51
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Huang J, Zheng Q, Wang S, Wei X, Li F, Ma Y. High-Throughput RNA Sequencing Reveals NDUFC2-AS lncRNA Promotes Adipogenic Differentiation in Chinese Buffalo ( Bubalus bubalis L). Genes (Basel) 2019; 10:genes10090689. [PMID: 31500202 PMCID: PMC6770997 DOI: 10.3390/genes10090689] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
The buffalo (Bubalus bubalis L.) is prevalent in China and the increasing demand for meat production has changed its role from being a beast of burden to a meat source. The low fat deposition level has become one of the main barriers for its use in meat production. It is urgent to reveal factors involved in fat deposition in buffalo. This study performed RNA sequencing to investigate both long noncoding RNAs (lncRNAs) and mRNAs of adipose tissues in young and adult buffalos. A total of 124 lncRNAs and 2008 mRNAs showed differential expression patterns between young and adult samples. Coexpression analysis and functional enrichment revealed 585 mRNA–lncRNA pairs with potential function in fat deposition. After validation by qRT-PCR, we focused on a lncRNA transcribed from the ubiquinone oxidoreductase subunit C2 (NDUFC2) antisense (AS) strand which showed high correlation with thyroid hormone responsive protein (THRSP). NDUFC2-AS lncRNA is highly expressed in adipose tissue and maturation adipocytes and mainly exists in the nucleus. Functional assays demonstrated that NDUFC2-AS lncRNA promotes adipogenic differentiation by upregulating the expression levels of THRSP and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo. These results indicate that NDUFC2-AS lncRNA promotes fat deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Qiuzhi Zheng
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Shuzhe Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Fen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China.
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52
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Bonnet S, Boucherat O, Paulin R, Wu D, Hindmarch CCT, Archer SL, Song R, Moore JB, Provencher S, Zhang L, Uchida S. Clinical value of non-coding RNAs in cardiovascular, pulmonary, and muscle diseases. Am J Physiol Cell Physiol 2019; 318:C1-C28. [PMID: 31483703 DOI: 10.1152/ajpcell.00078.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although a majority of the mammalian genome is transcribed to RNA, mounting evidence indicates that only a minor proportion of these transcriptional products are actually translated into proteins. Since the discovery of the first non-coding RNA (ncRNA) in the 1980s, the field has gone on to recognize ncRNAs as important molecular regulators of RNA activity and protein function, knowledge of which has stimulated the expansion of a scientific field that quests to understand the role of ncRNAs in cellular physiology, tissue homeostasis, and human disease. Although our knowledge of these molecules has significantly improved over the years, we have limited understanding of their precise functions, protein interacting partners, and tissue-specific activities. Adding to this complexity, it remains unknown exactly how many ncRNAs there are in existence. The increased use of high-throughput transcriptomics techniques has rapidly expanded the list of ncRNAs, which now includes classical ncRNAs (e.g., ribosomal RNAs and transfer RNAs), microRNAs, and long ncRNAs. In addition, splicing by-products of protein-coding genes and ncRNAs, so-called circular RNAs, are now being investigated. Because there is substantial heterogeneity in the functions of ncRNAs, we have summarized the present state of knowledge regarding the functions of ncRNAs in heart, lungs, and skeletal muscle. This review highlights the pathophysiologic relevance of these ncRNAs in the context of human cardiovascular, pulmonary, and muscle diseases.
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Affiliation(s)
- Sébastien Bonnet
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Olivier Boucherat
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Roxane Paulin
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Danchen Wu
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Charles C T Hindmarch
- Queen's Cardiopulmonary Unit, Translational Institute of Medicine, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Stephen L Archer
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Rui Song
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Joseph B Moore
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Steeve Provencher
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Shizuka Uchida
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky.,Cardiovascular Innovation Institute, University of Louisville, Louisville, Kentucky
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53
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Gao Y, Li S, Lai Z, Zhou Z, Wu F, Huang Y, Lan X, Lei C, Chen H, Dang R. Analysis of Long Non-Coding RNA and mRNA Expression Profiling in Immature and Mature Bovine ( Bos taurus) Testes. Front Genet 2019; 10:646. [PMID: 31333723 PMCID: PMC6624472 DOI: 10.3389/fgene.2019.00646] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/18/2019] [Indexed: 01/08/2023] Open
Abstract
Testis development and spermatogenesis are strictly regulated by numbers of genes and non-coding genes. However, long non-coding RNAs (lncRNAs) as key regulators in multitudinous biological processes have not been systematically identified in bovine testes during sexual maturation. In this study, we comprehensively analyzed lncRNA and mRNA expression profiling of six bovine testes at 3 days after birth and 13 months by RNA sequencing. 23,735 lncRNAs and 22,118 mRNAs were identified, in which 540 lncRNAs (P-value < 0.05) and 3,525 mRNAs (P-adjust < 0.05) were significantly differentially expressed (DE) between two stages. Correspondingly, the results of RT-qPCR analysis showed well correlation with the transcriptome data. Moreover, GO and KEGG enrichment analyses showed that DE genes and target genes of DE lncRNAs were enriched in spermatogenesis. Furthermore, we constructed lncRNA–gene interaction networks; consequently, 15 DE lncRNAs and 12 cis-target genes were involved. The target genes (SPATA16, TCF21, ZPBP, PACRG, ATP8B3, COMP, ACE, and OSBP2) were found associated with bovine sexual maturation. In addition, the expression of lncRNAs and cis-target genes was detected in bovine Leydig cells, Sertoli cells, and spermatogonia. Our study identified and analyzed lncRNAs and mRNAs in testis tissues, suggesting that lncRNAs may regulate testis development and spermatogenesis. Our findings provided new insights for further investigation of biological function in bovine lncRNA.
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Affiliation(s)
- Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shipeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhenyu Lai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zihui Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fei Wu
- 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
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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54
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Ben-Arye T, Levenberg S. Tissue Engineering for Clean Meat Production. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00046] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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55
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ANGPTL8 regulates adipocytes differentiation and adipogenesis in bovine. Gene 2019; 707:93-99. [PMID: 31048067 DOI: 10.1016/j.gene.2019.04.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/20/2019] [Accepted: 04/17/2019] [Indexed: 12/17/2022]
Abstract
The formation of bovine adipose tissue involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms are largely unknown. Angiopoietin-like protein 8 (ANGPTL8) has been reported to be involved in the development of adipose tissue; however, the mechanism of adipogenesis which is regulated by ANGPTL8 has not been revealed in cattle. In this study, RT-qPCR and Oil Red O staining were performed to detect the expression of ANGPTL8 and adipocyte differentiation in bovine. We found that ANGPTL8 had a high expression level in adipose tissue and that the expression pattern was consistent with those of PPARγ, C/EBPα and LPL which are key regulators and transcription factors involved in preadipocyte differentiation and adipogenesis. The overexpression of ANGPTL8 by the adenovirus vector promoted lipid droplet formation in adipocytes. Thus, we speculated that ANGPTL8 could significantly enhance lipid deposition. Moreover, the expression of LPL and SREBP1, key genes inhibiting adipogenesis, was significantly decreased by ANGPTL8 overexpression. These results suggested that ANGPTL8 promotes adipocyte differentiation. In conclusion, we consider that ANGPTL8 regulates adipocyte differentiation and adipogenesis in bovine.
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56
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Zhang Y, Tao Y, Liao Q. Long noncoding RNA: a crosslink in biological regulatory network. Brief Bioinform 2019; 19:930-945. [PMID: 28449042 DOI: 10.1093/bib/bbx042] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil. In this review, we will outline well-known associations between lncRNAs and other biological molecules, demonstrate the diverse bioinformatics approaches applied in prediction and analysis of lncRNA interaction and perform a case study for lncRNA linc00460 to concretely decipher the lncRNA regulatory network.
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Affiliation(s)
- Yuwei Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Tao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
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57
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Peng S, Song C, Li H, Cao X, Ma Y, Wang X, Huang Y, Lan X, Lei C, Chaogetu B, Chen H. Circular RNA SNX29 Sponges miR-744 to Regulate Proliferation and Differentiation of Myoblasts by Activating the Wnt5a/Ca 2+ Signaling Pathway. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:481-493. [PMID: 31051333 PMCID: PMC6495097 DOI: 10.1016/j.omtn.2019.03.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/16/2022]
Abstract
Myogenesis is a complex and precisely orchestrated process that is highly regulated by several non-coding RNAs and signal pathways. Circular RNAs (circRNAs) represent a novel subclass of endogenous non-coding RNAs that have been identified in multiple species and tissues and play a vital role in post-transcriptional regulation in eukaryotes, but the precise molecular mechanism of action remains largely unknown. Here, we screened a candidate circRNA derived from the SNX29 gene, termed circSNX29 from our previous circRNAs sequencing data of bovine skeletal muscle, and further characterized its regulation and function during muscle development. The overexpression of circSNX29 facilitated myoblasts differentiation and inhibited cell proliferation. Computational analysis using RNAhybrid showed the potential for circSNX29 to sponge to miR-744 with nine potential binding sites. We tested this via a luciferase screening assay and found that circSNX29 directly interacted with miR-744 and downregulation of miR-744 efficiently reversed the suppression of Wnt5a and CaMKIIδ. Importantly, through the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis, Fluo-4, AM, cell permeant-calcium ion fluorescent probing, and western blotting assays, we found that overexpression of Wnt5a and circSNX29 activated the non-canonical Wnt5a/Ca2+ pathway. Overall, the evidence generated by our study elucidates the regulatory mechanisms of circSNX29 to function as a sponge for miRNA-744 in bovine primary myoblasts.
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Affiliation(s)
- Shujun Peng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chengchuang Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiukai Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yilei Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaogang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, 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 712100, 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 712100, 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 712100, China
| | - Buren Chaogetu
- Animal Disease Control Center of Haixi Mongolian and Tibetan Autonomous Prefecture, Delingha 817000, 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 712100, China.
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58
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Liu M, Li B, Peng W, Ma Y, Huang Y, Lan X, Lei C, Qi X, Liu GE, Chen H. LncRNA-MEG3 promotes bovine myoblast differentiation by sponging miR-135. J Cell Physiol 2019; 234:18361-18370. [PMID: 30887511 DOI: 10.1002/jcp.28469] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/09/2019] [Accepted: 02/19/2019] [Indexed: 12/19/2022]
Abstract
Long noncoding RNA maternally expressed gene 3 (lncRNA-MEG3) is an important regulator in multiple biological functions. However, lncRNA-MEG3's function in cattle growth and regulatory mechanism on bovine skeletal muscle development has not yet been well studied. In this project, we first investigated lncRNA-MEG3's expression profile and detected that it was highly expressed in bovine skeletal muscle tissue and its RNA level was kept increasingly during the early phase of bovine primary myoblast differentiation. Using luciferase reporter assays, we identified the lncRNA-MEG3 core promoter containing putative transcription factor binding site for myocyte enhancer factor 2C (MEF2C). Interestingly, we found that LncRNA-MEG3 could significantly upregulate and downregulate myosin heavy chain ( MHC), myogenin ( MyoG), and MEF2C through overexpression and RNAi strategies, respectively. Using luciferase reporter assays, we also verified lncRNA-MEG3 as a miR-135 sponge. Overexpression of miR-135 markedly inhibited the wild type of lncRNA-MEG3, but not the mutant lncRNA-MEG3 reporter. The luciferase activity of miR-135 sensor could be rescued by lncRNA-MEG3 via competing for miRNA-135. In addition, the luciferase activity of MEF2C was significantly upregulated by the wild type of lncRNA-MEG3. This study, for the first time, revealed that lncRNA-MEG3 could promote bovine skeletal muscle differentiation via interacting with miRNA-135 and MEF2C. The results were valuable for further studies and applications of lncRNA related roles in beef molecular breeding.
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Affiliation(s)
- Mei Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China.,Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, Maryland
| | - Bo Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Wenwen Peng
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Yilei Ma
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Xinglei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, Maryland
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
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59
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Yue B, Li H, Liu M, Wu J, Li M, Lei C, Huang B, Chen H. Characterization of lncRNA-miRNA-mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle. Front Genet 2019; 10:91. [PMID: 30842787 PMCID: PMC6391848 DOI: 10.3389/fgene.2019.00091] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/29/2019] [Indexed: 01/14/2023] Open
Abstract
There is growing evidence that non-coding RNAs are emerging as critical regulators of skeletal muscle development. In order to reveal their functional roles and regulatory mechanisms, we constructed a lncRNA–miRNA–mRNA network according to the ceRNA (competitive endogenous RNA) theory, using our high-throughput sequencing data. Subsequently, the network analysis, GO (Gene Ontology) analysis, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed for functional annotation and exploration of lncRNA ceRNAs. The results uncovered a scale-free characteristics network which exhibited high functional specificity for bovine skeletal muscle development: co-expression lncRNAs were significantly enriched in muscle development related biological processes and the Wnt signaling pathway. Furthermore, GSEA (Gene Set Enrichment Analysis) indicated that the risk score has a tendency to associate with myogenesis, and differentially expressed RNAs were validated by qPCR, further confirming the credibility of our network. In summary, this study provides insights into lncRNA-mediated ceRNA function and mechanisms in bovine skeletal muscle development and will expand our understanding of lncRNA biology in mammals.
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Affiliation(s)
- Binglin Yue
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Mei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiyao Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingxun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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60
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Zhang M, Li F, Sun JW, Li DH, Li WT, Jiang RR, Li ZJ, Liu XJ, Han RL, Li GX, Wang YB, Tian YD, Kang XT, Sun GR. LncRNA IMFNCR Promotes Intramuscular Adipocyte Differentiation by Sponging miR-128-3p and miR-27b-3p. Front Genet 2019; 10:42. [PMID: 30804984 PMCID: PMC6378276 DOI: 10.3389/fgene.2019.00042] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Poultry meat quality is affected by many factors, among which intramuscular fat (IMF) is predominant. IMF content affects the tenderness, juiciness, and flavor of chicken. An increasing number of studies are focusing on the functions of lncRNAs in adipocyte differentiation. However, little is known about lncRNAs associated with intramuscular adipocyte differentiation. In the present study, we focused on an up-regulated lncRNA during intramuscular adipogenetic differentiation, which we named intramuscular fat-associated long non-coding RNA (IMFNCR). IMFNCR promotes intramuscular adipocyte differentiation. In-depth analyses showed that IMFNCR acts as a molecular sponge for miR-128-3p and miR-27b-3p and that PPARG is a direct target of miR-128-3p and miR-27b-3p in chicken. High-fat and high-protein diet inhibited chicken IMFNCR level in vivo. Moreover, IMFNCR level was positively correlated with PPARG mRNA level in chicken breast muscle tissues, a vital corollary to ceRNA function. Altogether, our research showed that IMFNCR acts as a ceRNA to sequester miR-128-3p and miR-27b-3p, leading to heightened PPARG expression, and thus promotes intramuscular adipocyte differentiation. Taken together, our findings may contribute to a more thorough understanding of chicken IMF deposition and the improvement of poultry meat quality.
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Affiliation(s)
- Meng Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.,The First Bethune Hospital, Jilin University, Changchun, China
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Jun-Wei Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Dong-Hua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Wen-Ting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Rui-Rui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Zhuan-Jian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Xiao-Jun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Rui-Li Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Guo-Xi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Yan-Bin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Ya-Dong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Xiang-Tao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Gui-Rong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
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61
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Lu C, Xing Y, Cai H, Shi Y, Liu J, Huang Y. Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos). BMC Genomics 2019; 20:36. [PMID: 30634898 PMCID: PMC6330444 DOI: 10.1186/s12864-018-5422-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. For example, human (Homo sapiens) (96,308 vs. 20,376) and mouse (Mus musculus) (87,774 vs. 22,630) have more lncRNA genes than protein-coding genes in the NONCODEv5 database. Recently, mammalian lncRNAs were reported to play critical roles in immune response to influenza A virus infections. Such observation inspired us to identify lncRNAs related to immune response to influenza A virus in duck, which is the most important natural host of influenza A viruses. RESULTS We explored features of 62,447 lncRNAs from human, mouse, chicken, zebrafish and elegans, and developed a pipeline to identify lncRNAs using the identified features with transcriptomic data. We then collected 151,970 assembled transcripts from RNA-Seq data of 21 individuals from three tissues and annotated 4094 duck lncRNAs. Comparing to duck protein-coding transcripts, we found that 4094 lncRNAs had smaller number of exons (2.4 vs. 10.2) and longer length of transcripts (1903.0 bp vs. 1686.9 bp) on average. Among them, 3586 (87.6%) lncRNAs located in intergenic regions and 619 lncRNAs showed differential expression in ducks infected by H5N1 virus when compared to control individuals. 58 lncRNAs were involved into two co-expressional modules related to anti-influenza A virus immune response. Moreover, we confirmed that eight lncRNAs showed remarkably differential expression both in vivo (duck individuals) and in vitro (duck embryo fibroblast cells, DEF cells) after infected with H5N1 viruses, implying they might play important roles in response to influenza A virus infection. CONCLUSIONS This study presented an example to annotate lncRNA in new species based on model species using transcriptome data. These data and analysis provide information for duck lncRNAs' function in immune response to influenza A virus.
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Affiliation(s)
- Chang Lu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanling Xing
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Han Cai
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Yirong Shi
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yinhua Huang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.
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Li M, Lu X, Xia H, Zhang C, Wang X, Chen Z, Zhang H, Qu K, Huang B, Moore S, Mao Y, Yang Z. In-depth characterization of the pituitary transcriptome in Simmental and Chinese native cattle. Domest Anim Endocrinol 2019; 66:35-42. [PMID: 30391830 DOI: 10.1016/j.domaniend.2018.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/10/2018] [Accepted: 09/21/2018] [Indexed: 12/15/2022]
Abstract
The pituitary gland is a key endocrine organ responsible for growth and development. To get closer to understanding important molecular mechanisms at work in the bovine pituitary and identifying the core genes controlling growth, in the present study we have analyzed the transcriptome profiling of the pituitary glands of two cattle breeds (Wenshan and Simmental cattle) with extreme growth differences using high-throughput RNA sequencing. Our study revealed that the overall gene expression levels are quite similar between the two breeds. A total of 18,065 annotated genes were identified, which accounted for 85% of the annotated genes in cattle. The five most abundant hormone genes (GH, PRL, POMC, CGA, and LHB) were relatively stable in both breeds, indicating their pivotal roles in maintaining the basic functions of the pituitary. In addition, 105 genes were identified as differentially expressed between Wenshan and Simmental pituitary glands, including 83 known and 22 novel genes. Functional association analyses of the differentially expressed genes between the breeds revealed 60 enriched gene ontology terms and 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Interestingly, the most enriched KEGG pathway, cell adhesion molecules, can modulate pituitary hormone secretion by cell-cell contact. Our findings demonstrated that SYTL2, SLC38A4, and NCAM2 are new candidates for crucial functions in the secretory pathways of the pituitary gland. These results will further understanding of the important molecular mechanisms at work in the bovine pituitary.
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Affiliation(s)
- Mingxun Li
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Xubin Lu
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Hailei Xia
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Chenglong Zhang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Zhi Chen
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Huimin Zhang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - Stephen Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia
| | - Yongjiang Mao
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China
| | - Zhangping Yang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou 225002, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225002, China.
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A novel long non-coding RNA, lncKBTBD10, involved in bovine skeletal muscle myogenesis. In Vitro Cell Dev Biol Anim 2018; 55:25-35. [PMID: 30465303 DOI: 10.1007/s11626-018-0306-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/25/2018] [Indexed: 12/27/2022]
Abstract
Accumulating evidence suggests that long non-coding RNAs (lncRNAs) play a crucial role in regulating skeletal muscle myogenesis, a highly coordinated multistep biological process. However, most studies of lncRNAs have focused on humans, mouse, and other model animals. In this study, we identified a novel lncRNA, named lncKBTBD10, located in the nucleus and involved in the proliferation and differentiation of bovine skeletal muscle satellite cells. Prediction of coding potential and in vitro translation system illustrated that lncKBTBD10 has no encoding capability. With the process of myogenic differentiation, the expression of lncKBTBD10 gradually increased. To elucidate the functions of lncKBTBD10 during myogenesis, the gain/loss-of-function experiments were performed. Results showed that the proliferation and differentiation of bovine skeletal muscle satellite cells were all suppressed whether lncKBTBD10 was knocked down or over-expressed. Furthermore, we found that lncKBTBD10 may affect its proximity gene KBTBD10 to involve in myogenesis. Results indicated that the protein level of KBTBD10 was all diminished after induced differentiation for 2 d in differentiation medium (DM2) whether lncKBTBD10 was knocked down or over-expressed. It may support why the altering of lncKBTBD10 can suppress the proliferation and differentiation of bovine skeletal muscle satellite cells. In short, our study elucidated that lncKBTBD10 could induce a decrease of KBTBD10 protein and further to affect bovine skeletal muscle myogenesis. The novel identified lncKBTBD10 may provide a reference for lncRNAs involved in myogenesis of bovine skeletal muscle.
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Zheng X, Ning C, Zhao P, Feng W, Jin Y, Zhou L, Yu Y, Liu J. Integrated analysis of long noncoding RNA and mRNA expression profiles reveals the potential role of long noncoding RNA in different bovine lactation stages. J Dairy Sci 2018; 101:11061-11073. [PMID: 30268606 DOI: 10.3168/jds.2018-14900] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
Abstract
Long noncoding RNA (lncRNA) play a critical role in mammary development and breast cancer biology. Despite their important role in the mammary gland, little is known of the roles of lncRNA in bovine lactation, particularly regarding the molecular processes underlying it. To characterize the role of lncRNA in bovine lactation, 4 samples of Holstein cow mammary gland tissue at peak and late lactation stages were examined after biopsy. We then profiled the transcriptome of the mammary gland using RNA sequencing technology. Further, functional lncRNA-mRNA coexpression pairs were constructed to infer the function of lncRNA using a generalized linear model, followed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. More than 1,000 putative lncRNA were identified, 117 of which were differentially expressed between peak and late lactation stages. Bovine lncRNA were shorter, with fewer exon numbers, and expressed at significantly lower levels than protein-coding genes. Seventy-two differentially expressed (DE) lncRNA were coexpressed with 340 different protein-coding genes. The KEGG pathway analysis showed that target mRNA for DE lncRNA were mainly related to lipid and glucose metabolism, including the peroxisome proliferator-activated receptors and 5' adenosine monophosphate-activated protein kinase signaling pathways. Further bioinformatics and integrative analyses revealed that 12 DE lncRNA potentially played important roles in bovine lactation. Our findings provide a valuable resource for future bovine transcriptome studies, facilitate the understanding of bovine lactation biology, and offer functional information for cattle lactation.
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Affiliation(s)
- X Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - C Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - P Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - W Feng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Y Jin
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - L Zhou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Y Yu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - J Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Du J, Zhang P, Zhao X, He J, Xu Y, Zou Q, Luo J, Shen L, Gu H, Tang Q, Li M, Jiang Y, Tang G, Bai L, Li X, Wang J, Zhang S, Zhu L. MicroRNA-351-5p mediates skeletal myogenesis by directly targeting lactamase-β and is regulated by lnc-mg. FASEB J 2018; 33:1911-1926. [PMID: 30216112 DOI: 10.1096/fj.201701394rrr] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Skeletal muscle is an important and complex organ with a variety of functions in humans and animals. Skeletal myogenesis is a multistep and complex process, and increasing evidence suggests that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) play critical roles in skeletal myogenesis. In this study the expression of miR-351-5p is dynamically regulated during skeletal myogenesis in vitro and in vivo. Cell-counting kit-8, qRT-PCR, and EdU immunofluorescence analysis showed that miR-351-5p overexpression promoted the proliferation and inhibited the differentiation of C2C12 myoblast, whereas inhibition of miR-351-5p had the opposite effect. In addition, miR-351-5p mediated the regulation of muscle fiber type transition in vivo. In vitro, loss of miR-351-5p in muscle tissues promoted muscle hypertrophy and increased slow-twitch fibers in the gastrocnemius muscles of mice. Luciferase reporter assay and functional analyses demonstrated that lactamase β ( LACTB) is a direct target of miR-351-5p involved in the regulation of skeletal myogenesis. Expression levels of a myogenesis-associated lncRNA ( lnc-mg) correlated negatively with miR-351-5p and positively with LACTB during C2C12 myoblast proliferation and differentiation. Further analyses showed that lnc-mg acted as a molecular sponge for miR-351-5p, demonstrating its involvement in the negative regulation of LACTB by miR-351-5p during skeletal myogenesis. These findings indicate that miRNA-351-5p functions in skeletal myogenesis by targeting LACTB and is regulated by lnc-mg, supporting the role of the competing endogenous RNA network in skeletal myogenesis.-Du, J., Zhang, P., Zhao, X., He, J., Xu, Y., Zou, Q., Luo, J., Shen, L., Gu, H., Tang, Q., Li, M., Jiang, Y., Tang, G., Bai, L., Li, X., Wang, J., Zhang, S., Zhu, L. MicroRNA-351-5p mediates skeletal myogenesis by directly targeting lactamase β and is regulated by lnc-mg.
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Affiliation(s)
- Jingjing Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Peiwen Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xue Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jin He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qin Zou
- College of Life and Science, Sichuan Agricultural University, Chengdu, China; and
| | - Jia Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hao Gu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanzhi Jiang
- College of Life and Science, Sichuan Agricultural University, Chengdu, China; and
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lin Bai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Rongchang, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Jia W, Xu B, Wu J. Circular RNA expression profiles of mouse ovaries during postnatal development and the function of circular RNA epidermal growth factor receptor in granulosa cells. Metabolism 2018; 85:192-204. [PMID: 29634953 DOI: 10.1016/j.metabol.2018.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
Abstract
PURPOSE Circular RNAs (circRNAs) are a class of noncoding RNAs that can regulate gene expression at the post-transcriptional level. The contribution of circRNAs in the regulation of granulosa cells (GCs) functions is not yet clear. The aim of this study was to analyze circRNA expression in adult and neonate ovaries, uncover the biological roles of circ_0002861 (circEGFR) and identify the mechanism by which it modulates follicular development. BASIC PROCEDURES The circRNA expression profiles of adult and neonatal mouse ovaries were explored by high-throughput sequencing. The function of circEGFR was measured by RNA fluorescence in situ hybridization, overexpression, knockdown, RNA immunoprecipitation and luciferase reporter assays in GCs. MAIN FINDINGS Numerous differentially expressed circRNAs were identified in adult and neonatal ovaries. Through circRNAs expression patterns and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, estrogen signaling was found to be upregulated in adult ovaries compared with neonate ovaries. Further analysis revealed that the expression of circEGFR (circ_0002861, ID: mmu_circ_0002861 in circBase) was increased in adult ovaries compared with neonate ovaries. circEGFR is formed by splicing from exons 14 and 15 of the epidermal growth factor receptor (EGFR) gene to produce a covalently linked 249-nucleotide circRNA. Overexpression of circEGFR increased estradiol (E2) production and GCs growth, whereas circEGFR knockdown enhanced progesterone production and inhibited (E2) secretion by GCs. Bioinformatic screening identified several binding sites for miR-125a-3p in the circEGFR sequence. RNA immunoprecipitation and luciferase reporter assays demonstrated that circEGFR may act as a sponge for miR-125a-3p, thus modulating Fyn expression. PRINCIPAL CONCLUSIONS These findings illustrate that circEGFR may play a vital role in ovarian GCs by modulating Fyn via competitive binding with miR-125a-3p. Our results suggest potential applications of circEGFR in reproductive and steroid-related disorder therapy.
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Affiliation(s)
- Wenchao Jia
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Xu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China; Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China.
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circFGFR4 Promotes Differentiation of Myoblasts via Binding miR-107 to Relieve Its Inhibition of Wnt3a. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:272-283. [PMID: 29858062 PMCID: PMC5992882 DOI: 10.1016/j.omtn.2018.02.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/25/2018] [Accepted: 02/27/2018] [Indexed: 12/19/2022]
Abstract
Muscle development is regulated under a series of complicate processes, and non-coding RNAs, such as microRNAs (miRNAs) and circular RNAs (circRNAs), have been reported to play important roles in regulating myoblast proliferation and differentiation. We found that miR-107 expression was high in skeletal muscle of Qinchuan cattle. Overexpression of miR-107 inhibited bovine myoblasts differentiation and protected cells from apoptosis. Wnt3a was identified as a target of miR-107 by luciferase activity, real-time qPCR, and western blotting assays. Knockdown of Wnt3a inhibited bovine myoblasts differentiation and apoptosis, and this effect was similar to miR-107 overexpression. We also found circFGFR4 to promote myoblasts differentiation and to induce cell apoptosis. Via luciferase screening and RNA pull-down assays, circFGFR4 was observed to sponge miR-107. Overexpression of circFGFR4 increased the expression of Wnt3a, whereas this effect was abolished by miR-107. These results demonstrated that circFGFR4 binding miR-107 promotes cell differentiation via targeting Wnt3a in bovine primary myoblasts.
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68
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Li H, Wei X, Yang J, Dong D, Huang Y, Lan X, Plath M, Lei C, Qi X, Bai Y, Chen H. Developmental transcriptome profiling of bovine muscle tissue reveals an abundant GosB that regulates myoblast proliferation and apoptosis. Oncotarget 2018; 8:32083-32100. [PMID: 28404879 PMCID: PMC5458270 DOI: 10.18632/oncotarget.16644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/28/2017] [Indexed: 01/20/2023] Open
Abstract
The formation of bovine skeletal muscle involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms underlying differences in meat quality are largely unknown. We conducted transcriptome analysis of bovine muscle tissues to compare gene expression profiles between embryonic and adult stages. Total RNAs from skeletal muscle of Qinchuan cattle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using the Ribo-Zero RNA sequencing (RNA-Seq) method. We found a total of 19,695 genes to be expressed in fetal and adult stages, whereby 3,299 were expressed only in fetal, and 433 only in adult tissues. We characterized the role of a candidate gene (GosB), which was highly (but differentially) expressed in embryonic and adult skeletal muscle tissue. GosB increased the number of myoblasts in the S-phase of the cell cycle, and decreased the proportion of cells in the G0/G1 phase. GosB promoted the proliferation of myoblasts and protected them from apoptosis via regulating Bcl-2 expression and controlling the intracellular calcium concentration. Modulation of GosB expression in muscle tissue may emerge as a potential target in breeding strategies attempting to alter myoblast numbers in cattle.
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Affiliation(s)
- Hui Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xuefeng Wei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiameng Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dong Dong
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xinglei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan 463700, China
| | - Yueyu Bai
- Animal Health Supervision of Henan Province, Bureau of Animal Husbandry of Henan province, Zhengzhou, Henan 450008, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
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Long Noncoding RNA Sponges miR-454 to Promote Osteogenic Differentiation in Maxillary Sinus Membrane Stem Cells. IMPLANT DENT 2018; 26:178-186. [PMID: 28301382 DOI: 10.1097/id.0000000000000569] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Although increasing evidence has shown that long noncoding RNAs (lncRNAs) play an important regulatory role in pluripotency and differentiation of mesenchymal stem cells, little is known about the role of lncRNA in maxillary sinus membrane stem cells (MSMSCs). The goal of this study was to investigate the expression profile and function of lncRNAs on osteogenic differentiation of MSMSCs. MATERIALS AND METHODS By using lncRNA microarray, we identify a novel osteogenesis differentiation-related lncRNA of MSMSCs (lncRNA-MODR). The functional role of lncRNA-MODR in regulating osteogenesis was evaluated by quantitative real-time polymerase chain reaction, western blot, and alizarin red staining. Bioinformatic analyses of the predicted target genes (gene ontology, pathway, and network analysis) were applied for further study of lncRNA-MODR. RESULTS We show that lncRNA-MODR is gradually upregulated during osteogenic differentiation. lncRNA-MODR overexpression upregulated, whereas lncRNA-MODR silencing decreased the expression of the osteogenic key marker, runt-related transcription factor 2 (RUNX2). In-depth analyses showed that lncRNA-MODR acts as a molecular sponge for microRNA-454 (miR-454) and that prevents RUNX2 from mi-454-mediated suppression. CONCLUSION The lncRNAs act as a competing endogenous RNA to sequester microRNA-454 (miR-454), leading to heightened RUNX2 expression and thus promotes osteogenesis of MSMSCs.
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Li CY, Li X, Liu Z, Ni W, Zhang X, Hazi W, Ma Q, Zhang Y, Cao Y, Qi J, Yao Y, Feng L, Wang D, Hou X, Yu S, Liu L, Zhang M, Hu S. Identification and characterization of long non-coding RNA in prenatal and postnatal skeletal muscle of sheep. Genomics 2018; 111:133-141. [PMID: 29366530 DOI: 10.1016/j.ygeno.2018.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/14/2017] [Accepted: 01/15/2018] [Indexed: 11/28/2022]
Abstract
lncRNAs are a class of transcriptional RNA molecules of >200 nucleotides in length. However, the overall expression pattern and function of lncRNAs in sheep muscle is not clear. Here, we identified 1566 lncRNAs and 404 differentially expressed lncRNAs in sheep muscle from prenatal (110 days of fetus) and postnatal (2 to 3 years old of adult sheep) developmental stages by using RNA-seq technology. Several lncRNAs were identified by using RT-PCR and DNA sequencing. The expression levels of several lncRNAs were confirmed by qRT-PCR. We analyzed the effect of lncRNAs that act cis to the target genes. lncRNA targeting genes were involved in signaling pathways associated with growth and development of muscle by GO and KEGG enrichment analysis. Through our study, we provide a comprehensive expression profile of muscle lncRNAs in sheep, which provides valuable resources for further understanding genetic regulation of muscle growth and development from the perspective of lncRNA.
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Affiliation(s)
- Cun-Yuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Qiman Ma
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yunfeng Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jiangjiao Qi
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Lin Feng
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
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Abstract
Bone regeneration is very important for the recovery of some diseases including osteoporosis and bone fracture trauma. It is a multiple-step- and multiple-gene-involved complex process, including the matrix secretion and calcium mineralization by osteoblasts differentiated from mesenchymal stem cells (MSCs) and the absorption of calcium and phosphorus by osteoclasts differentiated from hematopoietic stem cells. Long noncoding RNAs (lncRNAs) are a family of transcripts longer than 200 nt without or with very low protein-coding potential. Recent studies have demonstrated that lncRNAs are widely involved in the regulation of lineage commitment and differentiation of stem cells through multiple mechanisms. In this review, we will summarize the roles and molecular mechanism of lncRNAs including H19, MALAT1, MODR, HOTAIR, DANCR, MEG3, HoxA-AS3, and MIAT in osteogenesis ossification; lncRNA ZBED3-AS1 and CTA-941F9.9, DANCR, and HIT in chondrogenic differentiation; and lncRNA DANCR in osteoclast differentiation. These findings will facilitate the development and application of novel molecular drugs which regulate the balance of bone formation and absorption.
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72
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Li H, Yang J, Wei X, Song C, Dong D, Huang Y, Lan X, Plath M, Lei C, Ma Y, Qi X, Bai Y, Chen H. CircFUT10 reduces proliferation and facilitates differentiation of myoblasts by sponging miR-133a. J Cell Physiol 2018; 233:4643-4651. [PMID: 29044517 DOI: 10.1002/jcp.26230] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/29/2017] [Indexed: 12/28/2022]
Abstract
Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine, and mouse. However, knowledge on circRNAs in bovine muscle development is limited. We downloaded and analyzed the circRNAs sequencing data of bovine skeletal muscle tissue, and further characterized the role of a candidate circRNA (circFUT10) in muscle development. Quantitative real-time PCR (qPCR) and Western blot assays were used to confirm the expression of genes involved in myoblasts differentiation and proliferation. Flow cytometry was performed to assess cell cycle distribution and cell apoptosis. EdU incorporation and CCK-8 assay were performed to demonstrate cell proliferation. We demonstrated that circFUT10 was highly (but differentially) expressed in embryonic and adult skeletal muscle tissue. circFUT10 induced bovine primary myoblasts differentiation and increased the expression of MyoD, MyoG, and MyhC in mRNA and protein levels. circFUT10 increased the number of myoblasts in the G0/G1 phase of the cell cycle, and decreased the proportion of cells in the S-phase. circFUT10 inhibited the proliferation of myoblasts and promoted them apoptosis. Via a luciferase screening assay, circFUT10 is observed to sponge to miR-133a with three potential binding sites. Specifically, we show that circFUT10 regulated myoblasts differentiation and cell survival by directly binding to miR-133a and inhibiting miR-133a activity. Modulation of circFUT10 expression in muscle tissue may emerge as a potential target in breeding strategies attempting to control muscle development in cattle.
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Affiliation(s)
- Hui Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Jiameng Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xuefeng Wei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China.,Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, College of Life Sciences, Xinyang Normal University, Xinyang, Henan, P.R. China
| | - Chengchuang Song
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Dong Dong
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yun Ma
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, College of Life Sciences, Xinyang Normal University, Xinyang, Henan, P.R. China
| | - Xinglei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan, P.R. China
| | - Yueyu Bai
- Animal Health Supervision in Henan Province, Zhengzhou, Henan, P.R. China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
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73
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Li Y, Chen X, Sun H, Wang H. Long non-coding RNAs in the regulation of skeletal myogenesis and muscle diseases. Cancer Lett 2017; 417:58-64. [PMID: 29253523 DOI: 10.1016/j.canlet.2017.12.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/07/2017] [Indexed: 12/11/2022]
Abstract
Skeletal muscle myogenesis during development and the injury induced regeneration contribute to the formation and maintenance of muscle tissue. Emerging studies have demonstrated that long non-coding RNAs (lncRNAs) participate in the regulation of gene expression during skeletal myogenesis and their aberrant expression is associated with several muscular diseases. In this review, we summarize recent studies of lncRNAs in the regulation of myogenesis and muscle diseases with mechanistic characterization. These findings have greatly enhanced our understanding of gene regulatory mechanisms governing muscle formation and regeneration, which will eventually lead to novel therapeutics against various muscle diseases.
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Affiliation(s)
- Yuying Li
- Department of Chemical Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Xiaona Chen
- Department of Orthopaedics and Traumatology, Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Hao Sun
- Department of Chemical Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China.
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74
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Li C, Li X, Yao Y, Ma Q, Ni W, Zhang X, Cao Y, Hazi W, Wang D, Quan R, Hou X, Liu Z, Zhan Q, Liu L, Zhang M, Yu S, Hu S. Genome-wide analysis of circular RNAs in prenatal and postnatal muscle of sheep. Oncotarget 2017; 8:97165-97177. [PMID: 29228601 PMCID: PMC5722553 DOI: 10.18632/oncotarget.21835] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep. A total of 6113 circRNAs were detected from the RNA-seq data. Several circRNAs were identified using reverse transcription PCR, DNA sequencing and RNase R digestion experiments. The expression levels of several circRNAs in prenatal and postnatal muscle were confirmed by Real-Time RT-PCR. The gene ontology (GO) and KEGG enrichment analysis of the host gene of the circRNAs showed that these circRNAs were mainly involved in the growth and development of muscle related signaling pathways. These circRNAs might sponge microRNAs (miRNAs) in predicted circRNA-miRNA-mRNA networks. The circRNAs expression profiles in muscle provided an important reference for the study of circRNAs in sheep.
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Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qiman Ma
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qianqian Zhan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
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75
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Wei X, Li H, Yang J, Hao D, Dong D, Huang Y, Lan X, Plath M, Lei C, Lin F, Bai Y, Chen H. Circular RNA profiling reveals an abundant circLMO7 that regulates myoblasts differentiation and survival by sponging miR-378a-3p. Cell Death Dis 2017; 8:e3153. [PMID: 29072698 PMCID: PMC5680912 DOI: 10.1038/cddis.2017.541] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/15/2017] [Accepted: 09/08/2017] [Indexed: 01/11/2023]
Abstract
Circular RNAs (circRNAs) have been identified from various tissues and species, but their regulatory functions during developmental processes are not well understood. We examined circRNA expression profiles of two developmental stages of bovine skeletal muscle (embryonic and adult musculus longissimus) to provide first insights into their potential involvement in bovine myogenesis. We identified 12 981 circRNAs and annotated them to the Bos taurus reference genome, including 530 circular intronic RNAs (ciRNAs). One parental gene could generate multiple circRNA isoforms, with only one or two isoforms being expressed at higher expression levels. Also, several host genes produced different isoforms when comparing development stages. Most circRNA candidates contained two to seven exons, and genomic distances to back-splicing sites were usually less than 50 kb. The length of upstream or downstream flanking introns was usually less than 105 nt (mean≈11 000 nt). Several circRNAs differed in abundance between developmental stages, and real-time quantitative PCR (qPCR) analysis largely confirmed differential expression of the 17 circRNAs included in this analysis. The second part of our study characterized the role of circLMO7—one of the most down-regulated circRNAs when comparing adult to embryonic muscle tissue—in bovine muscle development. Overexpression of circLMO7 inhibited the differentiation of primary bovine myoblasts, and it appears to function as a competing endogenous RNA for miR-378a-3p, whose involvement in bovine muscle development has been characterized beforehand. Congruent with our interpretation, circLMO7 increased the number of myoblasts in the S-phase of the cell cycle and decreased the proportion of cells in the G0/G1 phase. Moreover, it promoted the proliferation of myoblasts and protected them from apoptosis. Our study provides novel insights into the regulatory mechanisms underlying skeletal muscle development and identifies a number of circRNAs whose regulatory potential will need to be explored in the future.
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Affiliation(s)
- Xuefeng Wei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hui Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiameng Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dan Hao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dong Dong
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengpeng Lin
- Bureau of Animal Husbandry of Biyang County, Biyang 463700, Henan, China
| | - Yueyu Bai
- Animal Health Supervision of Henan Province, Bureau of Animal Husbandry of Henan province, Zhengzhou, Henan 450008, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
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76
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Ren C, Deng M, Fan Y, Yang H, Zhang G, Feng X, Li F, Wang D, Wang F, Zhang Y. Genome-Wide Analysis Reveals Extensive Changes in LncRNAs during Skeletal Muscle Development in Hu Sheep. Genes (Basel) 2017; 8:genes8080191. [PMID: 28763026 PMCID: PMC5575655 DOI: 10.3390/genes8080191] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022] Open
Abstract
As an important type of noncoding RNA molecules, long non-coding RNAs (lncRNAs) act as versatile players in various biological processes. However, little is known about lncRNA regulators during sheep muscle growth. To explore functional lncRNAs during sheep muscle growth, we systematically investigated lncRNAs using strand-specific Ribo-Zero RNA sequencing at three key developmental stages in Hu sheep. A total of 6924 lncRNAs were obtained, and the differentially expressed lncRNAs and genes were screened from (control vs. experiment) fetus vs. lamb, lamb vs. adult, and fetus vs. adult comparisons, respectively. The quantitative real-time polymerase chain reaction (qRT-PCR) analysis results correlated well with the sequencing data. Moreover, functional annotation analysis based on the Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases showed that the target genes of the differentially expressed lncRNAs were significantly enriched in organ morphogenesis, skeletal system development as well as response to stimulus and some other terms related to muscle. Furthermore, a co-expression network of the differentially expressed target genes and lncRNAs was constructed and well-known muscle growth regulators such as retrotransposon-like 1 and Junctophilin-2 were included. Finally, we investigated the expression profiles of seven lncRNAs and their target genes, and found that they played vital roles in muscle growth. This study extends the sheep muscle lncRNA database and provides novel candidate regulators for future genetic and molecular studies on sheep muscle growth, which is helpful for optimizing the production of mutton.
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Affiliation(s)
- Caifang Ren
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mingtian Deng
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yixuan Fan
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hua Yang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Guomin Zhang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xu Feng
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fengzhe Li
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dan Wang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Wang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yanli Zhang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
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77
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Jin CF, Li Y, Ding XB, Li X, Zhang LL, Liu XF, Guo H. lnc133b, a novel, long non-coding RNA, regulates bovine skeletal muscle satellite cell proliferation and differentiation by mediating miR-133b. Gene 2017; 630:35-43. [PMID: 28757453 DOI: 10.1016/j.gene.2017.07.066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/18/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
Abstract
The proliferation and differentiation of skeletal muscle satellite cells is regulated by multiple regulatory factors including non-coding RNAs. It has been reported that miR-133b regulates myogenesis. In this study, we detected a novel lncRNA, lnc133b, which is completely complemented by mature miR-133b, indicating that lnc133b may regulate the expression of miR-133b by "sponge" miR-133b. A luciferase report assay confirmed that lnc133b interacts with miR-133b in regions complemented by miR-133b. We successfully constructed lnc133b gain/loss-of-function cell models by infecting LV-1nc133b and transfecting si-lnc133b into satellite cells. Results of quantitative real-time polymerase chain reaction (qRT-PCR) and 5-ethynyl-2'-deoxyuridine (EdU) assays showed that overexpression or inhibition of lnc133b could promote the proliferation or inhibition of satellite cell differentiation. The qRT-PCR results also showed that lnc133b negatively regulates miR-133b expression and a Western blot assay showed that lnc133b positively regulates IGF1R expression, indicating that the lnc133b/miR-133b/IGF1R axis is a potential pathway for promoting satellite cell proliferation and repressing their differentiation through the ceRNA mechanism. Building on the findings of previous reports, we constructed the lnc133b/miR-133b/FGFR1 & PP2AC pathway to improve the lnc133b regulation network regulating the proliferation and differentiation of satellite cells. The current study provides a new perspective for understanding the mechanism regulating satellite cell proliferation and differentiation through the interaction of miR-133b and lnc133b.
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Affiliation(s)
- Cong Fei Jin
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Yan Li
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiang Bin Ding
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Xin Li
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Lin Lin Zhang
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China
| | - Xin Feng Liu
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China.
| | - Hong Guo
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, China.
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78
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Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver. Sci Rep 2017; 7:6396. [PMID: 28743867 PMCID: PMC5527063 DOI: 10.1038/s41598-017-06634-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 06/14/2017] [Indexed: 12/22/2022] Open
Abstract
RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.
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79
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A lncRNA promotes myoblast proliferation by up-regulating GH1. In Vitro Cell Dev Biol Anim 2017; 53:699-705. [PMID: 28726188 DOI: 10.1007/s11626-017-0180-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/20/2017] [Indexed: 01/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are key regulatory factors for gene expression in a variety of biological processes; however, the role of lncRNAs in muscle formation and development is poorly understood, particularly in cattle. Here, we identified a highly expressed lncRNA in muscle, lncYYW, by high-throughput sequencing in bovine longissimus, scapular, intercostal, and gluteus muscles. The expression of lncYYW increased gradually during myoblast differentiation. Overexpression of lncYYW increased the number of cells in the DNA synthesis (S) stage of the cell cycle and upregulated the expression of two well-established myogenic markers, myogenin and myosin heavy chain. A microarray analysis showed that lncYYW positively regulates the expression of growth hormone 1 and its downstream genes, AKT1 and PIK3CD, in bovine myoblasts. This discovery provides a good foundation for further study of the mechanism of action of lncYYW during bovine myoblast development. Taken together, our results reveal a novel lncRNA associated with bovine myoblast proliferation and differentiation. This lncRNA will play a crucial and critical role in future studies of bovine muscle development.
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