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Lei S, Chen R, Shi H, Zhou S, She Y. lncRNA AK159072 Promotes Myoblast Proliferation and Muscle Regeneration Through Activation of Akt/Foxo1 Pathway. J Biochem Mol Toxicol 2025; 39:e70292. [PMID: 40341721 DOI: 10.1002/jbt.70292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 03/19/2025] [Accepted: 04/25/2025] [Indexed: 05/10/2025]
Abstract
Long non-coding RNAs (lncRNAs) are significant regulators of myoblast proliferation, migration and regeneration. In our previous research, we identified that lncRNA AK159072 was differentially expressed during myoblast development. In this study, we would like to explore the regulatory role and the mechanisms of AK159072 in proliferation. We discovered that AK159072 was increasingly expressed during myoblast proliferation and was located in both the nucleus and cytoplasm of proliferating C2C12 myoblasts. Overexpression of AK159072 promoted the expression of proliferation-related genes c-Myc, cyclin-dependent kinase 2 (CDK2), CDK4, and CDK6 in C2C12 myoblasts. Additionally, the cell viability and EdU-positive cells were increased, while the wound size was decreased after overexpression AK159072. In contrast, cell proliferation was attenuated when AK159072 was successfully silenced. Furthermore, the cross sectional area (CSA) and proliferative markers were decreased after knockdown of AK159072 in the mouse hind leg muscles with CTX-induced injury in vivo, indicating that knockdown of AK159072 may delay muscle regeneration. The study further demonstrated that Akt/Foxo1 pathway mediated the effects of AK159072 overexpression and knockdown in myoblasts. Taken together, our results suggested that AK159072 may regulate myoblast proliferation and muscle regeneration via Akt/Foxo1 pathway. The study suggestd that modulating the expression of AK159072 could be a potential therapeutic strategy for muscle injuries, this could have significant clinical relevance for conditions such as muscular dystrophy, sarcopenia, and other muscle disorders.
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Affiliation(s)
- Si Lei
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Rui Chen
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Huacai Shi
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Shanyao Zhou
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Yanling She
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, Guangdong, China
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2
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Li Y, Li C, Sun Q, Liu X, Chen F, Cheung Y, Zhao Y, Xie T, Chazaud B, Sun H, Wang H. Skeletal muscle stem cells modulate niche function in Duchenne muscular dystrophy mouse through YY1-CCL5 axis. Nat Commun 2025; 16:1324. [PMID: 39900599 PMCID: PMC11790879 DOI: 10.1038/s41467-025-56474-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 01/15/2025] [Indexed: 02/05/2025] Open
Abstract
Adult skeletal muscle stem cells (MuSCs) are indispensable for muscle regeneration and tightly regulated by macrophages (MPs) and fibro-adipogenic progenitors (FAPs) in their niche. Deregulated MuSC/MP/FAP interactions and the ensuing inflammation and fibrosis are hallmarks of dystrophic muscle. Here we demonstrate intrinsic deletion of transcription factor Yin Yang 1 (YY1) in MuSCs exacerbates dystrophic pathologies by altering composition and heterogeneity of MPs and FAPs. Further analysis reveals YY1 loss induces expression of immune genes in MuSCs, including C-C motif chemokine ligand 5 (Ccl5). Augmented CCL5 secretion promotes MP recruitment via CCL5/C-C chemokine receptor 5 (CCR5) crosstalk, which subsequently hinders FAP clearance through elevated Transforming growth factor-β1 (TGFβ1). Maraviroc-mediated pharmacological blockade of the CCL5/CCR5 axis effectively mitigates muscle dystrophy and improves muscle performance. Lastly, we demonstrate YY1 represses Ccl5 transcription by binding to its enhancer thus facilitating promoter-enhancer looping. Altogether, our study demonstrates the critical role of MuSCs in actively shaping their niche and provides novel insight into the therapeutic intervention of muscle dystrophy.
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MESH Headings
- YY1 Transcription Factor/metabolism
- YY1 Transcription Factor/genetics
- Animals
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscle, Skeletal/cytology
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/pathology
- Chemokine CCL5/metabolism
- Chemokine CCL5/genetics
- Mice
- Stem Cell Niche
- Receptors, CCR5/metabolism
- Receptors, CCR5/genetics
- Macrophages/metabolism
- Stem Cells/metabolism
- Mice, Inbred C57BL
- Transforming Growth Factor beta1/metabolism
- Male
- Mice, Inbred mdx
- Mice, Knockout
- Signal Transduction
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Grants
- 82172436 National Natural Science Foundation of China (National Science Foundation of China)
- 14115319, 14100620, 14106521, 14105823, 14120420, 14103522, 14105123 Research Grants Council, University Grants Committee (RGC, UGC)
- T13-602/21-N Research Grants Council, University Grants Committee (RGC, UGC)
- C6018-19GF Research Grants Council, University Grants Committee (RGC, UGC)
- 10210906, 08190626 Research Grants Council, University Grants Committee (RGC, UGC)
- AoE/M-402/20 Research Grants Council, University Grants Committee (RGC, UGC)
- STG1/E-403/24-N Research Grants Council, University Grants Committee (RGC, UGC)
- National Key R&D Program of China to H.W. (2022YFA0806003) Health and Medical Research Fund (HMRF) from Health Bureau of the Hong Kong Special Administrative Region, China to H.W. (10210906 and 08190626)
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Affiliation(s)
- Yang Li
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China
| | - Chuhan Li
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qiang Sun
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China
| | - Xingyuan Liu
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fengyuan Chen
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yeelo Cheung
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ting Xie
- Center for Tissue Regeneration and Engineering, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Bénédicte Chazaud
- Unité Physiopathologie et Génétique du Neurone et du Muscle, UMR CNRS 5261, Inserm U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Hao Sun
- Warshel Institute for Computational Biology, Faculty of Medicine, Chinese University of Hong Kong (Shenzhen), Guangdong, China.
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China.
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China.
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3
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Sun Q, Zhou Q, Qiao Y, Chen X, Sun H, Wang H. Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization. Nucleic Acids Res 2025; 53:gkae1271. [PMID: 39777468 PMCID: PMC11705077 DOI: 10.1093/nar/gkae1271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 11/10/2024] [Accepted: 12/12/2024] [Indexed: 01/30/2025] Open
Abstract
Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance. In this study, we investigate the potential role of RNA-binding proteins (RBPs) in TAD organization. By integrated analyses of global RBP binding and 3D genome mapping profiles from both K562 and HepG2 cells, our study unveils the prevalent enrichment of RBPs on TAD boundaries and define boundary-associated RBPs (baRBPs). We found that baRBP binding is correlated with enhanced TAD insulation strength and in a CTCF-independent manner. Moreover, baRBP binding is associated with nascent promoter transcription. Additional experimental testing was performed using RBFox2 as a paradigm. Knockdown of RBFox2 in K562 cells causes mild TAD reorganization. Moreover, RBFox2 enrichment on TAD boundaries is a conserved phenomenon in C2C12 myoblast (MB) cells. RBFox2 is downregulated and its bound boundaries are remodeled during MB differentiation into myotubes. Finally, transcriptional inhibition indeed decreases RBFox2 binding and disrupts TAD boundary insulation. Altogether, our findings demonstrate that RBPs can play an active role in modulating TAD organization through co-transcriptional association and synergistic actions with nascent promoter transcripts.
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Affiliation(s)
- Qiang Sun
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China
| | - Qin Zhou
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China
| | - Yulong Qiao
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China
| | - Xiaona Chen
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China
| | - Hao Sun
- Warshel Institute for Computational Biology, Faculty of Medicine, Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine Limited, Hong Kong Science Park, Hong Kong SAR, China
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Zhu J, Mo L, Li M, Wang Y, Zhang G, Tao Z, Liao X, Du M, He H. Long non-coding RNA Snhg15 promotes preosteoblast proliferation by interacting with and stabilizing nucleolin. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119847. [PMID: 39288892 DOI: 10.1016/j.bbamcr.2024.119847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 09/05/2024] [Accepted: 09/08/2024] [Indexed: 09/19/2024]
Abstract
The proliferation and mineralization of preosteoblasts is crucial for bone formation and has attracted extensive attentions for decades. However, the roles of numerous long non-coding RNAs (lncRNAs) in preosteoblasts have not been fully determined. This study aimed to investigate the function of lncRNA Snhg15 in preosteoblasts as well as the potential underlying mechanism. LncRNA Snhg15 was dynamically expressed during preosteoblast proliferation and mineralization, and its transcripts were localized mainly in the cytoplasm. LncRNA Snhg15 knockdown significantly inhibited the proliferation and mineralization of preosteoblasts in both a cellular model and a murine ectopic bone formation model. RNA-seq showed that lncRNA Snhg15 knockdown downregulated multiple proliferation-related genes, and cell cycle deregulation was verified by flow cytometry. Mechanistically, we found that lncRNA Snhg15 could bind to nucleolin (NCL), thereby block NCL ubiquitination and decrease its degradation. Furthermore, the overexpression of NCL in lncRNA Snhg15-knockdown preosteoblasts ameliorated GO/G1 phase cell cycle arrest. Moreover, experiments in an in situ bone formation model confirmed the negative effects of lncRNA Snhg15 deficiency on bone formation. In conclusion, this study revealed an important regulatory role of lncRNA Snhg15/NCL complex in preosteoblast proliferation and may provide insights into the molecular mechanisms underlying bone formation.
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Affiliation(s)
- Jiaqi Zhu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Lijuan Mo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Mengying Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China; Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, Jiangsu Province, China
| | - Yunlei Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Gengming Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhendong Tao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xiaozhu Liao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Mingyuan Du
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Hong He
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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5
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Gu S, Huang Q, Jie Y, Sun C, Wen C, Yang N. Transcriptomic and epigenomic landscapes of muscle growth during the postnatal period of broilers. J Anim Sci Biotechnol 2024; 15:91. [PMID: 38961455 PMCID: PMC11223452 DOI: 10.1186/s40104-024-01049-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/12/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Broilers stand out as one of the fastest-growing livestock globally, making a substantial contribution to animal meat production. However, the molecular and epigenetic mechanisms underlying the rapid growth and development of broiler chickens are still unclear. This study aims to explore muscle development patterns and regulatory networks during the postnatal rapid growth phase of fast-growing broilers. We measured the growth performance of Cornish (CC) and White Plymouth Rock (RR) over a 42-d period. Pectoral muscle samples from both CC and RR were randomly collected at day 21 after hatching (D21) and D42 for RNA-seq and ATAC-seq library construction. RESULTS The consistent increase in body weight and pectoral muscle weight across both breeds was observed as they matured, with CC outpacing RR in terms of weight at each stage of development. Differential expression analysis identified 398 and 1,129 genes in the two dimensions of breeds and ages, respectively. A total of 75,149 ATAC-seq peaks were annotated in promoter, exon, intron and intergenic regions, with a higher number of peaks in the promoter and intronic regions. The age-biased genes and breed-biased genes of RNA-seq were combined with the ATAC-seq data for subsequent analysis. The results spotlighted the upregulation of ACTC1 and FDPS at D21, which were primarily associated with muscle structure development by gene cluster enrichment. Additionally, a noteworthy upregulation of MUSTN1, FOS and TGFB3 was spotted in broiler chickens at D42, which were involved in cell differentiation and muscle regeneration after injury, suggesting a regulatory role of muscle growth and repair. CONCLUSIONS This work provided a regulatory network of postnatal broiler chickens and revealed ACTC1 and MUSTN1 as the key responsible for muscle development and regeneration. Our findings highlight that rapid growth in broiler chickens triggers ongoing muscle damage and subsequent regeneration. These findings provide a foundation for future research to investigate the functional aspects of muscle development.
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Affiliation(s)
- Shuang Gu
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Qiang Huang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Yuchen Jie
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan, 572025, China
| | - Chaoliang Wen
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Hainan, 572025, China
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding and Frontier Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China.
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Department of Animal Genetics and Breeding, College of Animal Science and Technology China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Hainan, 572025, China.
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Li X, Hou Z, Meng S, Jia Q, Xing S, Wang Z, Chen M, Xu H, Li M, Cai H. LncRNA BlncAD1 Modulates Bovine Adipogenesis by Binding to MYH10, PI3K/Akt Signaling Pathway, and miR-27a-5p/CDK6 Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11094-11110. [PMID: 38661523 DOI: 10.1021/acs.jafc.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Research on adipogenesis will help to improve the meat quality of livestock. Long noncoding RNAs (lncRNAs) are involved in mammalian adipogenesis as epigenetic modulators. In this study, we analyzed lncRNA expression during bovine adipogenesis and detected 195 differentially expressed lncRNAs, including lncRNA BlncAD1, which was significantly upregulated in mature bovine adipocytes. Gain- and loss-of-function experiments confirmed that BlncAD1 promoted the proliferation, apoptosis, and differentiation of bovine preadipocytes. RNA pull-down revealed that the nonmuscle myosin 10 (MYH10) is a potential binding protein of BlncAD1. Then, we elucidated that loss of BlncAD1 caused increased ubiquitination of MYH10, which confirmed that BlncAD1 regulates adipogenesis by enhancing the stability of the MYH10 protein. Western blotting was used to demonstrate that BlncAD1 activated the PI3K/Akt signaling pathway. Bioinformatic analysis and dual-luciferase reporter assays indicated that BlncAD1 competitively absorbed miR-27a-5p. The overexpression and interference of miR-27a-5p in bovine preadipocytes displayed that miR-27a-5p inhibited proliferation, apoptosis, and differentiation. Further results suggested that miR-27a-5p targeted the CDK6 gene and that BlncAD1 controlled the proliferation of bovine preadipocytes by modulating the miR-27a-5p/CDK6 axis. This study revealed the complex mechanisms of BlncAD1 underlying bovine adipogenesis for the first time, which would provide useful information for genetics and breeding improvement of Chinese beef cattle.
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Affiliation(s)
- Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhongyi Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shengbo Meng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Qihui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shanshan Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhitong Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengjuan Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Zhang S, Yang F, Huang Y, He L, Li Y, Wan YCE, Ding Y, Chan KM, Xie T, Sun H, Wang H. ATF3 induction prevents precocious activation of skeletal muscle stem cell by regulating H2B expression. Nat Commun 2023; 14:4978. [PMID: 37591871 PMCID: PMC10435463 DOI: 10.1038/s41467-023-40465-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 07/27/2023] [Indexed: 08/19/2023] Open
Abstract
Skeletal muscle stem cells (also called satellite cells, SCs) are important for maintaining muscle tissue homeostasis and damage-induced regeneration. However, it remains poorly understood how SCs enter cell cycle to become activated upon injury. Here we report that AP-1 family member ATF3 (Activating Transcription Factor 3) prevents SC premature activation. Atf3 is rapidly and transiently induced in SCs upon activation. Short-term deletion of Atf3 in SCs accelerates acute injury-induced regeneration, however, its long-term deletion exhausts the SC pool and thus impairs muscle regeneration. The Atf3 loss also provokes SC activation during voluntary exercise and enhances the activation during endurance exercise. Mechanistically, ATF3 directly activates the transcription of Histone 2B genes, whose reduction accelerates nucleosome displacement and gene transcription required for SC activation. Finally, the ATF3-dependent H2B expression also prevents genome instability and replicative senescence in SCs. Therefore, this study has revealed a previously unknown mechanism for preserving the SC population by actively suppressing precocious activation, in which ATF3 is a key regulator.
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Affiliation(s)
- Suyang Zhang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, China
| | - Feng Yang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yile Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liangqiang He
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yi Ching Esther Wan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518172, China
| | - Yingzhe Ding
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518172, China
| | - Ting Xie
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China.
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, New Territories, Hong Kong SAR, China.
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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: 0.3] [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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9
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Lockd promotes myoblast proliferation and muscle regeneration via binding with DHX36 to facilitate 5' UTR rG4 unwinding and Anp32e translation. Cell Rep 2022; 39:110927. [PMID: 35675771 DOI: 10.1016/j.celrep.2022.110927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/10/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Adult muscle stem cells, also known as satellite cells (SCs), play pivotal roles in muscle regeneration, and long non-coding RNA (lncRNA) functions in SCs remain largely unknown. Here, we identify a lncRNA, Lockd, which is induced in activated SCs upon acute muscle injury. We demonstrate that Lockd promotes SC proliferation; deletion of Lockd leads to cell-cycle arrest, and in vivo repression of Lockd in mouse muscles hinders regeneration process. Mechanistically, we show that Lockd directly interacts with RNA helicase DHX36 and the 5'end of Lockd possesses the strongest binding with DHX36. Furthermore, we demonstrate that Lockd stabilizes the interaction between DHX36 and EIF3B proteins; synergistically, this complex unwinds the RNA G-quadruplex (rG4) structure formed at Anp32e mRNA 5' UTR and promotes the translation of ANP32E protein, which is required for myoblast proliferation. Altogether, our findings identify a regulatory Lockd/DHX36/Anp32e axis that promotes myoblast proliferation and acute-injury-induced muscle regeneration.
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10
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Ma L, Chen W, Li S, Qin M, Zeng Y. Identification and functional prediction of long non-coding RNAs related to skeletal muscle development in Duroc pigs. Anim Biosci 2022; 35:1512-1523. [PMID: 35507853 PMCID: PMC9449383 DOI: 10.5713/ab.22.0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/23/2022] [Indexed: 12/04/2022] Open
Abstract
Objective The growth of pigs involves multiple regulatory mechanisms, and modern molecular breeding techniques can be used to understand the skeletal muscle growth and development to promote the selection process of pigs. This study aims to explore candidate lncRNAs and mRNAs related to skeletal muscle growth and development among Duroc pigs with different average daily gain (ADG). Methods A total of 8 pigs were selected and divided into two groups: H group (high-ADG) and L group (low-ADG). And followed by whole transcriptome sequencing to identify differentially expressed (DE) lncRNAs and mRNAs. Results In RNA-seq, 703 DE mRNAs (263 up-regulated and 440 down-regulated) and 74 DE lncRNAs (45 up-regulated and 29 down-regulated) were identified. In addition, 1,418 Transcription factors (TFs) were found. Compared with mRNAs, lncRNAs had fewer exons, shorter transcript length and open reading frame length. DE mRNAs and DE lncRNAs can form 417 lncRNA-mRNA pairs (antisense, cis and trans). DE mRNAs and target genes of lncRNAs were enriched in cellular processes, biological regulation, and regulation of biological processes. In addition, quantitative trait locus (QTL) analysis was used to detect the functions of DE mRNAs and lncRNAs, the most of DE mRNAs and target genes of lncRNAs were enriched in QTLs related to growth traits and skeletal muscle development. In single-nucleotide polymorphism/insertion-deletion (SNP/INDEL) analysis, 1,081,182 SNP and 131,721 INDEL were found, and transition was more than transversion. Over 60% of percentage were skipped exon events among alternative splicing events. Conclusion The results showed that different ADG among Duroc pigs with the same diet maybe due to the DE mRNAs and DE lncRNAs related to skeletal muscle growth and development.
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11
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An Emerging Role for Epigenetics in Cerebral Palsy. J Pers Med 2021; 11:jpm11111187. [PMID: 34834539 PMCID: PMC8625874 DOI: 10.3390/jpm11111187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 12/29/2022] Open
Abstract
Cerebral palsy is a set of common, severe, motor disabilities categorized by a static, nondegenerative encephalopathy arising in the developing brain and associated with deficits in movement, posture, and activity. Spastic CP, which is the most common type, involves high muscle tone and is associated with altered muscle function including poor muscle growth and contracture, increased extracellular matrix deposition, microanatomic disruption, musculoskeletal deformities, weakness, and difficult movement control. These muscle-related manifestations of CP are major causes of progressive debilitation and frequently require intensive surgical and therapeutic intervention to control. Current clinical approaches involve sophisticated consideration of biomechanics, radiologic assessments, and movement analyses, but outcomes remain difficult to predict. There is a need for more precise and personalized approaches involving omics technologies, data science, and advanced analytics. An improved understanding of muscle involvement in spastic CP is needed. Unfortunately, the fundamental mechanisms and molecular pathways contributing to altered muscle function in spastic CP are only partially understood. In this review, we outline evidence supporting the emerging hypothesis that epigenetic phenomena play significant roles in musculoskeletal manifestations of CP.
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12
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Wang Y, Luo W, Huang L, Xiao J, Song X, Li F, Ma Y, Wang X, Jin F, Liu P, Zhu Y, Kitazato K, Wang Y, Ren Z. A novel lncRNA linc-AhRA negatively regulates innate antiviral response in murine microglia upon neurotropic herpesvirus infection. Am J Cancer Res 2021; 11:9623-9651. [PMID: 34646390 PMCID: PMC8490526 DOI: 10.7150/thno.64880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Microglia are the primary cellular source of type I interferons (I-IFNs) in the brain upon neurotropic virus infection. Although the I-IFN-based antiviral innate immune response is crucial for eliminating viruses, overproduction led to immune disorders. Therefore, the relatively long-lasting I-IFNs must be precisely controlled, but the regulatory mechanism for the innate antiviral response in microglia remains largely unknown. Long non-coding RNAs (lncRNAs) are being recognized as crucial factors in numerous diseases, but their regulatory roles in the innate antiviral response in microglia are undefined. Methods: The high-throughput RNA sequencing was performed to obtain differentially expressed lncRNAs (DELs) in primary microglia infected with or without the neurotropic herpes simplex virus type 1 (HSV-1). We selected four DELs ranked in the top 15 in basic level and their fold change induced by HSV-1, i.e., FPKMHSV-1/FPKMCells.We subsequently found a key lncRNA affecting the innate antiviral response of microglia significantly. We next used dual-luciferase reporter assays, bioinformatical tools, and truncation mutants of both lncRNA and targeted proteins to elucidate the downstream and upstream mechanism of action of lncRNA. Further, we established microglia-specific knock-in (KI) mice to investigate the role of lncRNA in vivo. Results: We identified a long intergenic non-coding RNA, linc-AhRA, involved in regulating the innate antiviral response in murine microglia. linc-AhRA is activated by aryl hydrocarbon receptor (AhR) and restricts I-IFN production in microglia upon neurotropic herpesvirus infection and innate immune stimulation. Mechanistically, linc-AhRA binds to both tripartite motif-containing 27 (TRIM27) and TANK-binding kinase 1 (TBK1) through its conserved 117nt fragment as a molecular scaffold to enhance TRIM27-TBK1 interaction. This interaction facilitates the TRIM27-mediated ubiquitination of TBK1 and results in ubiquitin-proteasome-dependent degradation of TBK1. Consequently, linc-AhRA suppresses I-IFN production through facilitating TBK1 degradation and limits the microglial innate immune response against neurotropic herpesvirus infection. Microglia-specific KI of linc-AhRA mice shows a weakened antiviral immune response upon neurotropic herpesvirus challenge due to a reduction of TBK1 in microglia. Conclusion: Our findings indicate that linc-AhRA is a negative regulator of I-IFN production in microglia to avoid excessive autoimmune responses. These findings uncover a previously unappreciated role for lncRNA conserved fragments in the innate antiviral response, providing a strong foundation for developing nucleotide drugs based on conserved functional fragments within lncRNAs.
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13
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Wang YC, Yao X, Ma M, Zhang H, Wang H, Zhao L, Liu S, Sun C, Li P, Wu Y, Li X, Jiang J, Li Y, Li Y, Ying H. miR-130b inhibits proliferation and promotes differentiation in myocytes via targeting Sp1. J Mol Cell Biol 2021; 13:422-432. [PMID: 33751053 PMCID: PMC8436675 DOI: 10.1093/jmcb/mjab012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 11/29/2022] Open
Abstract
Muscle regeneration after damage or during myopathies requires a fine cooperation between myoblast proliferation and myogenic differentiation. A growing body of evidence suggests that microRNAs play critical roles in myocyte proliferation and differentiation transcriptionally. However, the molecular mechanisms underlying the orchestration are not fully understood. Here, we showed that miR-130b is able to repress myoblast proliferation and promote myogenic differentiation via targeting Sp1 transcription factor. Importantly, overexpression of miR-130b is capable of improving the recovery of damaged muscle in a freeze injury model. Moreover, miR-130b expression is declined in the muscle of muscular dystrophy patients. Thus, these results indicated that miR-130b may play a role in skeletal muscle regeneration and myopathy progression. Together, our findings suggest that the miR-130b/Sp1 axis may serve as a potential therapeutic target for the treatment of patients with muscle damage or severe myopathies.
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Affiliation(s)
- Yu-Cheng Wang
- Shanghai Xuhui District Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai 200001, China
| | - Xiaohan Yao
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mei Ma
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huihui Zhang
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Wang
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Zhao
- Department of Neuromuscular Disease, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Shengnan Liu
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Sun
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng Li
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Wu
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xihua Li
- Department of Neuromuscular Disease, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Jingjing Jiang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai 200031, China
| | - Yuying Li
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Ying
- CAS Key laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China
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14
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Chen R, Lei S, She Y, Zhou S, Shi H, Li C, Jiang T. Lnc-GD2H Promotes Proliferation by Forming a Feedback Loop With c-Myc and Enhances Differentiation Through Interacting With NACA to Upregulate Myog in C2C12 Myoblasts. Front Cell Dev Biol 2021; 9:671857. [PMID: 34490239 PMCID: PMC8416608 DOI: 10.3389/fcell.2021.671857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/07/2021] [Indexed: 11/23/2022] Open
Abstract
In the present study, the roles of a novel long non-coding RNA (lncRNA), lnc-GD2H, in promoting C2C12 myoblast proliferation and differentiation and muscle regeneration were investigated by quantitative polymerase chain reaction, western blotting, Cell Counting Kit-8, 5-ethynyl-2′-deoxyuridine (EdU), immunofluorescence staining, luciferase reporter, mass spectrometry, pulldown, chromatin immunoprecipitation, RNA immunoprecipitation assay, wound healing assays, and cardiotoxin (CTX)-induced muscle injury assays. It was observed that lnc-GD2H promoted myoblast proliferation as evidenced by the enhancement of the proliferation markers c-Myc, CDK2, CDK4, and CDK6, percentage of EdU-positive cells, and rate of cell survival during C2C12 myoblast proliferation. Additional experiments confirmed that c-Myc bound to the lnc-GD2H promoter and regulated its transcription. lnc-GD2H promoted cell differentiation with enhanced MyHC immunostaining as well as increased expression of the myogenic marker genes myogenin (Myog), Mef2a, and Mef2c during myoblast differentiation. Additional assays indicated that lnc-GD2H interacted with NACA which plays a role of transcriptional regulation in myoblast differentiation, and the enrichment of NACA at the Myog promoter was impaired by lnc-GD2H. Furthermore, inhibition of lnc-GD2H impaired muscle regeneration after CTX-induced injury in mice. lnc-GD2H facilitated the expression of proliferating marker genes and formed a feedback loop with c-Myc during myoblast proliferation. In differentiating myoblasts, lnc-GD2H interacted with NACA to relieve the inhibitory effect of NACA on Myog, facilitating Myog expression to promote differentiation. The results provide evidence for the role of lncRNAs in muscle regeneration and are useful for developing novel therapeutic targets for muscle disorders.
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Affiliation(s)
- Rui Chen
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Si Lei
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yanling She
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Shanyao Zhou
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Huacai Shi
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Cheng Li
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Ting Jiang
- Department of Radiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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15
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Translational control by DHX36 binding to 5'UTR G-quadruplex is essential for muscle stem-cell regenerative functions. Nat Commun 2021; 12:5043. [PMID: 34413292 PMCID: PMC8377060 DOI: 10.1038/s41467-021-25170-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/06/2021] [Indexed: 12/30/2022] Open
Abstract
Skeletal muscle has a remarkable ability to regenerate owing to its resident stem cells (also called satellite cells, SCs). SCs are normally quiescent; when stimulated by damage, they activate and expand to form new fibers. The mechanisms underlying SC proliferative progression remain poorly understood. Here we show that DHX36, a helicase that unwinds RNA G-quadruplex (rG4) structures, is essential for muscle regeneration by regulating SC expansion. DHX36 (initially named RHAU) is barely expressed at quiescence but is highly induced during SC activation and proliferation. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration after damage. System-wide mapping in proliferating SCs reveals DHX36 binding predominantly to rG4 structures at various regions of mRNAs, while integrated polysome profiling shows that DHX36 promotes mRNA translation via 5′-untranslated region (UTR) rG4 binding. Furthermore, we demonstrate that DHX36 specifically regulates the translation of Gnai2 mRNA by unwinding its 5′ UTR rG4 structures and identify GNAI2 as a downstream effector of DHX36 for SC expansion. Altogether, our findings uncover DHX36 as an indispensable post-transcriptional regulator of SC function and muscle regeneration acting through binding and unwinding rG4 structures at 5′ UTR of target mRNAs. Skeletal muscle stem cells (or satellite cells, SCs) are normally quiescent but activate and expand in response to injury. Here the authors show that induction of DHX36 helicase during SC activation promotes mRNA translation by binding to 5′UTR mRNA G-quadruplexes (rG4) in targets including Gnai2 and unwinding them.
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16
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Huang Y, Qiao Y, Zhao Y, Li Y, Yuan J, Zhou J, Sun H, Wang H. Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. Brief Bioinform 2021; 22:6287336. [PMID: 34056657 DOI: 10.1093/bib/bbab195] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of major biological processes and their functional modes are dictated by their subcellular localization. Relative nuclear enrichment of lncRNAs compared to mRNAs is a prevalent phenomenon but the molecular mechanisms governing their nuclear retention in cells remain largely unknown. Here in this study, we harness the recently released eCLIP data for a large number of RNA-binding proteins (RBPs) in K562 and HepG2 cells and utilize multiple bioinformatics methods to comprehensively survey the roles of RBPs in lncRNA nuclear retention. We identify an array of splicing RBPs that bind to nuclear-enriched lincRNAs (large intergenic non-coding RNAs) thus may act as trans-factors regulating their nuclear retention. Further analyses reveal that these RBPs may bind with distinct core motifs, flanking sequence compositions, or secondary structures to drive lincRNA nuclear retention. Moreover, network analyses uncover potential co-regulatory RBP clusters and the physical interaction between HNRNPU and SAFB2 proteins in K562 cells is further experimentally verified. Altogether, our analyses reveal previously unknown factors and mechanisms that govern lincRNA nuclear localization in cells.
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Affiliation(s)
- Yile Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yulong Qiao
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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17
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Guiducci G, Stojic L. Long Noncoding RNAs at the Crossroads of Cell Cycle and Genome Integrity. Trends Genet 2021; 37:528-546. [PMID: 33685661 DOI: 10.1016/j.tig.2021.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/28/2020] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Abstract
The cell cycle is controlled by guardian proteins that coordinate the process of cell growth and cell division. Alterations in these processes lead to genome instability, which has a causal link to many human diseases. Beyond their well-characterized role of influencing protein-coding genes, an increasing body of evidence has revealed that long noncoding RNAs (lncRNAs) actively participate in regulation of the cell cycle and safeguarding of genome integrity. LncRNAs are versatile molecules that act via a wide array of mechanisms. In this review, we discuss how lncRNAs are implicated in control of the cell cycle and maintenance of genome stability and how changes in lncRNA-regulatory networks lead to proliferative diseases such as cancer.
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Affiliation(s)
- Giulia Guiducci
- Barts Cancer Institute, Centre for Cancer Cell and Molecular Biology, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lovorka Stojic
- Barts Cancer Institute, Centre for Cancer Cell and Molecular Biology, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London EC1M 6BQ, UK.
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18
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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: 1.5] [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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19
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Li R, Li B, Cao Y, Li W, Dai W, Zhang L, Zhang X, Ning C, Li H, Yao Y, Tao J, Jia C, Wu W, Liu H. Long non-coding RNA Mir22hg-derived miR-22-3p promotes skeletal muscle differentiation and regeneration by inhibiting HDAC4. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:200-211. [PMID: 33767916 PMCID: PMC7957084 DOI: 10.1016/j.omtn.2021.02.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/22/2021] [Indexed: 12/31/2022]
Abstract
Emerging studies have indicated that long non-coding RNAs (lncRNAs) play important roles in skeletal muscle growth and development. Nevertheless, it remains challenging to understand the function and regulatory mechanisms of these lncRNAs in muscle biology and associated diseases. Here, we identify a novel lncRNA, Mir22hg, that is significantly upregulated during myoblast differentiation and is highly expressed in skeletal muscle. We validated that Mir22hg promotes myoblast differentiation in vitro. Mechanistically, Mir22hg gives rise to mature microRNA (miR)-22-3p, which inhibits its target gene, histone deacetylase 4 (HDAC4), thereby increasing the downstream myocyte enhancer factor 2C (MEF2C) and ultimately promoting myoblast differentiation. Furthermore, in vivo, we documented that Mir22hg knockdown delays repair and regeneration following skeletal muscle injury and further causes a significant decrease in weight following repair of an injured tibialis anterior muscle. Additionally, Mir22hg gives rise to miR-22-3p to restrict HDAC4 expression, thereby promoting the differentiation and regeneration of skeletal muscle. Given the conservation of Mir22hg between mice and humans, Mir22hg might constitute a promising new therapeutic target for skeletal muscle injury, skeletal muscle atrophy, as well as other skeletal muscle diseases.
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Affiliation(s)
- Rongyang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bojiang Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Yan Cao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weijian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weilong Dai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangliang Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Caibo Ning
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongqiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yilong Yao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jingli Tao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Jia
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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