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Luo W, Zhang H, Wan R, Cai Y, Liu Y, Wu Y, Yang Y, Chen J, Zhang D, Luo Z, Shang X. Biomaterials-Based Technologies in Skeletal Muscle Tissue Engineering. Adv Healthc Mater 2024; 13:e2304196. [PMID: 38712598 DOI: 10.1002/adhm.202304196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/26/2024] [Indexed: 05/08/2024]
Abstract
For many clinically prevalent severe injuries, the inherent regenerative capacity of skeletal muscle remains inadequate. Skeletal muscle tissue engineering (SMTE) seeks to meet this clinical demand. With continuous progress in biomedicine and related technologies including micro/nanotechnology and 3D printing, numerous studies have uncovered various intrinsic mechanisms regulating skeletal muscle regeneration and developed tailored biomaterial systems based on these understandings. Here, the skeletal muscle structure and regeneration process are discussed and the diverse biomaterial systems derived from various technologies are explored in detail. Biomaterials serve not merely as local niches for cell growth, but also as scaffolds endowed with structural or physicochemical properties that provide tissue regenerative cues such as topographical, electrical, and mechanical signals. They can also act as delivery systems for stem cells and bioactive molecules that have been shown as key participants in endogenous repair cascades. To achieve bench-to-bedside translation, the typical effect enabled by biomaterial systems and the potential underlying molecular mechanisms are also summarized. Insights into the roles of biomaterials in SMTE from cellular and molecular perspectives are provided. Finally, perspectives on the advancement of SMTE are provided, for which gene therapy, exosomes, and hybrid biomaterials may hold promise to make important contributions.
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Affiliation(s)
- Wei Luo
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Hanli Zhang
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Renwen Wan
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Yuxi Cai
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Yinuo Liu
- The Second Clinical Medical College of Nanchang University, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Yang Wu
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Yimeng Yang
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Jiani Chen
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, Hong Kong
| | - Zhiwen Luo
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
| | - Xiliang Shang
- Department of Sports Medicine Huashan Hospital, Fudan University, Shanghai, 200040, P. R. China
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2
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Guo Y, Geng W, Chen Z, Zhi Y, Zhang K, Li Z, Li G, Kang X, Tian W, Li H, Liu X. LncRNA lncMGR regulates skeletal muscle development and regeneration by recruiting CDK9 and sponging miRNAs. Int J Biol Macromol 2024; 266:131049. [PMID: 38522687 DOI: 10.1016/j.ijbiomac.2024.131049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/31/2024] [Accepted: 03/02/2024] [Indexed: 03/26/2024]
Abstract
Long non-coding RNAs (lncRNAs) play an essential role in vertebrate myogenesis and muscle diseases. However, the dynamic expression patterns, biological functions, and mechanisms of lncRNAs in skeletal muscle development and regeneration remain largely unknown. In this study, a novel lncRNA (named lncMGR) was differentially expressed during breast muscle development in fast- and slow-growing chickens. Functionally, lncMGR promoted myoblast differentiation, inhibited myoblast proliferation in vitro, and promoted myofiber hypertrophy and injury repair in vivo. Mechanistically, lncMGR increased the mRNA and protein expression of skeletal muscle myosin heavy chain 1 A (MYH1A) via both transcriptional and post-transcriptional regulation. Nuclear lncMGR recruited cyclin-dependent kinase 9 (CDK9) to the core transcriptional activation region of the MYH1A gene to activate MYH1A transcription. Cytoplasmic lncMGR served as a competitive endogenous RNA (ceRNA) to competitively absorb miR-2131-5p away from MYH1A and subsequently protected the MYH1A from miR-2131-5p-mediated degradation. Besides miR-2131-5p, cytoplasmic lncMGR could also sponge miR-143-3p to reconcile the antagonist between the miR-2131-5p/MYH1A-mediated inhibition effects and miR-143-3p-mediated promotion effects on myoblast proliferation, thereby inhibiting myoblast proliferation. Collectively, lncMGR could recruit CDK9 and sponge multiple miRNAs to regulate skeletal muscle development and regeneration, and could be a therapeutic target for muscle diseases.
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Affiliation(s)
- Yulong Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Wanzhuo Geng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhimin Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Yihao Zhi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ke Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China.
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China.
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China; International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450002, China.
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3
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Biferali B, Mocciaro E, Runfola V, Gabellini D. Long non-coding RNAs and their role in muscle regeneration. Curr Top Dev Biol 2024; 158:433-465. [PMID: 38670715 DOI: 10.1016/bs.ctdb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
In mammals, most of the genome is transcribed to generate a large and heterogeneous variety of non-protein coding RNAs, that are broadly grouped according to their size. Long noncoding RNAs include a very large and versatile group of molecules. Despite only a minority of them has been functionally characterized, there is emerging evidence indicating long noncoding RNAs as important regulators of expression at multiple levels. Several of them have been shown to be modulated during myogenic differentiation, playing important roles in the regulation of skeletal muscle development, differentiation and homeostasis, and contributing to neuromuscular diseases. In this chapter, we have summarized the current knowledge about long noncoding RNAs in skeletal muscle and discussed specific examples of long noncoding RNAs (lncRNAs and circRNAs) regulating muscle stem cell biology. We have also discussed selected long noncoding RNAs involved in the most common neuromuscular diseases.
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Affiliation(s)
- Beatrice Biferali
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Mocciaro
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Runfola
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Gabellini
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Sato J, Satoh Y, Yamamoto T, Watanabe T, Matsubara S, Satake H, Kimura AP. PTBP2 binds to a testis-specific long noncoding RNA, Tesra, and activates transcription of the Prss42/Tessp-2 gene. Gene 2024; 893:147907. [PMID: 37858745 DOI: 10.1016/j.gene.2023.147907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently been proved to be functional in the testis. Tesra, a testis-specific lncRNA, was suggested to activate the transcription of Prss42/Tessp-2, a gene that is involved in meiotic progression, in mouse spermatocytes. To reveal the molecular mechanism underlying the activation, we searched for Tesra-binding proteins by a Ribotrap assay followed by LC-MS/MS analysis and identified polypyrimidine tract binding protein 2 (PTBP2) as a candidate. Analysis of public RNA-seq data and our qRT-PCR results indicated that Ptbp2 mRNA showed an expression pattern similar to the expression patterns of Tesra and Prss42/Tessp-2 during testis development. Moreover, PTBP2 was found to be associated with Tesra in testicular germ cells by RNA immunoprecipitation. To evaluate the effect of PTBP2 on the Prss42/Tessp-2 promoter, we established an in vitro reporter gene assay system in which Tesra expression could be induced by the Tet-on system and thereby Prss42/Tessp-2 promoter activity could be increased. In this system, the Prss42/Tessp-2 promoter activity was significantly decreased by the knockdown of PTBP2. These results suggest that PTBP2 contributes to Prss42/Tessp-2 transcriptional activation by Tesra in spermatocytes. The finding provides a precious example of a molecular mechanism of testis lncRNA functioning in spermatogenesis.
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Affiliation(s)
- Josei Sato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Takehiro Watanabe
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan.
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5
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Li M, Liu Q, Xie S, Fu C, Li J, Tian C, Li X, Li C. LncRNA TCONS_00323213 Promotes Myogenic Differentiation by Interacting with PKNOX2 to Upregulate MyoG in Porcine Satellite Cells. Int J Mol Sci 2023; 24:ijms24076773. [PMID: 37047747 PMCID: PMC10094759 DOI: 10.3390/ijms24076773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Myogenic differentiation is a complex biological process that is regulated by multiple factors, among which long noncoding RNAs (lncRNAs) play an essential role. However, in-depth studies on the regulatory mechanisms of long noncoding RNAs (lncRNAs) in myogenic differentiation are limited. In this study, we characterized the role of the novel lncRNA TCONS_00323213, which is upregulated during porcine skeletal muscle satellite cell (PSC) differentiation in myogenesis. We found that TCONS_00323213 affected the proliferation and differentiation of PSC in vitro. We performed quantitative polymerase chain reaction (qPCR), 5-ethynyl-20-deoxyuridine (EdU), western blotting, immunofluorescence staining, pull-down assays, and cleavage under targets and tagmentation (CUT and Tag) assays to clarify the effects and action mechanisms of TCONS_00323213. LncRNA TCONS_00323213 inhibited myoblast proliferation based on analyses of cell survival rates during PSC proliferation. Functional analyses revealed that TCONS_00323213 promotes cell differentiation and enhances myogenin (MyoG), myosin heavy chain (MyHC), and myocyte enhancer factor 2 (MEF2C) during myoblast differentiation. As determined by pull-down and RNA immunoprecipitation (RIP) assays, the lncRNA TCONS_00323213 interacted with PBX/Knotted Homeobox 2 (PKNOX2). CUT and Tag assays showed that PKNOX2 was significantly enriched on the MyoG promoter after lncRNA TCONS_00323213 knockdown. Our findings demonstrate that the interaction between lncRNA TCONS_00323213 and PKNOX2 relieves the inhibitory effect of PKNOX2 on the MyoG promoter, increases its expression, and promotes PSC differentiation. This novel role of lncRNA TCONS_00323213 sheds light on the molecular mechanisms by which lncRNAs regulate porcine myogenesis.
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Affiliation(s)
- Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Quan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Su Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Chong Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Tian
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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Hitachi K, Kiyofuji Y, Yamaguchi H, Nakatani M, Inui M, Tsuchida K. Simultaneous loss of skeletal muscle myosin heavy chain IIx and IIb causes severe skeletal muscle hypoplasia in postnatal mice. FASEB J 2023; 37:e22692. [PMID: 36515178 DOI: 10.1096/fj.202200581r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
The skeletal muscle myosin heavy chain (MyHC) is a fundamental component of the sarcomere structure and muscle contraction. Two of the three adult fast MyHCs, MyHC-IIx and MyHC-IIb, are encoded by Myh1 and Myh4, respectively. However, skeletal muscle disorders have not yet been linked to these genes in humans. MyHC-IIb is barely detectable in human skeletal muscles. Thus, to characterize the molecular function of skeletal muscle MyHCs in humans, investigation of the effect of simultaneous loss of MyHC-IIb and other MyHCs on skeletal muscle in mice is essential. Here, we generated double knockout (dKO) mice with simultaneous loss of adult fast MyHCs by introducing nonsense frameshift mutations into the Myh1 and Myh4 genes. The dKO mice appeared normal after birth and until 2 weeks of age but showed severe skeletal muscle hypoplasia after 2 weeks. In 3-week-old dKO mice, increased expression of other skeletal muscle MyHCs, such as MyHC-I, MyHC-IIa, MyHC-neo, and MyHC-emb, was observed. However, these expressions were not sufficient to compensate for the loss of MyHC-IIb and MyHC-IIx. Moreover, the aberrant sarcomere structure with altered expression of sarcomere components was observed in dKO mice. Our findings imply that the simultaneous loss of MyHC-IIb and MyHC-IIx is substantially detrimental to postnatal skeletal muscle function and will contribute to elucidating the molecular mechanisms of skeletal muscle wasting disorders caused by the loss of skeletal muscle MyHCs.
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Affiliation(s)
- Keisuke Hitachi
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake, Japan
| | - Yuri Kiyofuji
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake, Japan
| | - Hisateru Yamaguchi
- School of Nursing and Medical Care, Yokkaichi Nursing and Medical Care University, Yokkaichi, Japan
| | - Masashi Nakatani
- Faculty of Rehabilitation and Care, Seijoh University, Tokai, Japan
| | - Masafumi Inui
- Laboratory of Animal Regeneration Systemology, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kunihiro Tsuchida
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake, Japan
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7
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Chang MW, Yang JH, Tsitsipatis D, Yang X, Martindale J, Munk R, Pandey P, Banskota N, Romero B, Batish M, Piao Y, Mazan-Mamczarz K, De S, Abdelmohsen K, Wilson G, Gorospe M. Enhanced myogenesis through lncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter. Nucleic Acids Res 2022; 50:13026-13044. [PMID: 36533518 PMCID: PMC9825165 DOI: 10.1093/nar/gkac1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/16/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The mammalian transcriptome comprises a vast family of long noncoding (lnc)RNAs implicated in physiologic processes such as myogenesis, through which muscle forms during embryonic development and regenerates in the adult. However, the specific molecular mechanisms by which lncRNAs regulate human myogenesis are poorly understood. Here, we identified a novel muscle-specific lncRNA, lncFAM71E1-2:2 (lncFAM), which increased robustly during early human myogenesis. Overexpression of lncFAM promoted differentiation of human myoblasts into myotubes, while silencing lncFAM suppressed this process. As lncFAM resides in the nucleus, chromatin isolation by RNA purification followed by mass spectrometry (ChIRP-MS) analysis was employed to identify the molecular mechanisms whereby it might promote myogenesis. Analysis of lncFAM-interacting proteins revealed that lncFAM recruited the RNA-binding protein HNRNPL to the promoter of MYBPC2, in turn increasing MYBPC2 mRNA transcription and enhancing production of the myogenic protein MYBPC2. These results highlight a mechanism whereby a novel ribonucleoprotein complex, lncFAM-HNRNPL, elevates MYBPC2 expression transcriptionally to promote myogenesis.
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Affiliation(s)
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Nirad Banskota
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Myriam Gorospe
- To whom correspondence should be addressed. Tel: +1 410 454 8412;
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8
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Fu X, Zhuang CL, Hu P. Regulation of muscle stem cell fate. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:40. [PMID: 36456659 PMCID: PMC9715903 DOI: 10.1186/s13619-022-00142-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/29/2022] [Indexed: 12/03/2022]
Abstract
Skeletal muscle plays a critical role in human health. Muscle stem cells (MuSCs) serve as the major cell type contributing to muscle regeneration by directly differentiating to mature muscle cells. MuSCs usually remain quiescent with occasionally self-renewal and are activated to enter cell cycle for proliferation followed by differentiation upon muscle injury or under pathological conditions. The quiescence maintenance, activation, proliferation, and differentiation of MuSCs are tightly regulated. The MuSC cell-intrinsic regulatory network and the microenvironments work coordinately to orchestrate the fate transition of MuSCs. The heterogeneity of MuSCs further complicates the regulation of MuSCs. This review briefly summarizes the current progress on the heterogeneity of MuSCs and the microenvironments, epigenetic, and transcription regulations of MuSCs.
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Affiliation(s)
- Xin Fu
- grid.412987.10000 0004 0630 1330Spine Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Cheng-le Zhuang
- grid.412538.90000 0004 0527 0050Colorectal Cancer Center/Department of Gastrointestinal Surgery, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, 200072 China
| | - Ping Hu
- grid.412987.10000 0004 0630 1330Spine Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China ,grid.412538.90000 0004 0527 0050Colorectal Cancer Center/Department of Gastrointestinal Surgery, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, 200072 China ,Guangzhou Laboratory, Guanghzou International Bio Lsland, No. 9 XingDaoHuan Road, Guangzhou, 510005 China ,grid.9227.e0000000119573309Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101 China
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9
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Chen W, Chen W, Liu P, Qian S, Tao S, Huang M, Xu W, Li C, Chen X, Lin H, Qin Z, Lu J, Xie S. Role of lncRNA Has2os in Skeletal Muscle Differentiation and Regeneration. Cells 2022; 11:3497. [PMID: 36359891 PMCID: PMC9655701 DOI: 10.3390/cells11213497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 09/26/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate a series of physiological processes and play an important role in development, metabolism and disease. Our previous studies showed that lncRNAs involved in skeletal muscle differentiation. Here, we demonstrated that lncRNA Has2os is highly expressed in skeletal muscle and significantly elevated during skeletal cell differentiation. The knockdown of Has2os inhibited myocyte fusion and impeded the expression of the myogenic factors MyHC and Mef2C. Mechanically, Has2os regulates skeletal muscle differentiation by inhibiting the JNK/MAPK signaling pathway. Furthermore, we also revealed that Has2os is involved in the early stage of regeneration after muscle injury, and the JNK/MAPK signaling pathway is activated at both protein and mRNA levels during early repair. Our results demonstrate the new function of lncRNA Has2os, which plays crucial roles during skeletal muscle differentiation and muscle regeneration, providing a basis for the therapy of lncRNA-related muscle diseases.
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Affiliation(s)
- Wanxin Chen
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Weicai Chen
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Peng Liu
- Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Shiyu Qian
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Mengchun Huang
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Wanyi Xu
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Cuiping Li
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Xiaoyan Chen
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Huizhu Lin
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Zhenshu Qin
- Department of Trauma Orthopaedics, Chenzhou First People’s Hospital Affiliated to South China University, Chenzhou 423000, China
| | - Jianxi Lu
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Shujuan Xie
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
- Vaccine Research Institute of Sun Yat-Sen University, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
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10
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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11
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Identification and characterization of long non-coding RNAs in juvenile and adult skeletal muscle of largemouth bass (Micropterus salmoides). Comp Biochem Physiol B Biochem Mol Biol 2022; 261:110748. [PMID: 35460873 DOI: 10.1016/j.cbpb.2022.110748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a class of transcriptional RNA molecules, which play critical roles in diverse biological processes. However, little is known about the overall expression pattern and roles of lncRNAs in skeletal muscle of largemouth bass (LMB). Here, we constructed two skeletal muscle RNA libraries to find lncRNAs that may involve in the regulation of skeletal muscle development between juvenile and adult LMB. A total of 16,147 lncRNAs and 4611 differentially expressed lncRNAs were identified. Among these identified lncRNAs, 10 lncRNAs were randomly selected to confirm their expression by real-time qPCR both in libraries, which were consistent with the RNA sequencing results. The target mRNAs of lncRNAs were predicted for GO enrichment analysis. Results showed that these targets associated with growth and development of muscle, such as skeletal muscle fiber development, myoblast proliferation and differentiation. Importantly, correlation analysis of lncRNA-miRNA-mRNA regulatory network revealed that several lncRNAs targeted miRNAs which are closely involved in the regulation of muscle development. It is the first time to identify a number of lncRNA that correlate with skeletal muscle development in LMB. Our results not only provide a comprehensive expression profile of muscle lncRNAs in this species, but also provide a theoretical basis for further elaborating genetic regulation mechanism of muscle growth and development, and pave the way for the future molecular assisted breeding in carnivorous fishes.
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12
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The Functional Role of Long Non-Coding RNA in Myogenesis and Skeletal Muscle Atrophy. Cells 2022; 11:cells11152291. [PMID: 35892588 PMCID: PMC9332450 DOI: 10.3390/cells11152291] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
Skeletal muscle is a pivotal organ in humans that maintains locomotion and homeostasis. Muscle atrophy caused by sarcopenia and cachexia, which results in reduced muscle mass and impaired skeletal muscle function, is a serious health condition that decreases life longevity in humans. Recent studies have revealed the molecular mechanisms by which long non-coding RNAs (lncRNAs) regulate skeletal muscle mass and function through transcriptional regulation, fiber-type switching, and skeletal muscle cell proliferation. In addition, lncRNAs function as natural inhibitors of microRNAs and induce muscle hypertrophy or atrophy. Intriguingly, muscle atrophy modifies the expression of thousands of lncRNAs. Therefore, although their exact functions have not yet been fully elucidated, various novel lncRNAs associated with muscle atrophy have been identified. Here, we comprehensively review recent knowledge on the regulatory roles of lncRNAs in skeletal muscle atrophy. In addition, we discuss the issues and possibilities of targeting lncRNAs as a treatment for skeletal muscle atrophy and muscle wasting disorders in humans.
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13
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A novel LncRNA PTH-AS upregulates interferon-related DNA damage resistance signature genes and promotes metastasis in human breast cancer xenografts. J Biol Chem 2022; 298:102065. [PMID: 35618021 PMCID: PMC9198338 DOI: 10.1016/j.jbc.2022.102065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are important tissue-specific regulators of gene expression, and their dysregulation can induce aberrant gene expression leading to various pathological conditions, including cancer. Although many lncRNAs have been discovered by computational analysis, most of these are as yet unannotated. Herein, we describe the nature and function of a novel lncRNA detected downstream of the human parathyroid hormone (PTH) gene in both extremely rare ectopic PTH-producing retroperitoneal malignant fibrous histiocytoma and parathyroid tumors with PTH overproduction. This novel lncRNA, which we have named "PTH-AS," has never been registered in a public database, and here, we investigated for the first time its exact locus, length, transcription direction, polyadenylation, and nuclear localization. Microarray and Gene Ontology analyses demonstrated that forced expression of PTH-AS in PTH-nonexpressing human breast cancer T47D cells did not induce the ectopic expression of the nearby PTH gene but did significantly upregulate Janus kinase-signal transducer and activator of transcription pathway-related genes such as cancer-promoting interferon-related DNA damage resistance signature (IRDS) genes. Importantly, we show that PTH-AS expression not only enhanced T47D cell invasion and resistance to the DNA-damaging drug doxorubicin but also promoted lung metastasis rather than tumor growth in a mouse xenograft model. In addition, PTH-AS-expressing T47D tumors showed increased macrophage infiltration that promoted angiogenesis, similar to IRDS-associated cancer characteristics. Although the detailed molecular mechanism remains imperfectly understood, we conclude that PTH-AS may contribute to tumor development, possibly through IRDS gene upregulation.
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14
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He C, Liu M, Ding Q, Yang F, Xu T. Upregulated miR-9-5p inhibits osteogenic differentiation of bone marrow mesenchymal stem cells under high glucose treatment. J Bone Miner Metab 2022; 40:208-219. [PMID: 34750680 DOI: 10.1007/s00774-021-01280-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Diabetic osteoporosis (DOP) is a chronic diabetic complication, which is attributed to high glucose (HG)-induced dysfunction of bone marrow mesenchymal stem cells (BMSCs). Studies have revealed that microRNAs (miRNAs) play critical roles in osteogenic differentiation of BMSCs in DOP. Here, the role of miR-9-5p in DOP progression was explored. MATERIALS AND METHODS The rat model of DOP was established by intraperitoneal injection of streptozotocin (STZ). BMSCs were treated with high glucose (HG) to establish in vitro models. Gene expression in BMSCs and bone tissues of rats was tested by RT-qPCR. The degree of osteogenic differentiation of BMSCs was examined by Alizarin Red staining and ALP activity analysis. The protein levels of collagen-I (COL1), osteocalcin (OCN), osteopontin (OPN), runt-related transcription factor-2 (RUNX2), and DEAD-Box Helicase 17 (DDX17) in BMSCs were evaluated by western blotting. The interaction between miR-9-5p and DDX17 was identified by luciferase reporter assay. H&E staining was used to test morphological structure of femurs of rats with STZ treatment. RESULTS MiR-9-5p was overexpressed in HG-treated BMSCs, while DDX17 was downregulated. Functionally, miR-9-5p knockdown promoted BMSCs osteogenic differentiation under HG condition. Mechanically, miR-9-5p targeted DDX17. DDX17 knockdown reversed the effect of miR-9-5p silencing on osteogenic differentiation of HG-treated BMSCs. In in vivo studies, miR-9-5p downregulation ameliorated the DOP condition of rats and miR-9-5p expression was negatively correlated with DDX17 expression in bone tissues of rats with STZ treatment. CONCLUSION MiR-9-5p knockdown promotes HG-induced osteogenic differentiation BMSCs in vitro and mitigates the DOP condition of rats in vivo by targeting DDX17.
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Affiliation(s)
- Chuanmei He
- Department of Nephrology, The Affiliated Lianyungang No.2 Hospital of Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Mingming Liu
- Department of Orthopedics, The Affiliated Lianyungang No.2 Hospital of Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Qun Ding
- Department of Endocrinology, The Affiliated Lianyungang No.2 Hospital of Bengbu Medical College, 41 Hailian East Road, Haizhou District, Lianyungang, 222000, Jiangsu, China
| | - Fumeng Yang
- Department of Laboratory, The Affiliated Lianyungang No.2 Hospital of Bengbu Medical College, Lianyungang, 222000, Jiangsu, China
| | - Tongdao Xu
- Department of Endocrinology, The Affiliated Lianyungang No.2 Hospital of Bengbu Medical College, 41 Hailian East Road, Haizhou District, Lianyungang, 222000, Jiangsu, China.
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15
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García-Pérez I, Molsosa-Solanas A, Perelló-Amorós M, Sarropoulou E, Blasco J, Gutiérrez J, Garcia de la serrana D. The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream ( Sparus aurata) Fast Skeletal Muscle. Cells 2022; 11:428. [PMID: 35159240 PMCID: PMC8834446 DOI: 10.3390/cells11030428] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are an emerging group of ncRNAs that can modulate gene expression at the transcriptional or translational levels. In the present work, previously published transcriptomic data were used to identify lncRNAs expressed in gilthead sea bream skeletal muscle, and their transcription levels were studied under different physiological conditions. Two hundred and ninety lncRNAs were identified and, based on transcriptomic differences between juveniles and adults, a total of seven lncRNAs showed potential to be important for muscle development. Our data suggest that the downregulation of most of the studied lncRNAs might be linked to increased myoblast proliferation, while their upregulation might be necessary for differentiation. However, with these data, as it is not possible to propose a formal mechanism to explain their effect, bioinformatic analysis suggests two possible mechanisms. First, the lncRNAs may act as sponges of myoblast proliferation inducers microRNAs (miRNAs) such as miR-206, miR-208, and miR-133 (binding energy MEF < -25.0 kcal). Secondly, lncRNA20194 had a strong predicted interaction towards the myod1 mRNA (ndG = -0.17) that, based on the positive correlation between the two genes, might promote its function. Our study represents the first characterization of lncRNAs in gilthead sea bream fast skeletal muscle and provides evidence regarding their involvement in muscle development.
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Affiliation(s)
- Isabel García-Pérez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Anna Molsosa-Solanas
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Miquel Perelló-Amorós
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71003 Crete, Greece;
| | - Josefina Blasco
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Joaquim Gutiérrez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Daniel Garcia de la serrana
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
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16
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A novel promoter-associated non-coding small RNA paGLI1 recruits FUS/P65 to transactivate GLI1 gene expression and promotes infiltrating glioma progression. Cancer Lett 2022; 530:68-84. [DOI: 10.1016/j.canlet.2022.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/29/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022]
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17
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García-Padilla C, Domínguez JN, Lodde V, Munk R, Abdelmohsen K, Gorospe M, Jiménez-Sábado V, Ginel A, Hove-Madsen L, Aránega AE, Franco D. Identification of atrial-enriched lncRNA Walras linked to cardiomyocyte cytoarchitecture and atrial fibrillation. FASEB J 2022; 36:e22051. [PMID: 34861058 PMCID: PMC8684585 DOI: 10.1096/fj.202100844rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023]
Abstract
Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia in humans. Genetic and genomic analyses have recently demonstrated that the homeobox transcription factor Pitx2 plays a fundamental role regulating expression of distinct growth factors, microRNAs and ion channels leading to morphological and molecular alterations that promote the onset of AF. Here we address the plausible contribution of long non-coding (lnc)RNAs within the Pitx2>Wnt>miRNA signaling pathway. In silico analyses of annotated lncRNAs in the vicinity of the Pitx2, Wnt8 and Wnt11 chromosomal loci identified five novel lncRNAs with differential expression during cardiac development. Importantly, three of them, Walaa, Walras, and Wallrd, are evolutionarily conserved in humans and displayed preferential atrial expression during embryogenesis. In addition, Walrad displayed moderate expression during embryogenesis but was more abundant in the right atrium. Walaa, Walras and Wallrd were distinctly regulated by Pitx2, Wnt8, and Wnt11, and Wallrd was severely elevated in conditional atrium-specific Pitx2-deficient mice. Furthermore, pro-arrhythmogenic and pro-hypertrophic substrate administration to primary cardiomyocyte cell cultures consistently modulate expression of these lncRNAs, supporting distinct modulatory roles of the AF cardiovascular risk factors in the regulation of these lncRNAs. Walras affinity pulldown assays revealed its association with distinct cytoplasmic and nuclear proteins previously involved in cardiac pathophysiology, while loss-of-function assays further support a pivotal role of this lncRNA in cytoskeletal organization. We propose that lncRNAs Walaa, Walras and Wallrd, distinctly regulated by Pitx2>Wnt>miRNA signaling and pro-arrhythmogenic and pro-hypertrophic factors, are implicated in atrial arrhythmogenesis, and Walras additionally in cardiomyocyte cytoarchitecture.
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Affiliation(s)
- Carlos García-Padilla
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Jorge N. Domínguez
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Valeria Lodde
- Laboratory of Genetics and Genomics, National Institute on Aging IRP, National Institutes of Health, Baltimore, Maryland, USA,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging IRP, National Institutes of Health, Baltimore, Maryland, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging IRP, National Institutes of Health, Baltimore, Maryland, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging IRP, National Institutes of Health, Baltimore, Maryland, USA
| | | | - Antonino Ginel
- Department Cardiac Surgery, Hospital de Sant Pau, Barcelona, Spain,Biomedical Research Institute IIB Sant Pau, Barcelona, Spain
| | - Leif Hove-Madsen
- CIBERCV, Barcelona, Spain,Biomedical Research Institute IIB Sant Pau, Barcelona, Spain,Biomedical Research Institute Barcelona (IIBB-CSIC), Barcelona, Spain
| | - Amelia E. Aránega
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, Spain
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18
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Myoparr-Associated and -Independent Multiple Roles of Heterogeneous Nuclear Ribonucleoprotein K during Skeletal Muscle Cell Differentiation. Int J Mol Sci 2021; 23:ijms23010108. [PMID: 35008534 PMCID: PMC8744952 DOI: 10.3390/ijms23010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/17/2022] Open
Abstract
RNA-binding proteins (RBPs) regulate cell physiology via the formation of ribonucleic-protein complexes with coding and non-coding RNAs. RBPs have multiple functions in the same cells; however, the precise mechanism through which their pleiotropic functions are determined remains unknown. In this study, we revealed the multiple inhibitory functions of heterogeneous nuclear ribonucleoprotein K (hnRNPK) for myogenic differentiation. We first identified hnRNPK as a lncRNA Myoparr binding protein. Gain- and loss-of-function experiments showed that hnRNPK repressed the expression of myogenin at the transcriptional level. The hnRNPK-binding region of Myoparr was required to repress myogenin expression. Moreover, hnRNPK repressed the expression of a set of genes coding for aminoacyl-tRNA synthetases in a Myoparr-independent manner. Mechanistically, hnRNPK regulated the eIF2α/Atf4 pathway, one branch of the intrinsic pathways of the endoplasmic reticulum sensors, in differentiating myoblasts. Thus, our findings demonstrate that hnRNPK plays lncRNA-associated and -independent multiple roles during myogenic differentiation, indicating that the analysis of lncRNA-binding proteins will be useful for elucidating both the physiological functions of lncRNAs and the multiple functions of RBPs.
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19
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Mbadhi MN, Tang JM, Zhang JX. Histone Lysine Methylation and Long Non-Coding RNA: The New Target Players in Skeletal Muscle Cell Regeneration. Front Cell Dev Biol 2021; 9:759237. [PMID: 34926450 PMCID: PMC8678087 DOI: 10.3389/fcell.2021.759237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Satellite stem cell availability and high regenerative capacity have made them an ideal therapeutic approach for muscular dystrophies and neuromuscular diseases. Adult satellite stem cells remain in a quiescent state and become activated upon muscular injury. A series of molecular mechanisms succeed under the control of epigenetic regulation and various myogenic regulatory transcription factors myogenic regulatory factors, leading to their differentiation into skeletal muscles. The regulation of MRFs via various epigenetic factors, including DNA methylation, histone modification, and non-coding RNA, determine the fate of myogenesis. Furthermore, the development of histone deacetylation inhibitors (HDACi) has shown promising benefits in their use in clinical trials of muscular diseases. However, the complete application of using satellite stem cells in the clinic is still not achieved. While therapeutic advancements in the use of HDACi in clinical trials have emerged, histone methylation modulations and the long non-coding RNA (lncRNA) are still under study. A comprehensive understanding of these other significant epigenetic modulations is still incomplete. This review aims to discuss some of the current studies on these two significant epigenetic modulations, histone methylation and lncRNA, as potential epigenetic targets in skeletal muscle regeneration. Understanding the mechanisms that initiate myoblast differentiation from its proliferative state to generate new muscle fibres will provide valuable information to advance the field of regenerative medicine and stem cell transplant.
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Affiliation(s)
- Magdaleena Naemi Mbadhi
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Jing-Xuan Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Department of Physiology, Faculty of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
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20
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Xie SJ, Tao S, Diao LT, Li PL, Chen WC, Zhou ZG, Hu YX, Hou YR, Lei H, Xu WY, Chen WJ, Peng YW, Zhang Q, Xiao ZD. Characterization of Long Non-coding RNAs Modified by m 6A RNA Methylation in Skeletal Myogenesis. Front Cell Dev Biol 2021; 9:762669. [PMID: 34722547 PMCID: PMC8548731 DOI: 10.3389/fcell.2021.762669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023] Open
Abstract
Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in various biological processes, making it essential to profile m6A modification on a transcriptome-wide scale in developing muscle. Patterns of m6A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m6A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m6A-lncRNAs harbor the consensus m6A motif “DRACH” along lncRNA transcripts. Interestingly, we found that m6A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m6A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m6A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m6A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.
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Affiliation(s)
- Shu-Juan Xie
- Vaccine Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Pan-Long Li
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei-Cai Chen
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhi-Gang Zhou
- Department of Orthopedics, First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yan-Xia Hu
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ya-Rui Hou
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hang Lei
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wan-Yi Xu
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wen-Jie Chen
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yan-Wen Peng
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qi Zhang
- Vaccine Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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21
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Archacka K, Ciemerych MA, Florkowska A, Romanczuk K. Non-Coding RNAs as Regulators of Myogenesis and Postexercise Muscle Regeneration. Int J Mol Sci 2021; 22:ijms222111568. [PMID: 34768999 PMCID: PMC8583994 DOI: 10.3390/ijms222111568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 12/21/2022] Open
Abstract
miRNAs and lncRNAs do not encode proteins, but they play an important role in the regulation of gene expression. They differ in length, biogenesis, and mode of action. In this work, we focus on the selected miRNAs and lncRNAs involved in the regulation of myogenesis and muscle regeneration. We present selected miRNAs and lncRNAs that have been shown to control myogenic differentiation and show that manipulation of their levels could be used to improve myogenic differentiation of various types of stem and progenitor cells. Finally, we discuss how physical activity affects miRNA and lncRNA expression and how it affects muscle well-being.
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22
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Liu R, Li G, Ma H, Zhou X, Wang P, Zhao Y. Transcriptome profiling of the diaphragm in a controlled mechanical ventilation model reveals key genes involved in ventilator-induced diaphragmatic dysfunction. BMC Genomics 2021; 22:472. [PMID: 34172008 PMCID: PMC8227366 DOI: 10.1186/s12864-021-07741-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/25/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Ventilator-induced diaphragmatic dysfunction (VIDD) is associated with weaning difficulties, intensive care unit hospitalization (ICU), infant mortality, and poor long-term clinical outcomes. The expression patterns of long noncoding RNAs (lncRNAs) and mRNAs in the diaphragm in a rat controlled mechanical ventilation (CMV) model, however, remain to be investigated. RESULTS The diaphragms of five male Wistar rats in a CMV group and five control Wistar rats were used to explore lncRNA and mRNA expression profiles by RNA-sequencing (RNA-seq). Muscle force measurements and immunofluorescence (IF) staining were used to verify the successful establishment of the CMV model. A total of 906 differentially expressed (DE) lncRNAs and 2,139 DE mRNAs were found in the CMV group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine the biological functions or pathways of these DE mRNAs. Our results revealed that these DE mRNAs were related mainly related to complement and coagulation cascades, the PPAR signaling pathway, cholesterol metabolism, cytokine-cytokine receptor interaction, and the AMPK signaling pathway. Some DE lncRNAs and DE mRNAs determined by RNA-seq were validated by quantitative real-time polymerase chain reaction (qRT-PCR), which exhibited trends similar to those observed by RNA-sEq. Co-expression network analysis indicated that three selected muscle atrophy-related mRNAs (Myog, Trim63, and Fbxo32) were coexpressed with relatively newly discovered DE lncRNAs. CONCLUSIONS This study provides a novel perspective on the molecular mechanism of DE lncRNAs and mRNAs in a CMV model, and indicates that the inflammatory signaling pathway and lipid metabolism may play important roles in the pathophysiological mechanism and progression of VIDD.
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Affiliation(s)
- Ruining Liu
- Emergency Center, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China.,Hubei Clinical Research Center for Emergency and Resuscitation, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China
| | - Gang Li
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China
| | - Haoli Ma
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China
| | - Xianlong Zhou
- Emergency Center, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China.,Hubei Clinical Research Center for Emergency and Resuscitation, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China
| | - Pengcheng Wang
- Emergency Center, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China.,Hubei Clinical Research Center for Emergency and Resuscitation, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China
| | - Yan Zhao
- Emergency Center, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China. .,Hubei Clinical Research Center for Emergency and Resuscitation, Zhongnan Hospital of Wuhan University, 430071, Wuhan, China.
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Qiu J, Wu L, Chang Y, Sun H, Sun J. Alternative splicing transitions associate with emerging atrophy phenotype during denervation-induced skeletal muscle atrophy. J Cell Physiol 2021; 236:4496-4514. [PMID: 33319931 DOI: 10.1002/jcp.30167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/23/2020] [Accepted: 11/05/2020] [Indexed: 12/25/2022]
Abstract
Alternative splicing (AS) presents a key posttranscriptional regulatory mechanism associated with numerous physiological processes. However, little is known about its role in skeletal muscle atrophy. In this study, we used a rat model of denervated skeletal muscle atrophy and performed RNA-sequencing to analyze transcriptome profiling of tibialis anterior muscle at multiple time points following denervation. We found that AS is a novel mechanism involving muscle atrophy, which is independent changes at the transcript level. Bioinformatics analysis further revealed that AS transitions are associated with the appearance of the atrophic phenotype. Moreover, we found that the inclusion of multiple highly conserved exons of Obscn markedly increased at 3 days after denervation. In addition, we confirmed that this newly transcript inhibited C2C12 cell proliferation and exacerbated myotube atrophy. Finally, our study revealed that a large number of RNA-binding proteins were upregulated when the atrophy phenotype appeared. Our data emphasize the importance of AS in this process.
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Affiliation(s)
- Jiaying Qiu
- Department of Prenatal Screening and Diagnosis Center, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Liucheng Wu
- Laboratory Animal Center, Nantong University, Nantong, China
| | - Yan Chang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China
| | - Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China
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Chen M, Zhang L, Guo Y, Liu X, Song Y, Li X, Ding X, Guo H. A novel lncRNA promotes myogenesis of bovine skeletal muscle satellite cells via PFN1-RhoA/Rac1. J Cell Mol Med 2021; 25:5988-6005. [PMID: 33942976 PMCID: PMC8256363 DOI: 10.1111/jcmm.16427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 02/13/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022] Open
Abstract
Myogenesis, the process of skeletal muscle formation, is a highly coordinated multistep biological process. Accumulating evidence suggests that long non-coding RNAs (lncRNAs) are emerging as a gatekeeper in myogenesis. Up to now, most studies on muscle development-related lncRNAs are mainly focussed on humans and mice. In this study, a novel muscle highly expressed lncRNA, named lnc23, localized in nucleus, was found differentially expressed in different stages of embryonic development and myogenic differentiation. The knockdown and over-expression experiments showed that lnc23 positively regulated the myogenic differentiation of bovine skeletal muscle satellite cells. Then, TMT 10-plex labelling quantitative proteomics was performed to screen the potentially regulatory proteins of lnc23. Results indicated that lnc23 was involved in the key processes of myogenic differentiation such as cell fusion, further demonstrated that down-regulation of lnc23 may inhibit myogenic differentiation by reducing signal transduction and cell fusion among cells. Furthermore, RNA pulldown/LC-MS and RIP experiment illustrated that PFN1 was a binding protein of lnc23. Further, we also found that lnc23 positively regulated the protein expression of RhoA and Rac1, and PFN1 may negatively regulate myogenic differentiation and the expression of its interacting proteins RhoA and Rac1. Hence, we support that lnc23 may reduce the inhibiting effect of PFN1 on RhoA and Rac1 by binding to PFN1, thereby promoting myogenic differentiation. In short, the novel identified lnc23 promotes myogenesis of bovine skeletal muscle satellite cells via PFN1-RhoA/Rac1.
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Affiliation(s)
- Mingming Chen
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
| | - Linlin Zhang
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
| | - Yiwen Guo
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
| | - Xinfeng Liu
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
| | - Yingshen Song
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
| | - Xin Li
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
| | - Xiangbin Ding
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
| | - Hong Guo
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy HusbandryCollege of Animal Science and Veterinary MedicineTianjin Agricultural UniversityTianjinChina
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Hitachi K, Nakatani M, Kiyofuji Y, Inagaki H, Kurahashi H, Tsuchida K. An Analysis of Differentially Expressed Coding and Long Non-Coding RNAs in Multiple Models of Skeletal Muscle Atrophy. Int J Mol Sci 2021; 22:ijms22052558. [PMID: 33806354 PMCID: PMC7961583 DOI: 10.3390/ijms22052558] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
The loss of skeletal muscle mass (muscle atrophy or wasting) caused by aging, diseases, and injury decreases quality of life, survival rates, and healthy life expectancy in humans. Although long non-coding RNAs (lncRNAs) have been implicated in skeletal muscle formation and differentiation, their precise roles in muscle atrophy remain unclear. In this study, we used RNA-sequencing (RNA-Seq) to examine changes in the expression of lncRNAs in four muscle atrophy conditions (denervation, casting, fasting, and cancer cachexia) in mice. We successfully identified 33 annotated lncRNAs and 18 novel lncRNAs with common expression changes in all four muscle atrophy conditions. Furthermore, an analysis of lncRNA–mRNA correlations revealed that several lncRNAs affected small molecule biosynthetic processes during muscle atrophy. These results provide novel insights into the lncRNA-mediated regulatory mechanism underlying muscle atrophy and may be useful for the identification of promising therapeutic targets.
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Affiliation(s)
- Keisuke Hitachi
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.); (Y.K.)
| | - Masashi Nakatani
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.); (Y.K.)
- Faculty of Rehabilitation and Care, Seijoh University, Tokai 476-0014, Japan
| | - Yuri Kiyofuji
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.); (Y.K.)
| | - Hidehito Inagaki
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake 470-1192, Japan; (H.I.); (H.K.)
- Division of Molecular Genetics, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan
| | - Hiroki Kurahashi
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake 470-1192, Japan; (H.I.); (H.K.)
- Division of Molecular Genetics, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan
| | - Kunihiro Tsuchida
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.); (Y.K.)
- Correspondence: ; Tel.: +81-(562)-93-9384
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Lnc-ORA interacts with microRNA-532-3p and IGF2BP2 to inhibit skeletal muscle myogenesis. J Biol Chem 2021; 296:100376. [PMID: 33548229 PMCID: PMC8289116 DOI: 10.1016/j.jbc.2021.100376] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscle is one of the most important organs of the animal body. Long noncoding RNAs play a crucial role in the regulation of skeletal muscle development via several mechanisms. We recently identified obesity-related lncRNA (lnc-ORA) in a search for long noncoding RNAs that influence adipogenesis, finding it impacted adipocyte differentiation by regulating the PI3K/protein kinase B/mammalian target of rapamycin pathway. However, whether lnc-ORA has additional roles, specifically in skeletal muscle myogenesis, is not known. Here, we found that lnc-ORA was significantly differentially expressed with age in mouse skeletal muscle tissue and predominantly located in the cytoplasm. Overexpression of lnc-ORA promoted C2C12 myoblast proliferation and inhibited myoblast differentiation. In contrast, lnc-ORA knockdown repressed myoblast proliferation and facilitated myoblast differentiation. Interestingly, silencing of lnc-ORA rescued dexamethasone-induced muscle atrophy in vitro. Furthermore, adeno-associated virus 9–mediated overexpression of lnc-ORA decreased muscle mass and the cross-sectional area of muscle fiber by upregulating the levels of muscle atrophy–related genes and downregulating the levels of myogenic differentiation–related genes in vivo. Mechanistically, lnc-ORA inhibited skeletal muscle myogenesis by acting as a sponge of miR-532-3p, which targets the phosphatase and tensin homolog gene; the resultant changes in phosphatase and tensin homolog suppressed the PI3K/protein kinase B signaling pathway. In addition, lnc-ORA interacted with insulin-like growth factor 2 mRNA-binding protein 2 and reduced the stability of myogenesis genes, such as myogenic differentiation 1 and myosin heavy chain. Collectively, these findings indicate that lnc-ORA could be a novel underlying regulator of skeletal muscle development.
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Rugowska A, Starosta A, Konieczny P. Epigenetic modifications in muscle regeneration and progression of Duchenne muscular dystrophy. Clin Epigenetics 2021; 13:13. [PMID: 33468200 PMCID: PMC7814631 DOI: 10.1186/s13148-021-01001-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a multisystemic disorder that affects 1:5000 boys. The severity of the phenotype varies dependent on the mutation site in the DMD gene and the resultant dystrophin expression profile. In skeletal muscle, dystrophin loss is associated with the disintegration of myofibers and their ineffective regeneration due to defective expansion and differentiation of the muscle stem cell pool. Some of these phenotypic alterations stem from the dystrophin absence-mediated serine-threonine protein kinase 2 (MARK2) misplacement/downregulation in activated muscle stem (satellite) cells and neuronal nitric oxide synthase loss in cells committed to myogenesis. Here, we trace changes in DNA methylation, histone modifications, and expression of regulatory noncoding RNAs during muscle regeneration, from the stage of satellite cells to myofibers. Furthermore, we describe the abrogation of these epigenetic regulatory processes due to changes in signal transduction in DMD and point to therapeutic treatments increasing the regenerative potential of diseased muscles based on this acquired knowledge.
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Affiliation(s)
- Anna Rugowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Alicja Starosta
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland
| | - Patryk Konieczny
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
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Sweeney BA, Petrov AI, Ribas CE, Finn RD, Bateman A, Szymanski M, Karlowski WM, Seemann SE, Gorodkin J, Cannone JJ, Gutell RR, Kay S, Marygold S, dos Santos G, Frankish A, Mudge JM, Barshir R, Fishilevich S, Chan PP, Lowe TM, Seal R, Bruford E, Panni S, Porras P, Karagkouni D, Hatzigeorgiou AG, Ma L, Zhang Z, Volders PJ, Mestdagh P, Griffiths-Jones S, Fromm B, Peterson KJ, Kalvari I, Nawrocki EP, Petrov AS, Weng S, Bouchard-Bourelle P, Scott M, Lui LM, Hoksza D, Lovering RC, Kramarz B, Mani P, Ramachandran S, Weinberg Z. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res 2021; 49:D212-D220. [PMID: 33106848 PMCID: PMC7779037 DOI: 10.1093/nar/gkaa921] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022] Open
Abstract
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.
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29
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Otsuka K, Matsubara S, Shiraishi A, Takei N, Satoh Y, Terao M, Takada S, Kotani T, Satake H, Kimura AP. A Testis-Specific Long Noncoding RNA, Start, Is a Regulator of Steroidogenesis in Mouse Leydig Cells. Front Endocrinol (Lausanne) 2021; 12:665874. [PMID: 33897623 PMCID: PMC8061315 DOI: 10.3389/fendo.2021.665874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022] Open
Abstract
The testis expresses many long noncoding RNAs (lncRNAs), but their functions and overview of lncRNA variety are not well understood. The mouse Prss/Tessp locus contains six serine protease genes and two lncRNAs that have been suggested to play important roles in spermatogenesis. Here, we found a novel testis-specific lncRNA, Start (Steroidogenesis activating lncRNA in testis), in this locus. Start is 1822 nucleotides in length and was found to be localized mostly in the cytosol of germ cells and Leydig cells, although nuclear localization was also observed. Start-knockout (KO) mice generated by the CRISPR/Cas9 system were fertile and showed no morphological abnormality in adults. However, in adult Start-KO testes, RNA-seq and qRT-PCR analyses revealed an increase in the expression of steroidogenic genes such as Star and Hsd3b1, while ELISA analysis revealed that the testosterone levels in serum and testis were significantly low. Interestingly, at 8 days postpartum, both steroidogenic gene expression and testosterone level were decreased in Start-KO mice. Since overexpression of Start in two Leydig-derived cell lines resulted in elevation of the expression of steroidogenic genes including Star and Hsd3b1, Start is likely to be involved in their upregulation. The increase in expression of steroidogenic genes in adult Start-KO testes might be caused by a secondary effect via the androgen receptor autocrine pathway or the hypothalamus-pituitary-gonadal axis. Additionally, we observed a reduced number of Leydig cells at 8 days postpartum. Collectively, our results strongly suggest that Start is a regulator of steroidogenesis in Leydig cells. The current study provides an insight into the overall picture of the function of testis lncRNAs.
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Affiliation(s)
- Kai Otsuka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Natsumi Takei
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Miho Terao
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of NCCHD Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoya Kotani
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P. Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
- *Correspondence: Atsushi P. Kimura,
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30
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Joshi M, Rajender S. Long non-coding RNAs (lncRNAs) in spermatogenesis and male infertility. Reprod Biol Endocrinol 2020; 18:103. [PMID: 33126901 PMCID: PMC7599102 DOI: 10.1186/s12958-020-00660-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have a size of more than 200 bp and are known to regulate a host of crucial cellular processes like proliferation, differentiation and apoptosis by regulating gene expression. While small noncoding RNAs (ncRNAs) such as miRNAs, siRNAs, Piwi-interacting RNAs have been extensively studied in male germ cell development, the role of lncRNAs in spermatogenesis remains largely unknown. OBJECTIVE In this article, we have reviewed the biology and role of lncRNAs in spermatogenesis along with the tools available for data analysis. RESULTS AND CONCLUSIONS Till date, three microarray and four RNA-seq studies have been undertaken to identify lncRNAs in mouse testes or germ cells. These studies were done on pre-natal, post-natal, adult testis, and different germ cells to identify lncRNAs regulating spermatogenesis. In case of humans, five RNA-seq studies on different germ cell populations, including two on sperm, were undertaken. We compared three studies on human germ cells to identify common lncRNAs and found 15 lncRNAs (LINC00635, LINC00521, LINC00174, LINC00654, LINC00710, LINC00226, LINC00326, LINC00494, LINC00535, LINC00616, LINC00662, LINC00668, LINC00467, LINC00608, and LINC00658) to show consistent differential expression across these studies. Some of the targets of these lncRNAs included CENPB, FAM98B, GOLGA6 family, RPGR, TPM2, GNB5, KCNQ10T1, TAZ, LIN28A, CDKN2B, CDKN2A, CDKN1A, CDKN1B, CDKN1C, EZH2, SUZ12, VEGFA genes. A lone study on human male infertility identified 9879 differentially expressed lncRNAs with three (lnc32058, lnc09522, and lnc98497) of them showing specific and high expression in immotile sperm in comparison to normal motile sperm. A few lncRNAs (Mrhl, Drm, Spga-lncRNAs, NLC1-C, HongrES2, Tsx, LncRNA-tcam1, Tug1, Tesra, AK015322, Gm2044, and LncRNA033862) have been functionally validated for their roles in spermatogenesis. Apart from rodents and humans, studies on sheep and bull have also identified lncRNAs potentially important for spermatogenesis. A number of these non-coding RNAs are strong candidates for further research on their roles in spermatogenesis.
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Affiliation(s)
- Meghali Joshi
- Division of Endocrinology, Central Drug Research Institute, Lucknow, UP, India
| | - Singh Rajender
- Division of Endocrinology, Central Drug Research Institute, Lucknow, UP, India.
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Koutelou E, Farria AT, Dent SYR. Complex functions of Gcn5 and Pcaf in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194609. [PMID: 32730897 DOI: 10.1016/j.bbagrm.2020.194609] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
A wealth of biochemical and cellular data, accumulated over several years by multiple groups, has provided a great degree of insight into the molecular mechanisms of actions of GCN5 and PCAF in gene activation. Studies of these lysine acetyltransferases (KATs) in vitro, in cultured cells, have revealed general mechanisms for their recruitment by sequence-specific binding factors and their molecular functions as transcriptional co-activators. Genetic studies indicate that GCN5 and PCAF are involved in multiple developmental processes in vertebrates, yet our understanding of their molecular functions in these contexts remains somewhat rudimentary. Understanding the functions of GCN5/PCAF in developmental processes provides clues to the roles of these KATs in disease states. Here we will review what is currently known about the developmental roles of GCN5 and PCAF, as well as emerging role of these KATs in oncogenesis.
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Affiliation(s)
- Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America.
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Yoneda R, Ueda N, Uranishi K, Hirasaki M, Kurokawa R. Long noncoding RNA pncRNA-D reduces cyclin D1 gene expression and arrests cell cycle through RNA m 6A modification. J Biol Chem 2020; 295:5626-5639. [PMID: 32165496 PMCID: PMC7186179 DOI: 10.1074/jbc.ra119.011556] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Indexed: 12/18/2022] Open
Abstract
pncRNA-D is an irradiation-induced 602-nt long noncoding RNA transcribed from the promoter region of the cyclin D1 (CCND1) gene. CCND1 expression is predicted to be inhibited through an interplay between pncRNA-D and RNA-binding protein TLS/FUS. Because the pncRNA-D-TLS interaction is essential for pncRNA-D-stimulated CCND1 inhibition, here we studied the possible role of RNA modification in this interaction in HeLa cells. We found that osmotic stress induces pncRNA-D by recruiting RNA polymerase II to its promoter. pncRNA-D was highly m6A-methylated in control cells, but osmotic stress reduced the methylation and also arginine methylation of TLS in the nucleus. Knockdown of the m6A modification enzyme methyltransferase-like 3 (METTL3) prolonged the half-life of pncRNA-D, and among the known m6A recognition proteins, YTH domain-containing 1 (YTHDC1) was responsible for binding m6A of pncRNA-D Knockdown of METTL3 or YTHDC1 also enhanced the interaction of pncRNA-D with TLS, and results from RNA pulldown assays implicated YTHDC1 in the inhibitory effect on the TLS-pncRNA-D interaction. CRISPR/Cas9-mediated deletion of candidate m6A site decreased the m6A level in pncRNA-D and altered its interaction with the RNA-binding proteins. Of note, a reduction in the m6A modification arrested the cell cycle at the G0/G1 phase, and pncRNA-D knockdown partially reversed this arrest. Moreover, pncRNA-D induction in HeLa cells significantly suppressed cell growth. Collectively, these findings suggest that m6A modification of the long noncoding RNA pncRNA-D plays a role in the regulation of CCND1 gene expression and cell cycle progression.
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Affiliation(s)
- Ryoma Yoneda
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama 350-1241, Japan
| | - Naomi Ueda
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama 350-1241, Japan
| | - Kousuke Uranishi
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama 350-1241, Japan
| | - Masataka Hirasaki
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama 350-1241, Japan
| | - Riki Kurokawa
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama 350-1241, Japan.
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Chellini L, Frezza V, Paronetto MP. Dissecting the transcriptional regulatory networks of promoter-associated noncoding RNAs in development and cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:51. [PMID: 32183847 PMCID: PMC7079525 DOI: 10.1186/s13046-020-01552-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/25/2020] [Indexed: 12/31/2022]
Abstract
In-depth analysis of global RNA sequencing has enabled a comprehensive overview of cellular transcriptomes and revealed the pervasive transcription of divergent RNAs from promoter regions across eukaryotic genomes. These studies disclosed that genomes encode a vast repertoire of RNAs beyond the well-known protein-coding messenger RNAs. Furthermore, they have provided novel insights into the regulation of eukaryotic epigenomes, and transcriptomes, including the identification of novel classes of noncoding transcripts, such as the promoter-associated noncoding RNAs (pancRNAs). PancRNAs are defined as transcripts transcribed within few hundred bases from the transcription start sites (TSSs) of protein-coding or non-coding genes. Unlike the long trans-acting ncRNAs that regulate expression of target genes located in different chromosomal domains and displaying their function both in the nucleus and in the cytoplasm, the pancRNAs operate as cis-acting elements in the transcriptional regulation of neighboring genes. PancRNAs are very recently emerging as key players in the epigenetic regulation of gene expression programs in development and diseases. Herein, we review the complex epigenetic network driven by pancRNAs in eukaryotic cells, their impact on physiological and pathological states, which render them promising targets for novel therapeutic strategies.
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Affiliation(s)
- Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
| | - Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Santa Lucia Foundation, 00143, Rome, Italy. .,Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135, Rome, Italy.
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Long Non-Coding RNA H19 Promotes Porcine Satellite Cell Differentiation by Interacting with TDP43. Genes (Basel) 2020; 11:genes11030259. [PMID: 32121115 PMCID: PMC7140797 DOI: 10.3390/genes11030259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in fundamental and diverse biological processes, including myogenesis. However, the molecular mechanisms involved in this process remain largely unexplored. This study found that H19 affected the differentiation of porcine satellite cells (PSCs) by directly binding to the DNA/RNA-binding protein TDP43. Functional analyses showed that TDP43 knockdown decreased PSC differentiation, whereas TDP43 overexpression exerted opposite effects in vitro. Furthermore, rescue experiments demonstrated that TDP43 can rescue the decrease in PSC differentiation caused by H19 knockdown. Mechanistically, H19 may act as a scaffold to recruit TDP43 to the promoters of MYOD and thereby activate the transcription of MYOD, leading to PSC differentiation. In summary, we elucidate the molecular mechanism by which H19 and TDP43 regulate myogenesis.
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Hitachi K, Nakatani M, Funasaki S, Hijikata I, Maekawa M, Honda M, Tsuchida K. Expression Levels of Long Non-Coding RNAs Change in Models of Altered Muscle Activity and Muscle Mass. Int J Mol Sci 2020; 21:ijms21051628. [PMID: 32120896 PMCID: PMC7084395 DOI: 10.3390/ijms21051628] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle is a highly plastic organ that is necessary for homeostasis and health of the human body. The size of skeletal muscle changes in response to intrinsic and extrinsic stimuli. Although protein-coding RNAs including myostatin, NF-κβ, and insulin-like growth factor-1 (IGF-1), have pivotal roles in determining the skeletal muscle mass, the role of long non-coding RNAs (lncRNAs) in the regulation of skeletal muscle mass remains to be elucidated. Here, we performed expression profiling of nine skeletal muscle differentiation-related lncRNAs (DRR, DUM1, linc-MD1, linc-YY1, LncMyod, Neat1, Myoparr, Malat1, and SRA) and three genomic imprinting-related lncRNAs (Gtl2, H19, and IG-DMR) in mouse skeletal muscle. The expression levels of these lncRNAs were examined by quantitative RT-PCR in six skeletal muscle atrophy models (denervation, casting, tail suspension, dexamethasone-administration, cancer cachexia, and fasting) and two skeletal muscle hypertrophy models (mechanical overload and deficiency of the myostatin gene). Cluster analyses of these lncRNA expression levels were successfully used to categorize the muscle atrophy models into two sub-groups. In addition, the expression of Gtl2, IG-DMR, and DUM1 was altered along with changes in the skeletal muscle size. The overview of the expression levels of lncRNAs in multiple muscle atrophy and hypertrophy models provides a novel insight into the role of lncRNAs in determining the skeletal muscle mass.
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Affiliation(s)
- Keisuke Hitachi
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.)
| | - Masashi Nakatani
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.)
| | - Shiori Funasaki
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.)
| | - Ikumi Hijikata
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.)
| | - Mizuki Maekawa
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.)
| | - Masahiko Honda
- Department of Biochemistry, Kindai University Faculty of Medicine, Osaka-Sayama 589-8511, Japan;
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center Research Institute, Suita 564-8565, Japan
| | - Kunihiro Tsuchida
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, Toyoake 470-1192, Japan; (K.H.); (M.N.)
- Correspondence: ; Tel.: +81-562-93-9384
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MEG3 Promotes Differentiation of Porcine Satellite Cells by Sponging miR-423-5p to Relieve Inhibiting Effect on SRF. Cells 2020; 9:cells9020449. [PMID: 32075310 PMCID: PMC7072828 DOI: 10.3390/cells9020449] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Although thousands of long noncoding RNAs (lncRNAs) have been identified in porcine growth and development, the regulation mechanisms of functional lncRNAs have not been well explored. In this study, using 5′- and 3′-rapid amplification of cDNA ends (RACE) assays, we obtained two different variants of lncRNA maternally expressed gene 3 (MEG3), namely, MEG3 v1 and MEG3 v2, that were both highly expressed in porcine skeletal muscle and in the early stage of the differentiation of porcine satellite cells. Moreover, we identified the core transcript MEG3 v2. Functional analyses showed that MEG3 overexpression could effectively arrest myoblasts in the G1 phase, inhibit DNA replication, and promote myoblast differentiation, whereas MEG3 knockdown resulted in the opposite effects. Interestingly, the expression of serum response factor (SRF), a crucial transcription factor for myogenesis process, remarkably increased and decreased in mRNA and protein levels with the respective overexpression and knockdown of MEG3. Dual luciferase reporter assay showed that MEG3 could attenuate the decrease of luciferase activity of SRF induced by miR-423-5p in a dose-dependent manner. MEG3 overexpression could relieve the inhibitory effect on SRF and myoblast differentiation induced by miR-423-5p. In addition, results of RNA immunoprecipitation analysis suggested that MEG3 could act as a ceRNA for miR-423-5p. Our findings initially established a novel connection among MEG3, miR-423-5p, and SRF in porcine satellite cell differentiation. This novel role of MEG3 may shed new light on understanding of molecular regulation of lncRNA in porcine myogenesis.
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Martone J, Mariani D, Desideri F, Ballarino M. Non-coding RNAs Shaping Muscle. Front Cell Dev Biol 2020; 7:394. [PMID: 32117954 PMCID: PMC7019099 DOI: 10.3389/fcell.2019.00394] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 12/26/2019] [Indexed: 12/19/2022] Open
Abstract
In 1957, Francis Crick speculated that RNA, beyond its protein-coding capacity, could have its own function. Decade after decade, this theory was dramatically boosted by the discovery of new classes of non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and circular RNAs (circRNAs), which play a fundamental role in the fine spatio-temporal control of multiple layers of gene expression. Recently, many of these molecules have been identified in a plethora of different tissues, and they have emerged to be more cell-type specific than protein-coding genes. These findings shed light on how ncRNAs are involved in the precise tuning of gene regulatory mechanisms governing tissues homeostasis. In this review, we discuss the recent findings on the mechanisms used by lncRNAs and circRNAs to sustain skeletal and cardiac muscle formation, paying particular attention to the technological developments that, over the last few years, have aided their genome-wide identification and study. Together with lncRNAs and circRNAs, the emerging contribution of Piwi-interacting RNAs and transfer RNA-derived fragments to myogenesis will be also discussed, with a glimpse on the impact of their dysregulation in muscle disorders, such as myopathies, muscle atrophy, and rhabdomyosarcoma degeneration.
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Affiliation(s)
- Julie Martone
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Davide Mariani
- Center for Human Technologies, Italian Institute of Technology, Genoa, Italy
| | - Fabio Desideri
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
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Sweta S, Dudnakova T, Sudheer S, Baker AH, Bhushan R. Importance of Long Non-coding RNAs in the Development and Disease of Skeletal Muscle and Cardiovascular Lineages. Front Cell Dev Biol 2019; 7:228. [PMID: 31681761 PMCID: PMC6813187 DOI: 10.3389/fcell.2019.00228] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
The early mammalian embryo is characterized by the presence of three germ layers-the outer ectoderm, middle mesoderm and inner endoderm. The mesoderm is organized into paraxial, intermediate and lateral plate mesoderm. The musculature, vasculature and heart of the adult body are the major derivatives of mesoderm. Tracing back the developmental process to generate these specialized tissues has sparked much interest in the field of regenerative medicine focusing on generating specialized tissues to treat patients with degenerative diseases. Several Long Non-Coding RNAs (lncRNAs) have been identified as regulators of development, proliferation and differentiation of various tissues of mesodermal origin. A better understanding of lncRNAs that can regulate the development of these tissues will open potential avenues for their therapeutic utility and enhance our knowledge about disease progression and development. In this review, we aim to summarize the functions and mechanisms of lncRNAs regulating the early mesoderm differentiation, development and homeostasis of skeletal muscle and cardiovascular system with an emphasis on their therapeutic potential.
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Affiliation(s)
- Sweta Sweta
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Tatiana Dudnakova
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Smita Sudheer
- Department of Genomic Science, Central University of Kerala, Kasaragod, India
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Raghu Bhushan
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
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Zhang K, Zhang M, Yao Q, Han X, Zhao Y, Zheng L, Li G, Liu Q, Chang Y, Zhang P, Cui H, Shi Z, Chen T, Yao Z, Han T, Hong W. The hepatocyte-specifically expressed lnc-HSER alleviates hepatic fibrosis by inhibiting hepatocyte apoptosis and epithelial-mesenchymal transition. Theranostics 2019; 9:7566-7582. [PMID: 31695787 PMCID: PMC6831459 DOI: 10.7150/thno.36942] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/02/2019] [Indexed: 12/19/2022] Open
Abstract
Liver fibrosis leading to cirrhosis is one of the major health burdens worldwide with currently limited therapeutic options available. Long noncoding RNAs (lncRNAs) play important roles in various biological and pathological processes in a cell- or tissue-specific manner. However, there is still an important gap in the understanding of the role of hepatocyte-specific lncRNAs in liver fibrosis. Methods: The expressions of lnc-Hser in human and mice fibrotic livers as well as primary hepatocytes (HCs) of mice developing liver fibrosis were determined by real-time RT-PCR. The roles and mechanisms of lnc-Hser in HCs and liver fibrosis were determined in vitro and in vivo. Results: In this study, we have identified a hepatocyte-specifically expressed lnc-Hser, which was reduced in human and mice fibrotic livers as well as primary HCs of mice developing liver fibrosis. We have shown that silencing lnc-Hser aggravated liver fibrosis both in vitro and in vivo through inducing the epithelial-mesenchymal transition (EMT) and the apoptosis of HCs. In addition, knockdown of lnc-Hser promoted hepatic stellate cells (HSCs) activation through the signals derived from injured HCs. Mechanistically, we have revealed that lnc-Hser inhibited HCs apoptosis via the C5AR1-Hippo-YAP pathway and suppressed HCs EMT via the Notch signaling. Conclusions: Our work has identified a hepatocyte-specific lnc-HSER that regulates liver fibrosis, providing a proof that this molecule is a novel biomarker for damaged HCs and a potential target for anti-fibrotic therapy.
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Hitachi K, Inagaki H, Kurahashi H, Okada H, Tsuchida K, Honda M. Deficiency of Vgll2 Gene Alters the Gene Expression Profiling of Skeletal Muscle Subjected to Mechanical Overload. Front Sports Act Living 2019; 1:41. [PMID: 33344964 PMCID: PMC7739700 DOI: 10.3389/fspor.2019.00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 11/19/2022] Open
Affiliation(s)
- Keisuke Hitachi
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Hidehito Inagaki
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake, Japan
| | - Hiroki Kurahashi
- Genome and Transcriptome Analysis Center, Fujita Health University, Toyoake, Japan
| | - Hitoshi Okada
- Department of Biochemistry, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Kunihiro Tsuchida
- Division for Therapies against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Masahiko Honda
- Department of Biochemistry, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan.,Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
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Functions and Regulatory Mechanisms of lncRNAs in Skeletal Myogenesis, Muscle Disease and Meat Production. Cells 2019; 8:cells8091107. [PMID: 31546877 PMCID: PMC6769631 DOI: 10.3390/cells8091107] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/04/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
Myogenesis is a complex biological process, and understanding the regulatory network of skeletal myogenesis will contribute to the treatment of human muscle related diseases and improvement of agricultural animal meat production. Long noncoding RNAs (lncRNAs) serve as regulators in gene expression networks, and participate in various biological processes. Recent studies have identified functional lncRNAs involved in skeletal muscle development and disease. These lncRNAs regulate the proliferation, differentiation, and fusion of myoblasts through multiple mechanisms, such as chromatin modification, transcription regulation, and microRNA sponge activity. In this review, we presented the latest advances regarding the functions and regulatory activities of lncRNAs involved in muscle development, muscle disease, and meat production. Moreover, challenges and future perspectives related to the identification of functional lncRNAs were also discussed.
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Hitachi K, Tsuchida K. Data describing the effects of depletion of Myoparr, myogenin, Ddx17, and hnRNPK in differentiating C2C12 cells. Data Brief 2019; 25:104172. [PMID: 31321265 PMCID: PMC6612617 DOI: 10.1016/j.dib.2019.104172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/07/2019] [Accepted: 06/14/2019] [Indexed: 11/30/2022] Open
Abstract
Myoparr is a promoter-associated long non-coding RNA (lncRNA) that is expressed from the promoter region of myogenin gene. Myoparr is essential for the proper differentiation of skeletal muscle cells; it accomplishes this by activating the expression of myogenin and myogenic microRNAs (miRNAs). In this study, we provide the RNA-seq data describing the changes in gene expression induced by knockdown of Myoparr, myogenin, and two Myoparr-binding proteins (Ddx17 and hnRNPK) during skeletal muscle differentiation in C2C12 cells. Raw data files were deposited in Sequence Read Archive in DNA Data Bank of Japan (DDBJ) under the accession number DRA005527. These data are related to the research article "Myogenin promoter-associated lncRNA Myoparr is essential for myogenic differentiation" Hitachi et al., 2019.
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Affiliation(s)
- Keisuke Hitachi
- Division for Therapies Against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Kunihiro Tsuchida
- Division for Therapies Against Intractable Diseases, Institute for Comprehensive Medical Science (ICMS), Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
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Long Non-Coding RNA Myoparr Regulates GDF5 Expression in Denervated Mouse Skeletal Muscle. Noncoding RNA 2019; 5:ncrna5020033. [PMID: 30965639 PMCID: PMC6631233 DOI: 10.3390/ncrna5020033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscle is a highly plastic tissue and decreased skeletal muscle mass (muscle atrophy) results in deteriorated motor function and perturbed body homeostasis. Myogenin promoter-associated long non-coding RNA (lncRNA) Myoparr promotes skeletal muscle atrophy caused by surgical denervation; however, the precise molecular mechanism remains unclear. Here, we examined the downstream genes of Myoparr during muscle atrophy following denervation of tibialis anterior (TA) muscles in C57BL/6J mice. Myoparr knockdown affected the expression of 848 genes. Sixty-five of the genes differentially regulated by Myoparr knockdown coded secretory proteins. Among these 65 genes identified in Myoparr-depleted skeletal muscles after denervation, we focused on the increased expression of growth/differentiation factor 5 (GDF5), an inhibitor of muscle atrophy. Myoparr knockdown led to activated bone morphogenetic protein (BMP) signaling in denervated muscles, as indicated by the increased levels of phosphorylated Smad1/5/8. Our detailed evaluation of downstream genes of Myoparr also revealed that Myoparr regulated differential gene expression between myogenic differentiation and muscle atrophy. This is the first report demonstrating the in vivo role of Myoparr in regulating BMP signaling in denervated muscles. Therefore, lncRNAs that have inhibitory activity on BMP signaling may be putative therapeutic targets for skeletal muscle atrophy.
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