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Mei T, Hu Y, Zhang Y, Li Y. Hypoxia treatment and resistance training alters microRNA profiling in rats skeletal muscle. Sci Rep 2024; 14:8388. [PMID: 38600177 PMCID: PMC11006875 DOI: 10.1038/s41598-024-58996-7] [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: 10/11/2023] [Accepted: 04/05/2024] [Indexed: 04/12/2024] Open
Abstract
MicroRNAs (miRNAs) may play a crucial regulatory role in the process of muscle atrophy induced by high-altitude hypoxia and its amelioration through resistance training. However, research in this aspect is still lacking. Therefore, this study aimed to employ miRNA microarray analysis to investigate the expression profile of miRNAs in skeletal muscle from an animal model of hypoxia-induced muscle atrophy and resistance training aimed at mitigating muscle atrophy. The study utilized a simulated hypoxic environment (oxygen concentration at 11.2%) to induce muscle atrophy and established a rat model of resistance training using ladder climbing, with a total intervention period of 4 weeks. The miRNA expression profile revealed 9 differentially expressed miRNAs influenced by hypoxia (e.g., miR-341, miR-32-5p, miR-465-5p) and 14 differentially expressed miRNAs influenced by resistance training under hypoxic conditions (e.g., miR-338-5p, miR-203a-3p, miR-92b-3p) (∣log2(FC)∣ ≥ 1.5, p < 0.05). The differentially expressed miRNAs were found to target genes involved in muscle protein synthesis and degradation (such as Utrn, mdm2, eIF4E), biological processes (such as negative regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-dependent), and signaling pathways (such as Wnt signaling pathway, MAPK signaling pathway, ubiquitin-mediated proteolysis, mTOR signaling pathway). This study provides a foundation for understanding and further exploring the molecular mechanisms underlying hypoxia-induced rats muscle atrophy and the mitigation of atrophy through resistance training.
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Affiliation(s)
- Tao Mei
- China Institute of Sport and Health Science, Beijing Sport University, Beijing, China
| | - Yang Hu
- China Institute of Sport and Health Science, Beijing Sport University, Beijing, China
| | - Ying Zhang
- China Institute of Sport and Health Science, Beijing Sport University, Beijing, China
| | - Yanchun Li
- China Institute of Sport and Health Science, Beijing Sport University, Beijing, China.
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2
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Millet M, Auroux M, Beaudart C, Demonceau C, Ladang A, Cavalier E, Reginster JY, Bruyère O, Chapurlat R, Rousseau JC. Association of circulating hsa-miRNAs with sarcopenia: the SarcoPhAge study. Aging Clin Exp Res 2024; 36:70. [PMID: 38485856 PMCID: PMC10940485 DOI: 10.1007/s40520-024-02711-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVE To identify a microRNA signature associated to sarcopenia in community-dwelling older adults form the SarcoPhAge cohort. METHODS In a screening phase by next generation sequencing (NGS), we compared the hsa-miRome expression of 18 subjects with sarcopenia (79.6 ± 6.8 years, 9 men) and 19 healthy subjects without sarcopenia (77.1 ± 6 years, 9 men) at baseline. Thereafter, we have selected eight candidate hsa-miRNAs according to the NGS results and after a critical assessment of previous literature. In a validation phase and by real-time qPCR, we then analyzed the expression levels of these 8 hsa-miRNAs at baseline selecting 92 healthy subjects (74.2 ± 10 years) and 92 subjects with sarcopenia (75.3 ± 6.8 years). For both steps, the groups were matched for age and sex. RESULTS In the validation phase, serum has-miRNA-133a-3p and has-miRNA-200a-3p were significantly decreased in the group with sarcopenia vs controls [RQ: relative quantification; median (interquartile range)]: -0.16 (-1.26/+0.90) vs +0.34 (-0.73/+1.33) (p < 0.01) and -0.26 (-1.07/+0.68) vs +0.27 (-0.55/+1.10) (p < 0.01) respectively. Has-miRNA-744-5p was decreased and has-miRNA-151a-3p was increased in the group with sarcopenia vs controls, but this barely reached significance: +0.16 (-1.34/+0.79) vs +0.44 (-0.31/+1.00) (p = 0.050) and +0.35 (-0.22/+0.90) vs +0.03 (-0.68/+0.75) (p = 0.054). CONCLUSION In subjects with sarcopenia, serum hsa-miRNA-133a-3p and hsa-miRNA-200a-3p expression were downregulated, consistent with their potential targets inhibiting muscle cells proliferation and differentiation.
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Affiliation(s)
| | - Maxime Auroux
- INSERM 1033, Lyon, France
- Hôpital E. Herriot, Hospices Civils de Lyon, Lyon, France
| | - Charlotte Beaudart
- Clinical Pharmacology and Toxicology Research Unit (URPC), NARILIS, Department of Biomedical Sciences, Faculty of Medicine, University of Namur, Namur, Belgium
- WHO Collaborating Center for Epidemiology of Musculoskeletal Health and Aging, Division of Public Health, Epidemiology and Health Economics, University of Liège, Liege, Belgium
| | - Céline Demonceau
- WHO Collaborating Center for Epidemiology of Musculoskeletal Health and Aging, Division of Public Health, Epidemiology and Health Economics, University of Liège, Liege, Belgium
| | - Aurélie Ladang
- Department of Clinical Chemistry, CHU de Liège, University of Liège, Liege, Belgium
| | - Etienne Cavalier
- Department of Clinical Chemistry, CHU de Liège, University of Liège, Liege, Belgium
| | - Jean-Yves Reginster
- WHO Collaborating Center for Epidemiology of Musculoskeletal Health and Aging, Division of Public Health, Epidemiology and Health Economics, University of Liège, Liege, Belgium
| | - Olivier Bruyère
- WHO Collaborating Center for Epidemiology of Musculoskeletal Health and Aging, Division of Public Health, Epidemiology and Health Economics, University of Liège, Liege, Belgium
| | - Roland Chapurlat
- INSERM 1033, Lyon, France
- PMO, Lyon, France
- Hôpital E. Herriot, Hospices Civils de Lyon, Lyon, France
- University of Lyon, Lyon, France
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Sun X, Zhang T, Li L, Tu K, Yu T, Wu B, Zhou L, Tian J, Liu Z. MicroRNA expression signature in the striated and smooth adductor muscles of Yesso scallop Patinopecten yessoensis. Genomics 2022; 114:110409. [PMID: 35714827 DOI: 10.1016/j.ygeno.2022.110409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/25/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022]
Abstract
Increasing evidences point to the potential role of microRNAs (miRNAs) in muscle growth and development in animals. However, knowledge on the identity of miRNAs and their targets in molluscs remains largely unknown. Scallops have one large adductor muscle, composed of fast (striated) and slow (smooth) muscle types, which display great differences in muscle fibers, meat quality, cell types and molecular components. In the present study, we performed a comprehensive investigation of miRNA transcriptomes in fast and slow adductor muscles of Yesso scallop Patinopecten yessoensis. As a result, 47 differentially expressed miRNAs representing ten miRNA families were identified between the striated and smooth adductor muscles. The KEGG enrichment analysis of their target genes were mainly associated with amino acid metabolism, energy metabolism and glycan biosynthesis. The target genes of miR-133 and miR-71 were validated by the dual-luciferase reporter assays and miRNA antagomir treatment in vivo. The identification and functional validation of these different miRNAs in scallops will greatly help our understanding of miRNA regulatory mechanism that achieves the unique muscle phenotypes in scallops. The present findings provide the direct evidences for muscle-specific miRNAs involved in muscle growth and differentiation in molluscs.
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Affiliation(s)
- Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Tianshi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Li Li
- National Oceanographic Center, Qingdao 266104, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian 351100, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao, China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Jiteng Tian
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Qingdao 266071, China.
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4
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Begum S, Gnanasree SM, Anusha N, Senthilkumaran B. Germ cell markers in fishes - A review. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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MicroRNA-dependent regulation of targeted mRNAs for improved muscle texture in crisp grass carp fed with broad bean. Food Res Int 2022; 155:111071. [DOI: 10.1016/j.foodres.2022.111071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/19/2022]
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Liu S, Yang Q, Chen Y, Liu Q, Wang W, Song J, Zheng Y, Liu W. Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone. Front Genet 2021; 12:695699. [PMID: 34421998 PMCID: PMC8375321 DOI: 10.3389/fgene.2021.695699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
17α-Methyltestosterone (MT) is a synthetic androgen. The objective of this study was to explore the effects of exogenous MT on the growth and gonadal development of female rare minnow Gobiocypris rarus. Female G. rarus groups were exposed to 25–100 ng/L of MT for 7 days. After exposure for 7 days, the total weight and body length were significantly decreased in the 50-ng/L MT groups. The major oocytes in the ovaries of the control group were vitellogenic oocytes (Voc) and cortical alveolus stage oocytes (Coc). In the MT exposure groups, some fish had mature ovaries with a relatively lower proportion of mature oocytes, and the diameter of the perinucleolar oocytes (Poc) was decreased compared with those of the control group. Ovarian VTG, FSH, LH, 11-KT, E2, and T were significantly increased after exposure to 50 ng/L of MT for 7 days. Unigenes (73,449), 24 known mature microRNAs (miRNAs), and 897 novel miRNAs in the gonads of G. rarus were found using high-throughput sequencing. Six mature miRNAs (miR-19, miR-183, miR-203, miR-204, miR-205, and miR-96) as well as six differentially expressed genes (fabp3, mfap4, abca1, foxo3, tgfb1, and zfp36l1) that may be associated with ovarian development and innate immune response were assayed using qPCR. Furthermore, the miR-183 cluster and miR-203 were differentially expressed in MT-exposed ovaries of the different G. rarus groups. This study provides some information about the role of miRNA–mRNA pairs in the regulation of ovarian development and innate immune system, which will facilitate future studies of the miRNA–RNA-associated regulation of teleost reproduction.
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Affiliation(s)
- Shaozhen Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qiong Yang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yue Chen
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qing Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Weiwei Wang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Jing Song
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
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7
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Differences in DNA methylation between slow and fast muscle in Takifugu rubripes. Gene 2021; 801:145853. [PMID: 34274464 DOI: 10.1016/j.gene.2021.145853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/22/2021] [Accepted: 07/13/2021] [Indexed: 12/20/2022]
Abstract
Fish skeletal muscle is comprised of fast muscle (FM) and slow muscle (SM), which constitutes 60% of total the body mass. Fish skeletal muscle can affect fish swimming activity, which is important for aquaculture due to its growth-potentiating effects. DNA methylation can influence gene expression level. We previously identified multiple differentially expressed genes (DEGs) between FM and SM in Takifugu rubripes. However, it is unknown if the expression levels of these DEGs are influenced by DNA methylation. In the present study, we used DNA methylation sequencing to study the DNA methylation profiles of FM and SM in T. rubripes. SM had higher overall methylation levels than FM. A total of 8479 differentially methylated genes (DMGs) and 3407 DMGs containing differentially methylated regions (DMRs) in the promoter regions between FM and SM were identified. After enrichment analysis, we found functionally relevant DMGs between FM and SM, including Kapca, Plcd3a, Plcd1, Pi3k, Tsp4b and Pgfrb in the hedgehog signaling pathway and phosphatidylinositol (PI)-related pathways. Due to the different methylation levels of these genes between FM and SM, the expression levels of Kapca, Plcd3a, Plcd1, Pi3k, and Tsp4b were higher in FM and Pgfrb was higher in SM. There were differences in the hedgehog signaling pathway and PI-related pathways between FM and SM. In SM, the cytokine-cytokine receptor interaction promoted focal adhesion, while ECM-receptor interactions promoted focal adhesion in FM. These results provide information regarding the difference between FM and SM in T. rubripes.
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8
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Dong J, Li J, Hu J, Sun C, Tian Y, Li W, Yan N, Sun C, Sheng X, Yang S, Shi Q, Ye X. Comparative Genomics Studies on the dmrt Gene Family in Fish. Front Genet 2020; 11:563947. [PMID: 33281869 PMCID: PMC7689362 DOI: 10.3389/fgene.2020.563947] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/16/2020] [Indexed: 01/15/2023] Open
Abstract
Doublesex and mab-3-related transcription factor (dmrt) genes are widely distributed across various biological groups and play critical roles in sex determination and neural development. Here, we applied bioinformatics methods to exam cross-species changes in the dmrt family members and evolutionary relationships of the dmrt genes based on genomes of 17 fish species. All the examined fish species have dmrt1-5 while only five species contained dmrt6. Most fish harbored two dmrt2 paralogs (dmrt2a and dmrt2b), with dmrt2b being unique to fish. In the phylogenetic tree, 147 DMRT are categorized into eight groups (DMRT1-DMRT8) and then clustered in three main groups. Selective evolutionary pressure analysis indicated purifying selections on dmrt1-3 genes and the dmrt1-3-2(2a) gene cluster. Similar genomic conservation patterns of the dmrt1-dmrt3-dmrt2(2a) gene cluster with 20-kb upstream/downstream regions in fish with various sex-determination systems were observed except for three regions with remarkable diversity. Synteny analysis revealed that dmrt1, dmrt2a, dmrt2b, and dmrt3-5 were relatively conserved in fish during the evolutionary process. While dmrt6 was lost in most species during evolution. The high conservation of the dmrt1-dmrt3-dmrt2(2a) gene cluster in various fish genomes suggests their crucial biological functions while various dmrt family members and sequences across fish species suggest different biological roles during evolution. This study provides a molecular basis for fish dmrt functional analysis and may serve as a reference for in-depth phylogenomics.
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Affiliation(s)
- Junjian Dong
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI Group, Shenzhen, China
| | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Wuhui Li
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Ningning Yan
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chengxi Sun
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xihui Sheng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI Group, Shenzhen, China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fisheries Resources Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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9
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Galagali H, Kim JK. The multifaceted roles of microRNAs in differentiation. Curr Opin Cell Biol 2020; 67:118-140. [PMID: 33152557 DOI: 10.1016/j.ceb.2020.08.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are major drivers of cell fate specification and differentiation. The post-transcriptional regulation of key molecular factors by microRNAs contributes to the progression of embryonic and postembryonic development in several organisms. Following the discovery of lin-4 and let-7 in Caenorhabditis elegans and bantam microRNAs in Drosophila melanogaster, microRNAs have emerged as orchestrators of cellular differentiation and developmental timing. Spatiotemporal control of microRNAs and associated protein machinery can modulate microRNA activity. Additionally, adaptive modulation of microRNA expression and function in response to changing environmental conditions ensures that robust cell fate specification during development is maintained. Herein, we review the role of microRNAs in the regulation of differentiation during development.
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Affiliation(s)
- Himani Galagali
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
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10
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Zucko D, Boris-Lawrie K. Circular RNAs Are Regulators of Diverse Animal Transcriptomes: One Health Perspective. Front Genet 2020; 11:999. [PMID: 33193584 PMCID: PMC7531264 DOI: 10.3389/fgene.2020.00999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Derived from linear (parental) precursor mRNA, circRNA are recycled exons and introns whose ends are ligated. By titrating microRNAs and RNA binding proteins, circRNA interconnect networks of competing endogenous RNAs. Without altering chromosomal DNA, circRNA regulates skeletal muscle development and proliferation, lactation, ovulation, brain development, and responses to infections and metabolic stress. This review integrates emerging knowledge of circRNA activity coming from genome-wide characterizations in many clades of animals. circRNA research addresses one of the main pillars of the One Health vision – to improve the health and productivity of food animals and generate translational knowledge in animal species.
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Affiliation(s)
- Dora Zucko
- Department of Veterinary and Biomedical Sciences, Veterinary Medicine Graduate Program, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, Veterinary Medicine Graduate Program, University of Minnesota Twin Cities, Saint Paul, MN, United States
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11
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Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age. Genes (Basel) 2020; 11:genes11020172. [PMID: 32041309 PMCID: PMC7073773 DOI: 10.3390/genes11020172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
Studies of the gene and miRNA expression profiles associated with the postnatal late growth, development, and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA sequencing (RNA-seq) and microRNA sequencing (miRNA-seq) analyses to determine the differentially expressed (DE) unigenes and miRNAs from skeletal muscle tissues at 1, 3, 5, and 10 years in sika deer. A total of 51,716 unigenes, 171 known miRNAs, and 60 novel miRNAs were identified based on four mRNA and small RNA libraries. A total of 2,044 unigenes and 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 1,946 unigenes and 4 miRNAs were differentially expressed between adult and adolescent sika deer, and 2,209 unigenes and 1 miRNAs were differentially expressed between aged and adult sika deer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DE unigenes and miRNA were mainly related to energy and substance metabolism, processes that are closely associate with the growth, development, and aging of skeletal muscle. We also constructed mRNA–mRNA and miRNA–mRNA interaction networks related to the growth, development, and aging of skeletal muscle. The results show that mRNA (Myh1, Myh2, Myh7, ACTN3, etc.) and miRNAs (miR-133a, miR-133c, miR-192, miR-151-3p, etc.) may play important roles in muscle growth and development, and mRNA (WWP1, DEK, UCP3, FUS, etc.) and miRNAs (miR-17-5p, miR-378b, miR-199a-5p, miR-7, etc.) may have key roles in muscle aging. In this study, we determined the dynamic miRNA and unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent miRNAs and unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth, and maintenance and will also provide valuable information for sika deer genetic breeding.
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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Li L, Mao A, Wang P, Ning G, Cao Y, Wang Q. Endodermal pouch-expressed dmrt2b is important for pharyngeal cartilage formation. Biol Open 2018; 7:bio.035444. [PMID: 30341107 PMCID: PMC6310889 DOI: 10.1242/bio.035444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pharyngeal pouches, a series of outpocketings derived from the foregut endoderm, are essential for craniofacial skeleton formation. However, the molecular mechanisms underlying endodermal pouch-regulated head cartilage development are not fully understood. In this study, we find that zebrafish dmrt2b, a gene encoding Doublesex- and Mab-3-related transcription factor, is specifically expressed in endodermal pouches and required for normal pharyngeal cartilage development. Loss of dmrt2b doesn't affect cranial neural crest (CNC) specification and migration, but leads to prechondrogenic condensation defects by reducing cxcl12b expression after CNC cell movement into the pharyngeal arches. Moreover, dmrt2b inactivation results in reduced proliferation and impaired differentiation of CNC cells. We also show that dmrt2b suppresses crossveinless 2 expression in endodermal pouches to maintain BMP/Smad signaling in the arches, thereby facilitating CNC cell proliferation and chondrogenic differentiation. This work provides insight into how transcription factors expressed in endodermal pouches regulate pharyngeal skeleton development through tissue-tissue interactions.
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Affiliation(s)
- Linwei Li
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Aihua Mao
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Wang
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Guozhu Ning
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Cao
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Wang
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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Pinto RA, Almeida-Santos J, Lourenço R, Saúde L. Identification of Dmrt2a downstream genes during zebrafish early development using a timely controlled approach. BMC DEVELOPMENTAL BIOLOGY 2018; 18:14. [PMID: 29914374 PMCID: PMC6006574 DOI: 10.1186/s12861-018-0173-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/25/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Dmrt2a is a zinc finger like transcription factor with several roles during zebrafish early development: left-right asymmetry, synchronisation of the somite clock genes and fast muscle differentiation. Despite the described functions, Dmrt2a mechanism of action is unknown. Therefore, with this work, we propose to identify Dmrt2a downstream genes during zebrafish early development. RESULTS We generated and validated a heat-shock inducible transgenic line, to timely control dmrt2a overexpression, and dmrt2a mutant lines. We characterised dmrt2a overexpression phenotype and verified that it was very similar to the one described after knockdown of this gene, with left-right asymmetry defects and desynchronisation of somite clock genes. Additionally, we identified a new phenotype of somite border malformation. We generated several dmrt2a mutant lines, but we only detected a weak to negligible phenotype. As dmrt2a has a paralog gene, dmrt2b, with similar functions and expression pattern, we evaluated the possibility of redundancy. We found that dmrt2b does not seem to compensate the lack of dmrt2a. Furthermore, we took advantage of one of our mutant lines to confirm dmrt2a morpholino specificity, which was previously shown to be a robust knockdown tool in two independent studies. Using the described genetic tools to perform and validate a microarray, we were able to identify six genes downstream of Dmrt2a: foxj1b, pxdc1b, cxcl12b, etv2, foxc1b and cyp1a. CONCLUSIONS In this work, we generated and validated several genetic tools for dmrt2a and identified six genes downstream of this transcription factor. The identified genes will be crucial to the future understanding of Dmrt2a mechanism of action in zebrafish.
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Affiliation(s)
- Rita Alexandra Pinto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - José Almeida-Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal.,Present address: Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Raquel Lourenço
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal.,Present address: CEDOC, NOVA Medical School, Universidade Nova de Lisboa, 1150-190, Lisboa, Portugal
| | - Leonor Saúde
- Instituto de Medicina Molecular e Instituto de Histologia e Biologia do Desenvolvimento, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal.
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15
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Ouyang H, Chen X, Li W, Li Z, Nie Q, Zhang X. Circular RNA circSVIL Promotes Myoblast Proliferation and Differentiation by Sponging miR-203 in Chicken. Front Genet 2018; 9:172. [PMID: 29868120 PMCID: PMC5964199 DOI: 10.3389/fgene.2018.00172] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 04/27/2018] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs), expressed abundantly and universally in various eukaryotes, are involved in growth and development of animals. Our previous study on circRNA sequencing revealed that circSVIL, an exonic circular, expressed differentially among skeletal muscle at 11 embryo age (E11), 16 embryo age (E16), and 1 day post-hatch (P1). In this study, we aim to investigate the effect of circSVIL on the development of skeletal muscle. We detected the expression level of circSVIL in embryonic leg muscle during E10 to P1. As a result, we found that circSVIL had a high expression level during late embryonic development of skeletal muscle. Through dual-luciferase assay, RNA immunoprecipitation and biotin-coupled miRNA pull down, we found chicken circSVIL could functions as miR-203 sponges and upregulated the mRNA level of c-JUN and MEF2C. In chicken, circSVIL could promote the proliferation and differentiation of myoblast, and antagonize the functions of miR-203. Altogether our data suggest that circSVIL promotes the embryonic skeletal muscle development by sequestering miR-203 in chicken.
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Affiliation(s)
- Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiaolan Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Weimin Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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16
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The dysregulated autophagy signaling is partially responsible for defective podocyte development in wt1a mutant zebrafish. AQUACULTURE AND FISHERIES 2018. [DOI: 10.1016/j.aaf.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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17
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Guo W, Xie B, Xiong S, Liang X, Gui JF, Mei J. miR-34a Regulates Sperm Motility in Zebrafish. Int J Mol Sci 2017; 18:E2676. [PMID: 29232857 PMCID: PMC5751278 DOI: 10.3390/ijms18122676] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/29/2017] [Accepted: 12/07/2017] [Indexed: 01/03/2023] Open
Abstract
Increasing attention has been focused on the role of microRNAs in post-transcription regulation during spermatogenesis. Recently, the miR-34 family has been shown to be involved in the spermatogenesis, but the clear function of the miR-34 family in spermatogenesis is still obscure. Here we analyzed the function of miR-34a, a member of the miR-34 family, during spermatogenesis using miR-34a knockout zebrafish generated by the clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) system. miR-34a knockout zebrafish showed no obvious defects on testis morphology and sperm quantity. However, we found a significant increase in progressive sperm motility that is one of the pivotal factors influencing in vitro fertilization rates, in the knockout zebrafish. Moreover, breeding experiments showed that, when miR-34a-knockout male zebrafish mated with the wide-type females, they had a higher fertilization rate than did the wide-type males. Glycogen synthase kinase-3a (gsk3a), a potential sperm motility regulatory gene was predicted to be targeted by miR-34a, which was further supported by luciferase reporter assays, since a significant decrease of luciferase activity was detected upon ectopic overexpression of miR-34a. Our findings suggest that miR-34a downregulates gsk3a by targeting its 3' untranslated region, and miR-34a/gsk3a interaction modulates sperm motility in zebrafish. This study will help in understanding in the role of the miR-34 family during spermatogenesis and will set paths for further studies.
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Affiliation(s)
- Wenjie Guo
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Binyue Xie
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shuting Xiong
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xufang Liang
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jian-Fang Gui
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jie Mei
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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18
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Mok GF, Lozano-Velasco E, Münsterberg A. microRNAs in skeletal muscle development. Semin Cell Dev Biol 2017; 72:67-76. [PMID: 29102719 DOI: 10.1016/j.semcdb.2017.10.032] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
A fundamental process during both embryo development and stem cell differentiation is the control of cell lineage determination. In developing skeletal muscle, many of the diffusible signaling molecules, transcription factors and more recently non-coding RNAs that contribute to this process have been identified. This has facilitated advances in our understanding of the molecular mechanisms underlying the control of cell fate choice. Here we will review the role of non-coding RNAs, in particular microRNAs (miRNAs), in embryonic muscle development and differentiation, and in satellite cells of adult muscle, which are essential for muscle growth and regeneration. Some of these short post-transcriptional regulators of gene expression are restricted to skeletal muscle, but their expression can also be more widespread. In addition, we discuss a few examples of long non-coding RNAs, which are numerous but much less well understood.
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Affiliation(s)
- Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Estefania Lozano-Velasco
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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