primarily played roles in MAPK signaling pathways and fatty acid biosynthesis. The prediction of circRNA–microRNA–mRNAs networks revealed that circRNAs might be the regulators that mainly functioned in rabbits’ muscle neuron development and metabolic processes. Our work provides a catalog of circRNAs regulating skeletal muscle development at key growth stages in rabbits and might give a new insight into rabbit breeding.
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Wang J, Li B, Yang X, Liang C, Raza SHA, Pan Y, Zhang K, Zan L. Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle. Front Vet Sci 2022; 9:925590. [PMID: 36032309 PMCID: PMC9404375 DOI: 10.3389/fvets.2022.925590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
As the main product of livestock, muscle itself plays an irreplaceable role in maintaining animal body movement and regulating metabolism. Therefore, it is of great significance to explore its growth, development and regeneration to improve the meat yield and quality of livestock. In this study, we attempted to use RNA-seq and ATAC-seq techniques to identify differentially expressed genes (DEGs) specifically expressed in bovine skeletal muscle as potential candidates for studying the regulatory mechanisms of muscle development. Microarray data from 8 tissue samples were selected from the GEO database for analysis. First, we obtained gene modules related to each tissue through WGCNA analysis. Through Gene Ontology (GO) functional annotation, the module of lightyellow (MElightyellow) was closely related to muscle development, and 213 hub genes were screened as follow-up research targets. Further, the difference analysis showed that, except for PREB, all other candidate hub genes were up-regulated (muscle group vs. other-group). ATAC-seq analysis showed that muscle-specific accessible chromatin regions were mainly located in promoter of genes related to muscle structure development (GO:0061061), muscle cell development (GO:0055001) and muscle system process (GO:0003012), which were involved in cAMP, CGMP-PKG, MAPK, and other signaling pathways. Next, we integrated the results of RNA-seq and ATAC-seq analysis, and 54 of the 212 candidate hub genes were identified as key regulatory genes in skeletal muscle development. Finally, through motif analysis, 22 of the 54 key genes were found to be potential target genes of transcription factor MEF2C. Including CAPN3, ACTN2, MB, MYOM3, SRL, CKM, ALPK3, MAP3K20, UBE2G1, NEURL2, CAND2, DOT1L, HRC, MAMSTR, FSD2, LRRC2, LSMEM1, SLC29A2, FHL3, KLHL41, ATXN7L2, and PDRG1. This provides a potential reference for studying the molecular mechanism of skeletal muscle development in mammals.
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Affiliation(s)
- Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Bingzhi Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xinran Yang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | | | - Yueting Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China
- *Correspondence: Linsen Zan
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Zhang N, Xu G, Sun P, Wang S, Zhu Y, Duan S, Jiang M, Li H, Wei X, Ma Y. Buffalo long non-coding RNA gene11007 promotes myoblasts proliferation. Front Vet Sci 2022; 9:857044. [PMID: 36032282 PMCID: PMC9404873 DOI: 10.3389/fvets.2022.857044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Buffalo meat is of good quality because it is lean and tender, and could bring significant cardiovascular benefits. The underlying difference in muscle development and meat quality is a complex and precisely orchestrated process which has been demonstrated to be regulated by long non-coding RNAs (lncRNAs). However, the regulatory role of lncRNAs in the growth and development of buffalo skeletal muscle is still unclear. In this study, the Ribo-Zero RNA-Seq method was used to explore the lncRNA expression profiles of buffalo myoblasts during the proliferation and differentiation phases. A specific set of 9,978 lncRNAs was found. By comparing the expression profiles of lncRNAs, it was found that there were 1,576 differentially expressed lncRNAs (DELs) during buffalo myoblast differentiation. Twelve DELs were chosen and subsequently verified in eight different buffalo tissues during fetal and adult stages by using qPCR. Gene11007 was found to be one of the most down-regulated lncRNAs during buffalo myoblasts differentiation and it was subsequently characterized. EdU, CCK-8, qPCR and western blotting assays showed that gene11007 promoted the proliferation of buffalo myoblasts but it had no effect on cell differentiation. Our research may enrich the genome annotations of buffalo and provide a new molecular target for the in-depth understanding of the regulation of lncRNAs in skeletal muscle.
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Affiliation(s)
- Ning Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Gaoxiao Xu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Ping Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Shuzhe Wang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yunchang Zhu
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, China
| | - Saixing Duan
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Mingsheng Jiang
- 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
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, China
- *Correspondence: Xuefeng Wei
| | - Yun Ma
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, China
- Yun Ma
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Liu Y, Wang R, Ding S, Deng L, Zhang Y, Li J, Shi Z, Wu Z, Liang K, Yan X, Liu W, Du Y. Engineered meatballs via scalable skeletal muscle cell expansion and modular micro-tissue assembly using porous gelatin micro-carriers. Biomaterials 2022; 287:121615. [PMID: 35679644 DOI: 10.1016/j.biomaterials.2022.121615] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 11/02/2022]
Abstract
The emerging field of cultured meat faces several technical hurdles, including the scale-up production of quality muscle and adipose progenitor cells, and the differentiation and bioengineering of these cellular materials into large, meat-like tissue. Here, we present edible, 3D porous gelatin micro-carriers (PoGelat-MCs), as efficient cell expansion scaffolds, as well as modular tissue-engineering building blocks for lab-grown meat. PoGelat-MC culture in spinner flasks, not only facilitated the scalable expansion of porcine skeletal muscle satellite cells and murine myoblasts, but also triggered their spontaneous myogenesis, in the absence of myogenic reagents. Using 3D-printed mold and transglutaminase, we bio-assembled pork muscle micro-tissues into centimeter-scale meatballs, which exhibited similar mechanical property and higher protein content compared to conventional ground pork meatballs. PoGelat-MCs also supported the expansion and differentiation of 3T3L1 murine pre-adipocytes into mature adipose micro-tissues, which could be used as modular assembly unit for engineered fat-containing meat products. Together, our results highlight PoGelat-MCs, in combination with dynamic bioreactors, as a scalable culture system to produce large quantity of highly-viable muscle and fat micro-tissues, which could be further bio-assembled into ground meat analogues.
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Affiliation(s)
- Ye Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Rui Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Shijie Ding
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Liping Deng
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Yuanyuan Zhang
- Beijing CytoNiche Biotechnology Co. Ltd, Beijing, 100195, China
| | - Junyang Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Ziao Shi
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Zhongyuan Wu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kaini Liang
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Xiaojun Yan
- Beijing CytoNiche Biotechnology Co. Ltd, Beijing, 100195, China
| | - Wei Liu
- Beijing CytoNiche Biotechnology Co. Ltd, Beijing, 100195, China
| | - Yanan Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 10084, China.
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Li C, Shen H, Liu M, Li S, Luo Y. Natural antisense RNA Foxk1-AS promotes myogenic differentiation by inhibiting Foxk1 activity. Cell Commun Signal 2022; 20:77. [PMID: 35642035 PMCID: PMC9158385 DOI: 10.1186/s12964-022-00896-2] [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: 04/05/2022] [Accepted: 04/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background Natural antisense RNAs are RNA molecules that are transcribed from the opposite strand of either protein-coding or non-protein coding genes and have the ability to regulate the expression of their sense gene or several related genes. However, the roles of natural antisense RNAs in the maintenance and myogenesis of muscle stem cells remain largely unexamined. Methods We analysed myoblast differentiation and regeneration by overexpression and knockdown of Foxk1-AS using lentivirus and adeno-associated virus infection in C2C12 cells and damaged muscle tissues. Muscle injury was induced by BaCl2 and the regeneration and repair of damaged muscle tissues was assessed by haematoxylin–eosin staining and quantitative real-time PCR. The expression of myogenic differentiation-related genes was verified via quantitative real-time PCR, Western blotting and immunofluorescence staining. Results We identified a novel natural antisense RNA, Foxk1-AS, which is transcribed from the opposite strand of Foxk1 DNA and completely incorporated in the 3′ UTR of Foxk1. Foxk1-AS targets Foxk1 and functions as a regulator of myogenesis. Overexpression of Foxk1-AS strongly inhibited the expression of Foxk1 in C2C12 cells and in tibialis anterior muscle tissue and promoted myoblast differentiation and the regeneration of muscle fibres damaged by BaCl2. Furthermore, overexpression of Foxk1-AS promoted the expression of Mef2c, which is an important transcription factor in the control of muscle gene expression and is negatively regulated by Foxk1. Conclusion The results indicated that Foxk1-AS represses Foxk1, thereby rescuing Mef2c activity and promoting myogenic differentiation of C2C12 cells and regeneration of damaged muscle fibres. Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00896-2.
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Affiliation(s)
- Chun Li
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204, People's Republic of China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Hao Shen
- School of Life Science, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Meng Liu
- School of Life Science, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China.
| | - Yuping Luo
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China.
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43
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Yang X, Ning Y, Abbas Raza SH, Mei C, Zan L. MEF2C Expression Is Regulated by the Post-transcriptional Activation of the METTL3-m 6A-YTHDF1 Axis in Myoblast Differentiation. Front Vet Sci 2022; 9:900924. [PMID: 35573410 PMCID: PMC9096896 DOI: 10.3389/fvets.2022.900924] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) plays an essential role in regulating gene expression. However, the effect of m6A on skeletal myoblast differentiation and the underlying mechanisms are still unclear. Here, we ascertained mRNA m6A methylation exhibited declined changes during bovine skeletal myoblast differentiation, and both MEF2C mRNA expression and m6A levels were significantly increased during myoblast differentiation. We found that MEF2C with mutated m6A sites significantly inhibited myoblast differentiation compared with wild-type MEF2C. METTL3 promoted MEF2C protein expression through posttranscriptional modification in an m6A-YTHDF1-dependent manner. Moreover, MEF2C promoted the expression of METTL3 by binding to its promoter. These results revealed that there is a positive feedback loop between these molecules in myoblast differentiation. Our study provided new insights into skeletal muscle differentiation and fusion, which may provide an RNA methylation-based approach for molecular genetics and breeding in livestock as well as for the treatment of muscle-related diseases.
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Affiliation(s)
- Xinran Yang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yue Ning
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,College of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, China
| | | | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China
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44
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Wu P, Zhou K, Zhang J, Ling X, Zhang X, Zhang L, Li P, Wei Q, Zhang T, Wang X, Zhang G. Identification of crucial circRNAs in skeletal muscle during chicken embryonic development. BMC Genomics 2022; 23:330. [PMID: 35484498 PMCID: PMC9052468 DOI: 10.1186/s12864-022-08588-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background Chicken provides humans with a large amount of animal protein every year, in which skeletal muscle plays a leading role. The embryonic skeletal muscle development determines the number of muscle fibers and will affect the muscle production of chickens. CircRNAs are involved in a variety of important biological processes, including muscle development. However, studies on circRNAs in the chicken embryo muscle development are still lacking. Results In the study, we collected chicken leg muscles at 14 and 20-day embryo ages both in the fast- and slow-growing groups for RNA-seq. We identified 245 and 440 differentially expressed (DE) circRNAs in the comparison group F14vsF20 and S14vsS20 respectively. GO enrichment analysis for the host genes of DE circRNAs showed that biological process (BP) terms in the top 20 related to growth in F14vsF20 were found such as positive regulation of transcription involved in G1/S phase of mitotic cell cycle, multicellular organismal macromolecule metabolic process, and multicellular organismal metabolic process. In group S14vsS20, we also found some BP terms associated with growth in the top 20 including actomyosin structure organization, actin cytoskeleton organization and myofibril assembly. A total of 7 significantly enriched pathways were obtained, containing Adherens junction and Tight junction. Further analysis of those pathways found three crucial host genes MYH9, YBX3, IGF1R in both fast- and slow-growing groups, three important host genes CTNNA3, AFDN and CREBBP only in the fast-growing group, and six host genes FGFR2, ACTN2, COL1A2, CDC42, DOCK1 and MYL3 only in the slow-growing group. In addition, circRNA-miRNA network also revealed some key regulation pairs such as novel_circ_0007646-miR-1625-5p, novel_circ_0007646-miR-1680-5p, novel_circ_0008913-miR-148b-5p, novel_circ_0008906-miR-148b-5p and novel_circ_0001640-miR-1759-3p. Conclusions Comprehensive analysis of circRNAs and their targets would contribute to a better understanding of the molecular mechanisms in poultry skeletal muscle and it also plays an important guiding role in the next research. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08588-4.
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Affiliation(s)
- Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Kaizhi Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xuanze Ling
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xinchao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Li Zhang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China
| | - Peifeng Li
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China
| | - Qingyu Wei
- College of Animal Science, Shanxi Agricultural University, Taiyuan, 030032, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xinglong Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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Identification and characterization of circular RNAs in Longissimus dorsi muscle tissue from two goat breeds using RNA-Seq. Mol Genet Genomics 2022; 297:817-831. [DOI: 10.1007/s00438-022-01887-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
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Zhang RM, Pan Y, Zou CX, An Q, Cheng JR, Li PJ, Zheng ZH, Pan Y, Feng WY, Yang SF, Shi DS, Wei YM, Deng YF. CircUBE2Q2 promotes differentiation of cattle muscle stem cells and is a potential regulatory molecule of skeletal muscle development. BMC Genomics 2022; 23:267. [PMID: 35387588 PMCID: PMC8985345 DOI: 10.1186/s12864-022-08518-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Background The growth and development of muscle stem cells (MuSCs) are significant events known to affect muscle plasticity, disease, meat production, and meat quality, which involves the types and functions of mRNA and non-coding RNA. Here, MuSCs were cultured from Guangxi fetal cattle. RNA sequencing was used to analyze the RNA expression of mRNA and non-coding RNAs during the cell proliferation and differentiation phases. Results Two thousand one hundred forty-eight mRNAs and 888 non-coding RNAs were differentially expressed between cell proliferation and differentiation phases, including 113 miRNAs, 662 lncRNAs, and 113 circRNAs. RT-qPCR verified the differential expression levels of mRNAs and non-coding RNAs, and the differentially expressed circUBE2Q2 was subsequently characterized. Expression profile analysis revealed that circUBE2Q2 was abundant in muscle tissues and intramuscular fat. The expression of cricUBE2Q2 was also significantly upregulated during MuSCs myogenic differentiation and SVFs adipogenic differentiation and decreased with age in cattle muscle tissue. Finally, the molecular mechanism of circUBE2Q2 regulating MuSCs function that affects skeletal muscle development was investigated. The results showed that circUBE2Q2 could serve as a sponge for miR-133a, significantly promoting differentiation and apoptosis of cultured MuSCs, and inhibiting proliferation of MuSCs. Conclusions CircUBE2Q2 is associated with muscle growth and development and induces MuSCs myogenic differentiation through sponging miR-133a. This study will provide new clues for the mechanisms by which mRNAs and non-coding RNAs regulate skeletal muscle growth and development, affecting muscle quality and diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08518-4.
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Affiliation(s)
- Rui-Men Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yu Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Chao-Xia Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qiang An
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Juan-Ru Cheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Peng-Ju Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Zi-Hua Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yan Pan
- Guangxi Agricultural Vocational University, Nanning, 530007, Guangxi, China
| | - Wan-You Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Su-Fang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.,International Zhuang Medical Hospital Affiliated to Guangxi University Chinese Medicine, Nanning, 530000, Guangxi, China
| | - De-Shun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Ying-Ming Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Yan-Fei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.
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Xiong Z, Wang M, You S, Chen X, Lin J, Wu J, Shi X. Transcription Regulation of Tceal7 by the Triple Complex of Mef2c, Creb1 and Myod. BIOLOGY 2022; 11:biology11030446. [PMID: 35336819 PMCID: PMC8945367 DOI: 10.3390/biology11030446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary We have previously reported a striated muscle-specific gene during embryogenesis, Tceal7. Our studies have characterized the 0.7 kb promoter of the Tceal7 gene, which harbors important E-box motifs driving the LacZ reporter in the myogenic lineage. However, the underlying mechanism regulating the dynamic expression of Tceal7 during skeletal muscle regeneration is still elusive. In the present work, we have defined a cluster of Mef2#3–CRE#3–E#4 motifs through bioinformatic analysis and transcription assays. Our studies suggested that the triple complex of Mef2c, Creb1 and Myod binds to the Mef2#3–CRE#3–E#4 cluster region, therefore driving the dynamic expression of Tceal7 during skeletal muscle regeneration. The novel mechanism may throw new light on understanding transcription regulation in skeletal muscle myogenesis. Abstract Tceal7 has been identified as a direct, downstream target gene of MRF in the skeletal muscle. The overexpression of Tceal7 represses myogenic proliferation and promotes cell differentiation. Previous studies have defined the 0.7 kb upstream fragment of the Tceal7 gene. In the present study, we have further determined two clusters of transcription factor-binding motifs in the 0.7 kb promoter: CRE#2–E#1–CRE#1 in the proximal region and Mef2#3–CRE#3–E#4 in the distal region. Utilizing transcription assays, we have also shown that the reporter containing the Mef2#3–CRE#3–E#4 motifs is synergistically transactivated by Mef2c and Creb1. Further studies have mapped out the protein–protein interaction between Mef2c and Creb1. In summary, our present studies support the notion that the triple complex of Mef2c, Creb1 and Myod interacts with the Mef2#3–CRE#3–E#4 motifs in the distal region of the Tceal7 promoter, thereby driving Tceal7 expression during skeletal muscle development and regeneration.
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Affiliation(s)
- Zhenzhen Xiong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Z.X.); (M.W.); (S.Y.); (X.C.); (J.W.)
| | - Mengni Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Z.X.); (M.W.); (S.Y.); (X.C.); (J.W.)
| | - Shanshan You
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Z.X.); (M.W.); (S.Y.); (X.C.); (J.W.)
| | - Xiaoyan Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Z.X.); (M.W.); (S.Y.); (X.C.); (J.W.)
| | - Jiangguo Lin
- Research Department of Medical Sciences, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China;
- Department of Emergency Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jianhua Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Z.X.); (M.W.); (S.Y.); (X.C.); (J.W.)
| | - Xiaozhong Shi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Z.X.); (M.W.); (S.Y.); (X.C.); (J.W.)
- Correspondence: ; Tel.: +86-20-39380620
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Attwaters M, Hughes SM. Cellular and molecular pathways controlling muscle size in response to exercise. FEBS J 2022; 289:1428-1456. [PMID: 33755332 DOI: 10.1111/febs.15820] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022]
Abstract
From the discovery of ATP and motor proteins to synaptic neurotransmitters and growth factor control of cell differentiation, skeletal muscle has provided an extreme model system in which to understand aspects of tissue function. Muscle is one of the few tissues that can undergo both increase and decrease in size during everyday life. Muscle size depends on its contractile activity, but the precise cellular and molecular pathway(s) by which the activity stimulus influences muscle size and strength remain unclear. Four correlates of muscle contraction could, in theory, regulate muscle growth: nerve-derived signals, cytoplasmic calcium dynamics, the rate of ATP consumption and physical force. Here, we summarise the evidence for and against each stimulus and what is known or remains unclear concerning their molecular signal transduction pathways and cellular effects. Skeletal muscle can grow in three ways, by generation of new syncytial fibres, addition of nuclei from muscle stem cells to existing fibres or increase in cytoplasmic volume/nucleus. Evidence suggests the latter two processes contribute to exercise-induced growth. Fibre growth requires increase in sarcolemmal surface area and cytoplasmic volume at different rates. It has long been known that high-force exercise is a particularly effective growth stimulus, but how this stimulus is sensed and drives coordinated growth that is appropriately scaled across organelles remains a mystery.
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Affiliation(s)
- Michael Attwaters
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, UK
| | - Simon M Hughes
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, UK
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Nikonova E, Mukherjee A, Kamble K, Barz C, Nongthomba U, Spletter ML. Rbfox1 is required for myofibril development and maintaining fiber type-specific isoform expression in Drosophila muscles. Life Sci Alliance 2022; 5:5/4/e202101342. [PMID: 34996845 PMCID: PMC8742874 DOI: 10.26508/lsa.202101342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Protein isoform transitions confer muscle fibers with distinct properties and are regulated by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to contribute to normal muscle development and physiology in vertebrates, although the detailed mechanisms remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity in Drosophila Rbfox1 is differentially expressed among muscle fiber types, and RNAi knockdown causes a hypercontraction phenotype that leads to behavioral and eclosion defects. Misregulation of fiber type-specific gene and splice isoform expression, notably loss of an indirect flight muscle-specific isoform of Troponin-I that is critical for regulating myosin activity, leads to structural defects. We further show that Rbfox1 directly binds the 3'-UTR of target transcripts, regulates the expression level of myogenic transcription factors myocyte enhancer factor 2 and Salm, and both modulates expression of and genetically interacts with the CELF family RNA-binding protein Bruno1 (Bru1). Rbfox1 and Bru1 co-regulate fiber type-specific alternative splicing of structural genes, indicating that regulatory interactions between FOX and CELF family RNA-binding proteins are conserved in fly muscle. Rbfox1 thus affects muscle development by regulating fiber type-specific splicing and expression dynamics of identity genes and structural proteins.
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Affiliation(s)
- Elena Nikonova
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
| | - Amartya Mukherjee
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Ketaki Kamble
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Christiane Barz
- Muscle Dynamics Group, Max Planck Institute of Biochemistry, Martinsried-Planegg, Germany
| | - Upendra Nongthomba
- Department of Molecular Reproduction, Development and Genetics (MRDG), Indian Institute of Science, Bangalore, India
| | - Maria L Spletter
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Martinsried-Planegg, Germany
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Cao X, Cheng J, Huang Y, Lan X, Lei C, Chen H. Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq. Front Vet Sci 2022; 8:782409. [PMID: 34977215 PMCID: PMC8715921 DOI: 10.3389/fvets.2021.782409] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Annotating regulatory elements could benefit the interpretation of the molecular mechanism of genome-wide association study (GWAS) hits. In this work, we performed transposase-accessible chromatin with sequencing (ATAC-seq) to annotate the cattle muscle genome's functional elements. A total of 10,023 and 11,360 peaks were revealed in muscle genomes of adult and embryo cattle, respectively. The two peak sets produced 8,850 differentially accessible regions (DARs), including 2,515 promoters and 4,319 putative enhancers. These functional elements were associated with the cell cycle, muscle development, and lipid metabolism. A total of 15 putative enhancers were selected for a dual-luciferase reporter assay, and 12 of them showed enhancer activity in cattle myoblasts. Interestingly, the GeneHancer database has annotated the interactions of eight active enhancers with gene promoters, such as embryo-specific peak1053 (log2FC = 1.81, embryo/adult, E/A) with ligand-dependent nuclear receptor corepressor-like protein (LCORL) and embryo-specific peak4218 (log2FC = 1.81) with FERM domain-containing 8 (FRMD8). A total of 295 GWAS loci from the animal QTL database were mapped to 183 putative enhancers, including rs109554838 (associated with cattle body weight and average daily gain) to peak1053 and rs110294629 (associated with beef shear force and tenderness score) to peak4218. Notably, peak4218 has been found to be involved in mouse embryo development. Deleting peak4218 clearly reduced luciferase activity (P = 3.30E-04). Our comparative enhancer map is expected to benefit the area of beef cattle breeding.
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Affiliation(s)
- Xiukai Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Jie Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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