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Liu L, Tang L, Wang Y, Liu S, Zhang Y. Expression of ITPR2 regulated by lncRNA-NONMMUT020270.2 in LPS-stimulated HT22 cells. Heliyon 2024; 10:e33491. [PMID: 39040287 PMCID: PMC11260991 DOI: 10.1016/j.heliyon.2024.e33491] [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: 03/04/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Background Long non-coding RNA (lncRNA)-NONMMUT020270.2 is downregulated and co-expressed with inositol 1,4,5-trisphosphate receptor type 2 (ITPR2) in the hippocampus of Alzheimer's disease (AD) mice. However, whether the expression of ITPR2 was regulated by lncRNA-NONMMUT020270.2 remains unclear. we aimed to investigate regulating relationship of lncRNA-NONMMUT020270.2 and ITPR2. Methods HT22 cells were firstly transfected with the pcDNA3.1-lncRNA-NONMMUT020270.2 overexpression plasmid or with the lncRNA-NONMMUT020270.2 smart silencer, and then were stimulated with lipopolysaccharide (LPS) for 24h. The mRNA expression levels of lncRNA-NONMMUT020270.2 and ITPR2 were measured by reverse transcription-quantitative PCR. Cell viability was assessed using a Cell Counting Kit 8 assay. The expression of Aβ1-42 was detected by ELISA. The expression levels of p-tau, caspase-1, and inositol trisphosphate receptor (IP3R) proteins were detected by western-blotting. Nuclear morphological changes were detected by Hoechst staining. Flow cytometry and Fluo-3/AM were carried out to determine cell apoptosis and the intracellular Ca2+. Results LPS significantly decreased cell viability, and ITPR2 mRNA and IP3R protein expression levels. While it markedly enhanced the expression levels of p-tau and Aβ1-42, cell apoptosis rate, as well as intracellular Ca2+ concentration (P < 0.05). In addition, lncRNA-NONMMUT020270.2 overexpression significantly increased the expressions levels of ITPR2 mRNA and IP3R protein (P < 0.05), and inhibited expression of p-tau and Aβ1-42, cell apoptosis rate, and reduced intracellular Ca2+ concentration (P < 0.05). By contrast, lncRNA-NONMMUT020270.2 silencing notably downregulated expressions levels of ITPR2 mRNA and IP3R protein (P < 0.05), and elevated expression levels of p-tau and Aβ1-42, cell apoptosis rate, and intracellular Ca2+ concentration (P < 0.05). Conclusion lncRNA-NONMMUT020270.2 was positively correlated with ITPR2 expression in LPS-induced cell. Downregulating the lncRNA-NONMMUT020270.2 and ITPR2 may promote cell apoptosis and increase intracellular Ca2+ concentration.
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Affiliation(s)
- Lan Liu
- Medical College, Tibet University, Lhasa, Tibet, 850000, People's Republic of China
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Liang Tang
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative Diseases, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Yan Wang
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Neurodegenerative Diseases, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yongcang Zhang
- Medical College, Tibet University, Lhasa, Tibet, 850000, People's Republic of China
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2
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Gibril BAA, Xiong X, Chai X, Xu Q, Gong J, Xu J. Unlocking the Nexus of Sirtuins: A Comprehensive Review of Their Role in Skeletal Muscle Metabolism, Development, and Disorders. Int J Biol Sci 2024; 20:3219-3235. [PMID: 38904020 PMCID: PMC11186354 DOI: 10.7150/ijbs.96885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
The sirtuins constitute a group of histone deacetylases reliant on NAD+ for their activity that have gained recognition for their critical roles as regulators of numerous biological processes. These enzymes have various functions in skeletal muscle biology, including development, metabolism, and the body's response to disease. This comprehensive review seeks to clarify sirtuins' complex role in skeletal muscle metabolism, including glucose uptake, fatty acid oxidation, mitochondrial dynamics, autophagy regulation, and exercise adaptations. It also examines their critical roles in developing skeletal muscle, including myogenesis, the determination of muscle fiber type, regeneration, and hypertrophic responses. Moreover, it sheds light on the therapeutic potential of sirtuins by examining their impact on a range of skeletal muscle disorders. By integrating findings from various studies, this review outlines the context of sirtuin-mediated regulation in skeletal muscle, highlighting their importance and possible consequences for health and disease.
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Affiliation(s)
| | | | | | | | | | - Jiguo Xu
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China
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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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4
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Zhang C, Jiang M, Liu J, Wu B, Liu C. Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L. PLANT MOLECULAR BIOLOGY 2024; 114:47. [PMID: 38632206 DOI: 10.1007/s11103-024-01434-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/25/2024] [Indexed: 04/19/2024]
Abstract
Natural Antisense Transcripts (NATs) are a kind of complex regulatory RNAs that play crucial roles in gene expression and regulation. However, the NATs in Cannabis Sativa L., a widely economic and medicinal plant rich in cannabinoids remain unknown. In this study, we comprehensively predicted C. sativa NATs genome-wide using strand-specific RNA sequencing (ssRNA-Seq) data, and validated the expression profiles by strand-specific quantitative reverse transcription PCR (ssRT-qPCR). Consequently, a total of 307 NATs were predicted in C. sativa, including 104 cis- and 203 trans- NATs. Functional enrichment analysis demonstrated the potential involvement of the C. sativa NATs in DNA polymerase activity, RNA-DNA hybrid ribonuclease activity, and nucleic acid binding. Finally, 18 cis- and 376 trans- NAT-ST pairs were predicted to produce 621 cis- and 5,679 trans- small interfering RNA (nat-siRNAs), respectively. These nat-siRNAs were potentially involved in the biosynthesis of cannabinoids and cellulose. All these results will shed light on the regulation of NATs and nat-siRNAs in C. sativa.
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Affiliation(s)
- Chang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China
- School of Pharmaceutical Sciences, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, 100193, Beijing, China.
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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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6
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Mohammadi-Pilehdarboni H, Shenagari M, Joukar F, Naziri H, Mansour-Ghanaei F. Alzheimer's disease and microorganisms: the non-coding RNAs crosstalk. Front Cell Neurosci 2024; 17:1256100. [PMID: 38249527 PMCID: PMC10796784 DOI: 10.3389/fncel.2023.1256100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/25/2023] [Indexed: 01/23/2024] Open
Abstract
Alzheimer's disease (AD) is a complex, multifactorial disorder, influenced by a multitude of variables ranging from genetic factors, age, and head injuries to vascular diseases, infections, and various other environmental and demographic determinants. Among the environmental factors, the role of the microbiome in the genesis of neurodegenerative disorders (NDs) is gaining increased recognition. This paradigm shift is substantiated by an extensive body of scientific literature, which underscores the significant contributions of microorganisms, encompassing viruses and gut-derived bacteria, to the pathogenesis of AD. The mechanism by which microbial infection exerts its influence on AD hinges primarily on inflammation. Neuroinflammation, activated in response to microbial infections, acts as a defense mechanism for the brain but can inadvertently lead to unexpected neuropathological perturbations, ultimately contributing to NDs. Given the ongoing uncertainty surrounding the genetic factors underpinning ND, comprehensive investigations into environmental factors, particularly the microbiome and viral agents, are imperative. Recent advances in neuroscientific research have unveiled the pivotal role of non-coding RNAs (ncRNAs) in orchestrating various pathways integral to neurodegenerative pathologies. While the upstream regulators governing the pathological manifestations of microorganisms remain elusive, an in-depth exploration of the nuanced role of ncRNAs holds promise for the development of prospective therapeutic interventions. This review aims to elucidate the pivotal role of ncRNAs as master modulators in the realm of neurodegenerative conditions, with a specific focus on Alzheimer's disease.
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Affiliation(s)
- Hanieh Mohammadi-Pilehdarboni
- Faculty of Medicine and Dentistry and the School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Shenagari
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Farahnaz Joukar
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
| | - Hamed Naziri
- Department of Neurology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Fariborz Mansour-Ghanaei
- Gastrointestinal and Liver Diseases Research Center, Guilan University of Medical Sciences, Rasht, Iran
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Barbagallo C, Stella M, Ferrara C, Caponnetto A, Battaglia R, Barbagallo D, Di Pietro C, Ragusa M. RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases. EXPLORATION OF MEDICINE 2023:504-540. [DOI: 10.37349/emed.2023.00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.
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Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Angela Caponnetto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Rosalia Battaglia
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
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Barangi S, Hayes AW, Karimi G. The role of lncRNAs/miRNAs/Sirt1 axis in myocardial and cerebral injury. Cell Cycle 2023; 22:1062-1073. [PMID: 36703306 PMCID: PMC10081082 DOI: 10.1080/15384101.2023.2172265] [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: 10/05/2022] [Revised: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 01/28/2023] Open
Abstract
In recent years, researchers have begun to realize the importance of the role of non-coding RNAs in the treatment of cancer and cardiovascular and neurological diseases. LncRNAs and miRNAs are important non-coding RNAs, which regulate gene expression and activate mRNA translation through binding to diverse target sites. Their involvement in the regulation of protein function and the modulation of physiological and pathological conditions continues to be investigated. Sirtuins, especially Sirt1, have a critical function in regulating a variety of physiological processes such as oxidative stress, inflammation, apoptosis, and autophagy. The lncRNAs/miRNAs/Sirt1 axis may be a novel regulatory mechanism, which is involved in the progression and/or prevention of numerous diseases. This review focuses on recent findings on the crosstalk between non-coding RNAs and Sirt1 in myocardial and cerebral injuries and may provide some insight into the development of novel approaches in the treatment of these disorders.Abbreviation: BMECs, brain microvascular endothelial cells; C2dat1, calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D)-associated transcript 1; EPCs, endothelial progenitor cells; FOXOs, forkhead transcription factors; GAS5, growth arrest-specific 5; HAECs, human aortic endothelial cells; HAND2-AS1, HAND2 Antisense RNA 1; HIF-1α, hypoxia-inducible factor-1α; ILF3-AS1, interleukin enhancer-binding factor 3-antisense RNA 1; KLF3-AS1, KLF3 antisense RNA 1; LncRNA, long noncoding RNA; LUADT1, Lung Adenocarcinoma Associated Transcript 1; MALAT1, Metastasis-associated lung adenocarcinoma transcript 1; miRNA, microRNA; NEAT1, nuclear enriched abundant transcript 1; NF-κB, nuclear factor kappa B; OIP5-AS1, Opa-interacting protein 5-antisense transcript 1; Sirt1-AS, Sirt1 Antisense RNA; SNHG7, small nucleolar RNA host gene 7; SNHG8, small nucleolar RNA host gene 8; SNHG12, small nucleolar RNA host gene 12; SNHG15, small nucleolar RNA host gene 15; STAT3, signal transducers and activators of transcription 3; TUG1, taurine up-regulated gene 1; VSMCs, vascular smooth muscle cells; XIST, X inactive specific transcript; ZFAS1, ZNFX1 Antisense RNA 1.
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Affiliation(s)
- Samira Barangi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A. Wallace Hayes
- Michigan State University, East Lansing, MI, USA
- University of South Florida, Tampa, FL, USA
| | - Gholamreza Karimi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Zhao X, Ye J, Lin X, Xue H, Zou X, Liu G, Deng M, Sun B, Guo Y, Liu D, Li Y. Identification of Key Functional Genes and LncRNAs Influencing Muscle Growth and Development in Leizhou Black Goats. Genes (Basel) 2023; 14:genes14040881. [PMID: 37107639 PMCID: PMC10138011 DOI: 10.3390/genes14040881] [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: 03/01/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Meat yield and quality are important economic traits of livestock. Herein, longissimus dorsi (LD) muscles of Leizhou black goats aged 0, 3, and 6 months were used to identify differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) by high-throughput RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to analyze differentially expressed genes. Expression levels of regulator of calcineurin 1 (RCAN1) and olfactory receptor 2AP1 (OR2AP1) were significantly different in LD muscles of goats aged 0, 3, and 6 months, indicating potentially important roles in postnatal muscle development. Differentially expressed lncRNAs and mRNAs were mainly enriched in biological processes and pathways related to cellular energy metabolism, consistent with previous studies. Three lncRNAs, TCONS_00074191, TCONS_00074190, and TCONS_00078361, may play a cis-acting role with methyltransferase-like 11B (METTL11B) genes and participate in the methylation of goat muscle proteins. Some of the identified genes may provide valuable resources for future studies on postnatal meat development in goat muscles.
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Affiliation(s)
- Xiuhui Zhao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Junning Ye
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Xunkai Lin
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Huiwen Xue
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xian Zou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
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Yang C, Zhou X, Xue Y, Li D, Wang L, Zhong T, Dai D, Cao J, Guo J, Li L, Zhang H, Zhan S. Transcriptome Analysis Reveals the Profile of Long Non-Coding RNAs during Myogenic Differentiation in Goats. Int J Mol Sci 2023; 24:ijms24076370. [PMID: 37047345 PMCID: PMC10094361 DOI: 10.3390/ijms24076370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) are emerging as essential regulators of the growth and development of skeletal muscles. However, little is known about the expression profiles of lncRNAs during the proliferation and differentiation of skeletal muscle satellite cells (MuSCs) in goats. In this study, we investigate potential regulatory lncRNAs that govern muscle development by performing lncRNA expression profiling analysis during the proliferation (cultured in the growth medium, GM) and differentiation (cultured in the differentiation medium, DM1/DM5) of MuSCs. In total, 1001 lncRNAs were identified in MuSC samples, and 314 differentially expressed (DE) (FDR < 0.05, |log2FC| > 1) lncRNAs were screened by pairwise comparisons from three comparison groups (GM-vs-DM1, GM-vs-DM5, DM1-vs-DM5). Moreover, we identified the cis-, trans-, and antisense-regulatory target genes of DE lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these target genes were significantly enriched in muscle development-related GO terms and KEGG pathways. In addition, the network of interactions between DE lncRNAs and their target genes was identified, which included well-known myogenesis regulators such as Myogenic differentiation 1 (MyoD), Myogenin (MyoG), and Myosin heavy chain (MyHC). Meanwhile, competing endogenous RNA (ceRNA) network analysis showed that 237 DE lncRNAs could bind to 329 microRNAs (miRNAs), while miRNAs could target 564 mRNAs. Together, our results provide a genome-wide resource of lncRNAs that may contribute to myogenic differentiation in goats and lay the groundwork for future investigation into their functions during skeletal muscle development.
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Chen M, Lian D, Li Y, Zhao Y, Xu X, Liu Z, Zhang J, Zhang X, Wu S, Qi S, Deng S, Yu K, Lian Z. Global Long Noncoding RNA Expression Profiling of MSTN and FGF5 Double-Knockout Sheep Reveals the Key Gatekeepers of Skeletal Muscle Development. DNA Cell Biol 2023; 42:163-175. [PMID: 36917699 DOI: 10.1089/dna.2022.0574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Improving livestock and poultry growth rates and increasing meat production are urgently needed worldwide. Previously, we produced a myostatin (MSTN) and fibroblast growth factor 5 (FGF5) double-knockout (MF-/-) sheep by CRISPR Cas9 system to improve meat production, and also wool production. Both MF-/- sheep and the F1 generation (MF+/-) sheep showed an obvious "double-muscle" phenotype. In this study, we identified the expression profiles of long noncoding RNAs (lncRNAs) in wild-type and MF+/- sheep, then screened out the key candidate lncRNAs that can regulate myogenic differentiation and skeletal muscle development. These key candidate lncRNAs can serve as critical gatekeepers for muscle contraction, calcium ion transport and skeletal muscle cell differentiation, apoptosis, autophagy, and skeletal muscle inflammation, further revealing that lncRNAs play crucial roles in regulating muscle phenotype in MF+/- sheep. In conclusion, our newly identified lncRNAs may emerge as novel molecules for muscle development or muscle disease and provide a new reference for MSTN-mediated regulation of skeletal muscle development.
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Affiliation(s)
- Mingming Chen
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yan Li
- Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing, China
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xueling Xu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhimei Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Sujun Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyu Qi
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Kun Yu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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12
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Pulik Ł, Mierzejewski B, Sibilska A, Grabowska I, Ciemerych MA, Łęgosz P, Brzóska E. The role of miRNA and lncRNA in heterotopic ossification pathogenesis. Stem Cell Res Ther 2022; 13:523. [PMID: 36522666 PMCID: PMC9753082 DOI: 10.1186/s13287-022-03213-3] [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: 05/18/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Heterotopic ossification (HO) is the formation of bone in non-osseous tissues, such as skeletal muscles. The HO could have a genetic or a non-genetic (acquired) background, that is, it could be caused by musculoskeletal trauma, such as burns, fractures, joint arthroplasty (traumatic HO), or cerebral or spinal insult (neurogenetic HO). HO formation is caused by the differentiation of stem or progenitor cells induced by local or systemic imbalances. The main factors described so far in HO induction are TGFβ1, BMPs, activin A, oncostatin M, substance P, neurotrophin-3, and WNT. In addition, dysregulation of noncoding RNAs, such as microRNA or long noncoding RNA, homeostasis may play an important role in the development of HO. For example, decreased expression of miRNA-630, which is responsible for the endothelial-mesenchymal transition, was observed in HO patients. The reduced level of miRNA-421 in patients with humeral fracture was shown to be associated with overexpression of BMP2 and a higher rate of HO occurrence. Down-regulation of miRNA-203 increased the expression of runt-related transcription factor 2 (RUNX2), a crucial regulator of osteoblast differentiation. Thus, understanding the various functions of noncoding RNAs can reveal potential targets for the prevention or treatment of HO.
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Affiliation(s)
- Łukasz Pulik
- Department of Orthopaedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005, Warsaw, Poland.
| | - Bartosz Mierzejewski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Aleksandra Sibilska
- Department of Orthopaedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Maria Anna Ciemerych
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Paweł Łęgosz
- Department of Orthopaedics and Traumatology, Medical University of Warsaw, Lindley 4 St, 02-005, Warsaw, Poland
| | - Edyta Brzóska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
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13
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CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles. Sci Rep 2022; 12:15525. [PMID: 36109624 PMCID: PMC9477841 DOI: 10.1038/s41598-022-19782-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Here, we developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, we demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species.
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14
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Resveratrol Inhibits Proliferation and Differentiation of Porcine Preadipocytes by a Novel LincRNA-ROFM/miR-133b/AdipoQ Pathway. Foods 2022; 11:foods11172690. [PMID: 36076875 PMCID: PMC9455634 DOI: 10.3390/foods11172690] [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: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Resveratrol (RES) has a wide range of biological and pharmacological activities with various health benefits for humans as a food additive. In animal production, RES has been considered a potential functional feed additive for producing high-quality pork. Long noncoding RNAs (lncRNAs) have emerged as essential regulators of fat metabolism, and phytochemicals can regulate fat metabolism through lncRNA. However, it is unclear whether RES can improve back-fat thickness by regulating lncRNA. In this study, we identified a novel lncRNA, which was named a long intergenic non-protein coding RNA, a regulator of fat metabolism (LincRNA-ROFM), from our previous lncRNA sequencing data. LincRNA-ROFM can inhibit adipocyte proliferation and differentiation. In-depth analyses showed that LincRNA-ROFM acts as a molecular sponge for miR-133b, and adiponectin (AdipoQ) is a direct target of miR-133b in porcine preadipocytes. In addition, the expression of LincRNA-ROFM was positively correlated with AdipoQ. RES can promote the expression of LincRNA-ROFM by PPARα and C/EBPα. Altogether, our research showed that LincRNA-ROFM acts as a ceRNA to sequester miR-133b and is upregulated by RES, leading to heightened AdipoQ expression, and thus decreased adipocyte proliferation and differentiation, which reduces back-fat thickness of pigs. Taken together, the RES/LincRNA-ROFM/miR-133b/AdipoQ regulatory network preliminarily explains the mechanism of action of RES in inhibiting fat deposition, which provides new insight into the downstream mechanism of RES inhibition of fat deposits by regulating the lncRNA.
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15
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Epigenetic Alterations in Sports-Related Injuries. Genes (Basel) 2022; 13:genes13081471. [PMID: 36011382 PMCID: PMC9408207 DOI: 10.3390/genes13081471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
It is a well-known fact that physical activity benefits people of all age groups. However, highly intensive training, maladaptation, improper equipment, and lack of sufficient rest lead to contusions and sports-related injuries. From the perspectives of sports professionals and those performing regular–amateur sports activities, it is important to maintain proper levels of training, without encountering frequent injuries. The bodily responses to physical stress and intensive physical activity are detected on many levels. Epigenetic modifications, including DNA methylation, histone protein methylation, acetylation, and miRNA expression occur in response to environmental changes and play fundamental roles in the regulation of cellular activities. In the current review, we summarise the available knowledge on epigenetic alterations present in tissues and organs (e.g., muscles, the brain, tendons, and bones) as a consequence of sports-related injuries. Epigenetic mechanism observations have the potential to become useful tools in sports medicine, as predictors of approaching pathophysiological alterations and injury biomarkers that have already taken place.
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16
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Zhang P, Wu S, He Y, Li X, Zhu Y, Lin X, Chen L, Zhao Y, Niu L, Zhang S, Li X, Zhu L, Shen L. LncRNA-Mediated Adipogenesis in Different Adipocytes. Int J Mol Sci 2022; 23:ijms23137488. [PMID: 35806493 PMCID: PMC9267348 DOI: 10.3390/ijms23137488] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/01/2023] Open
Abstract
Long-chain noncoding RNAs (lncRNAs) are RNAs that do not code for proteins, widely present in eukaryotes. They regulate gene expression at multiple levels through different mechanisms at epigenetic, transcription, translation, and the maturation of mRNA transcripts or regulation of the chromatin structure, and compete with microRNAs for binding to endogenous RNA. Adipose tissue is a large and endocrine-rich functional tissue in mammals. Excessive accumulation of white adipose tissue in mammals can cause metabolic diseases. However, unlike white fat, brown and beige fats release energy as heat. In recent years, many lncRNAs associated with adipogenesis have been reported. The molecular mechanisms of how lncRNAs regulate adipogenesis are continually investigated. In this review, we discuss the classification of lncRNAs according to their transcriptional location. lncRNAs that participate in the adipogenesis of white or brown fats are also discussed. The function of lncRNAs as decoy molecules and RNA double-stranded complexes, among other functions, is also discussed.
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Affiliation(s)
- Peiwen Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuang Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxu He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinrong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Zhu
- College of Life Science, China West Normal University, Nanchong 637009, China;
| | - Xutao Lin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Z.); (L.S.); Tel.: +86-28-8629-1133 (L.Z. & L.S.)
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (S.W.); (Y.H.); (X.L.); (X.L.); (L.C.); (Y.Z.); (L.N.); (S.Z.); (X.L.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Z.); (L.S.); Tel.: +86-28-8629-1133 (L.Z. & L.S.)
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17
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Li C, Shen H, Liu M, Li S, Luo Y. Natural antisense RNA Foxk1-AS promotes myogenic differentiation by inhibiting Foxk1 activity. Cell Commun Signal 2022; 20:77. [PMID: 35642035 PMCID: PMC9158385 DOI: 10.1186/s12964-022-00896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background Natural antisense RNAs are RNA molecules that are transcribed from the opposite strand of either protein-coding or non-protein coding genes and have the ability to regulate the expression of their sense gene or several related genes. However, the roles of natural antisense RNAs in the maintenance and myogenesis of muscle stem cells remain largely unexamined. Methods We analysed myoblast differentiation and regeneration by overexpression and knockdown of Foxk1-AS using lentivirus and adeno-associated virus infection in C2C12 cells and damaged muscle tissues. Muscle injury was induced by BaCl2 and the regeneration and repair of damaged muscle tissues was assessed by haematoxylin–eosin staining and quantitative real-time PCR. The expression of myogenic differentiation-related genes was verified via quantitative real-time PCR, Western blotting and immunofluorescence staining. Results We identified a novel natural antisense RNA, Foxk1-AS, which is transcribed from the opposite strand of Foxk1 DNA and completely incorporated in the 3′ UTR of Foxk1. Foxk1-AS targets Foxk1 and functions as a regulator of myogenesis. Overexpression of Foxk1-AS strongly inhibited the expression of Foxk1 in C2C12 cells and in tibialis anterior muscle tissue and promoted myoblast differentiation and the regeneration of muscle fibres damaged by BaCl2. Furthermore, overexpression of Foxk1-AS promoted the expression of Mef2c, which is an important transcription factor in the control of muscle gene expression and is negatively regulated by Foxk1. Conclusion The results indicated that Foxk1-AS represses Foxk1, thereby rescuing Mef2c activity and promoting myogenic differentiation of C2C12 cells and regeneration of damaged muscle fibres. Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00896-2.
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Affiliation(s)
- Chun Li
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204, People's Republic of China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China
| | - Hao Shen
- School of Life Science, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Meng Liu
- School of Life Science, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China.
| | - Yuping Luo
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, People's Republic of China.
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18
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Juni RP, ’t Hart KC, Houtkooper RH, Boon R. Long non‐coding RNAs in cardiometabolic disorders. FEBS Lett 2022; 596:1367-1387. [DOI: 10.1002/1873-3468.14370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Rio P. Juni
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
| | - Kelly C. ’t Hart
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
- Laboratory Genetic Metabolic Diseases Amsterdam University Medical Centers; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Science, University of Amsterdam Frankfurt am Main Germany
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases Amsterdam University Medical Centers; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Science, University of Amsterdam Frankfurt am Main Germany
| | - Reinier Boon
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
- Institute for Cardiovascular Regeneration Centre for Molecular Medicine Goethe University Frankfurt am Main Frankfurt am Main Germany
- German Centre for Cardiovascular Research DZHK Partner site Frankfurt Rhein/Main Frankfurt am Main Germany
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He ZZ, Zhao T, Qimuge N, Tian T, Yan W, Yi X, Jin J, Cai R, Yu T, Yang G, Pang W. COPS3 AS lncRNA enhances myogenic differentiation and maintains fast-type myotube phenotype. Cell Signal 2022; 95:110341. [DOI: 10.1016/j.cellsig.2022.110341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/28/2022]
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20
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Yang Y, Liu Y, Wang Y, Chao Y, Zhang J, Jia Y, Tie J, Hu D. Regulation of SIRT1 and Its Roles in Inflammation. Front Immunol 2022; 13:831168. [PMID: 35359990 PMCID: PMC8962665 DOI: 10.3389/fimmu.2022.831168] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/15/2022] [Indexed: 12/28/2022] Open
Abstract
The silent information regulator sirtuin 1 (SIRT1) protein, a highly conserved NAD+-dependent deacetylase belonging to the sirtuin family, is a post-translational regulator that plays a role in modulating inflammation. SIRT1 affects multiple biological processes by deacetylating a variety of proteins including histones and non-histone proteins. Recent studies have revealed intimate links between SIRT1 and inflammation, while alterations to SIRT1 expression and activity have been linked to inflammatory diseases. In this review, we summarize the mechanisms that regulate SIRT1 expression, including upstream activators and suppressors that operate on the transcriptional and post-transcriptional levels. We also summarize factors that influence SIRT1 activity including the NAD+/NADH ratio, SIRT1 binding partners, and post-translational modifications. Furthermore, we underscore the role of SIRT1 in the development of inflammation by commenting on the proteins that are targeted for deacetylation by SIRT1. Finally, we highlight the potential for SIRT1-based therapeutics for inflammatory diseases.
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Affiliation(s)
- Yunshu Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yang Liu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yunwei Wang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yongyi Chao
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jinxin Zhang
- Department of Emergency, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yanhui Jia
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jun Tie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Dahai Hu, ; Jun Tie,
| | - Dahai Hu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Dahai Hu, ; Jun Tie,
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21
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Zhan S, Xue Y, Yang L, Li D, Dai H, Zhong T, Wang L, Dai D, Li L, Zhang H. Transcriptome analysis reveals long non-coding natural antisense transcripts involved in muscle development in fetal goat (Capra hircus). Genomics 2022; 114:110284. [DOI: 10.1016/j.ygeno.2022.110284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/24/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022]
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22
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De la Fuente-Hernandez MA, Sarabia-Sanchez MA, Melendez-Zajgla J, Maldonado-Lagunas V. Role of lncRNAs into Mesenchymal Stromal Cell Differentiation. Am J Physiol Cell Physiol 2022; 322:C421-C460. [PMID: 35080923 DOI: 10.1152/ajpcell.00364.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Currently, findings support that 75% of the human genome is actively transcribed, but only 2% is translated into a protein, according to databases such as ENCODE (Encyclopedia of DNA Elements) [1]. The development of high-throughput sequencing technologies, computational methods for genome assembly and biological models have led to the realization of the importance of the previously unconsidered non-coding fraction of the genome. Along with this, noncoding RNAs have been shown to be epigenetic, transcriptional and post-transcriptional regulators in a large number of cellular processes [2]. Within the group of non-coding RNAs, lncRNAs represent a fascinating field of study, given the functional versatility in their mode of action on their molecular targets. In recent years, there has been an interest in learning about lncRNAs in MSC differentiation. The aim of this review is to address the signaling mechanisms where lncRNAs are involved, emphasizing their role in either stimulating or inhibiting the transition to differentiated cell. Specifically, the main types of MSC differentiation are discussed: myogenesis, osteogenesis, adipogenesis and chondrogenesis. The description of increasingly new lncRNAs reinforces their role as players in the well-studied field of MSC differentiation, allowing a step towards a better understanding of their biology and their potential application in the clinic.
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Affiliation(s)
- Marcela Angelica De la Fuente-Hernandez
- Facultad de Medicina, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio de Epigenética, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Miguel Angel Sarabia-Sanchez
- Facultad de Medicina, Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Laboratorio de Genómica Funcional del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Zhang L, Wang X. Lowly expressed LNC01136 fails to aid HIF-1α to induce BTG2 expression resulting in increased proliferation of retinal microvascular endothelial cells. Microvasc Res 2022; 141:104315. [PMID: 35007537 DOI: 10.1016/j.mvr.2022.104315] [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: 09/14/2021] [Revised: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Retinal neovascularization (RN), a major cause of blindness occurring in multiple types of ophthalmic diseases, is closely associated with hypoxic conditions. However, the underlying pathological mechanisms of RN have not been fully elucidated. BTG2 is anti-proliferative factor. The up-stream of BTG2 gene within 3000 bp expresses a long non-coding RNA, LNC01136. METHODS we initially compared the expression of BTG2 and LNC01136 in human retinal microvascular endothelial cells (hRMECs) with other eye-associated cells, including Muller cells, ARPE19 cells and RGC-5, in response to a hypoxia mimetic agent (CoCl2). FISH and PCR tests were performed to determine the enrichment of LNC01136 in different cellular components. LNC01136 were overexpressed or knockdown to determine the effect on BTG2 expression. Finally, ChIP, RIP and Co-IP assays were performed to determine the interaction among BTG2, HIF-1α, LNC01136 and CNOT7. RESULTS After the treatment with CoCl2, expression levels of BTG2 and LNC01136 were strongly induced in Muller cells, ARPE19 cells and RGC-5, but weakly in hRMECs. LNC01136 is prominently located in cell nucleus and aids HIF-1α to enhance transcription of BTG2, which consequently inhibits cell growth. The anti-proliferative effect of BTG2 is probably associated to the interaction with CNOT7 and the regulation of multiple cell cycle-related proteins. CONCLUSIONS This study revealed that LNC01136 is a cell growth suppressor by recruiting HIF-1α to induce BTG2 expression. However the low expression of LNC01136 in hRMECs compared to other eye-associated cells promoted hRMECs' proliferation, which is probably a cause of RN under hypoxia.
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Affiliation(s)
- Lixin Zhang
- Department of Ophthalmology, Hunan Children's Hospital, Changsha 410006, PR China
| | - Xilang Wang
- Department of Ophthalmology, Hunan Children's Hospital, Changsha 410006, PR China.
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Yang B, Xu B, Yang R, Fu J, Li L, Huo D, Chen J, Yang X, Tan C, Chen H, Wang X. Long Non-coding Antisense RNA DDIT4-AS1 Regulates Meningitic Escherichia coli-Induced Neuroinflammation by Promoting DDIT4 mRNA Stability. Mol Neurobiol 2022; 59:1351-1365. [PMID: 34985734 PMCID: PMC8882120 DOI: 10.1007/s12035-021-02690-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022]
Abstract
Our previous studies have shown that meningitic Escherichia coli can colonize the brain and cause neuroinflammation. Controlling the balance of inflammatory responses in the host central nervous system is particularly vital. Emerging evidence has shown the important regulatory roles of long non-coding RNAs (lncRNAs) in a wide range of biological and pathological processes. However, whether lncRNAs participate in the regulation of meningitic E. coli-mediated neuroinflammation remains unknown. In the present study, we characterized a cytoplasm-enriched antisense lncRNA DDIT4-AS1, which showed similar concordant expression patterns with its parental mRNA DDIT4 upon E. coli infection. DDIT4-AS1 modulated DDIT4 expression at both mRNA and protein levels. Mechanistically, DDIT4-AS1 promoted the stability of DDIT4 mRNA through RNA duplex formation. DDIT4-AS1 knockdown and DDIT4 knockout both attenuated E. coli-induced NF-κB signaling as well as pro-inflammatory cytokines expression, and DDIT4-AS1 regulated the inflammatory response by targeting DDIT4. In summary, our results show that DDIT4-AS1 promotes E. coli-induced neuroinflammatory responses by enhancing the stability of DDIT4 mRNA through RNA duplex formation, providing potential nucleic acid targets for new therapeutic interventions in the treatment of bacterial meningitis.
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Affiliation(s)
- Bo Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Bojie Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Ruicheng Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Jiyang Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Liang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Dong Huo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Jiaqi Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Xiaopei Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, China
- International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, China
- International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China.
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, Hubei, China.
- International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, China.
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Xu H, Liu YY, Li LS, Liu YS. Sirtuins at the Crossroads between Mitochondrial Quality Control and Neurodegenerative Diseases: Structure, Regulation, Modifications, and Modulators. Aging Dis 2022; 14:794-824. [PMID: 37191431 DOI: 10.14336/ad.2022.1123] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/23/2022] [Indexed: 04/03/2023] Open
Abstract
Sirtuins (SIRT1-SIRT7), a family of nicotinamide adenine dinucleotide (NAD+)-dependent enzymes, are key regulators of life span and metabolism. In addition to acting as deacetylates, some sirtuins have the properties of deacylase, decrotonylase, adenosine diphosphate (ADP)-ribosyltransferase, lipoamidase, desuccinylase, demalonylase, deglutarylase, and demyristolyase. Mitochondrial dysfunction occurs early on and acts causally in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Sirtuins are implicated in the regulation of mitochondrial quality control, which is highly associated with the pathogenesis of neurodegenerative diseases. There is growing evidence indicating that sirtuins are promising and well-documented molecular targets for the treatment of mitochondrial dysfunction and neurodegenerative disorders by regulating mitochondrial quality control, including mitochondrial biogenesis, mitophagy, mitochondrial fission/fusion dynamics, and mitochondrial unfolded protein responses (mtUPR). Therefore, elucidation of the molecular etiology of sirtuin-mediated mitochondrial quality control points to new prospects for the treatment of neurodegenerative diseases. However, the mechanisms underlying sirtuin-mediated mitochondrial quality control remain obscure. In this review, we update and summarize the current understanding of the structure, function, and regulation of sirtuins with an emphasis on the cumulative and putative effects of sirtuins on mitochondrial biology and neurodegenerative diseases, particularly their roles in mitochondrial quality control. In addition, we outline the potential therapeutic applications for neurodegenerative diseases of targeting sirtuin-mediated mitochondrial quality control through exercise training, calorie restriction, and sirtuin modulators in neurodegenerative diseases.
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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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Rauner M, Foessl I, Formosa MM, Kague E, Prijatelj V, Lopez NA, Banerjee B, Bergen D, Busse B, Calado Â, Douni E, Gabet Y, Giralt NG, Grinberg D, Lovsin NM, Solan XN, Ostanek B, Pavlos NJ, Rivadeneira F, Soldatovic I, van de Peppel J, van der Eerden B, van Hul W, Balcells S, Marc J, Reppe S, Søe K, Karasik D. Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. Front Endocrinol (Lausanne) 2021; 12:731217. [PMID: 34938269 PMCID: PMC8686830 DOI: 10.3389/fendo.2021.731217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare diseases in the skeletal field. Yet, interpreting results from human association studies remains a challenge. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary. Multiple unknowns exist for putative causal genes, including cellular localization of the molecular function. Intermediate traits ("endophenotypes"), e.g. molecular quantitative trait loci (molQTLs), are needed to identify mechanisms of underlying associations. Furthermore, index variants often reside in non-coding regions of the genome, therefore challenging for interpretation. Knowledge of non-coding variance (e.g. ncRNAs), repetitive sequences, and regulatory interactions between enhancers and their target genes is central for understanding causal genes in skeletal conditions. Animal models with deep skeletal phenotyping and cell culture models have already facilitated fine mapping of some association signals, elucidated gene mechanisms, and revealed disease-relevant biology. However, to accelerate research towards bridging the current gap between association and causality in skeletal diseases, alternative in vivo platforms need to be used and developed in parallel with the current -omics and traditional in vivo resources. Therefore, we argue that as a field we need to establish resource-sharing standards to collectively address complex research questions. These standards will promote data integration from various -omics technologies and functional dissection of human complex traits. In this mission statement, we review the current available resources and as a group propose a consensus to facilitate resource sharing using existing and future resources. Such coordination efforts will maximize the acquisition of knowledge from different approaches and thus reduce redundancy and duplication of resources. These measures will help to understand the pathogenesis of osteoporosis and other skeletal diseases towards defining new and more efficient therapeutic targets.
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Affiliation(s)
- Martina Rauner
- Department of Medicine III, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ines Foessl
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Endocrine Lab Platform, Medical University of Graz, Graz, Austria
| | - Melissa M. Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Erika Kague
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nerea Alonso Lopez
- Rheumatology and Bone Disease Unit, CGEM, Institute of Genetics and Cancer (IGC), Edinburgh, United Kingdom
| | - Bodhisattwa Banerjee
- Musculoskeletal Genetics Laboratory, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Dylan Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ângelo Calado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Eleni Douni
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Institute for Bioinnovation, B.S.R.C. “Alexander Fleming”, Vari, Greece
| | - Yankel Gabet
- Department of Anatomy & Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Natalia García Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Nika M. Lovsin
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Xavier Nogues Solan
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Barbara Ostanek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Nathan J. Pavlos
- Bone Biology & Disease Laboratory, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | | | - Ivan Soldatovic
- Institute of Medical Statistics and Informatic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wim van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Sjur Reppe
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Kent Søe
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
- Marcus Research Institute, Hebrew SeniorLife, Boston, MA, United States
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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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Multi-Systemic Alterations by Chronic Exposure to a Low Dose of Bisphenol A in Drinking Water: Effects on Inflammation and NAD +-Dependent Deacetylase Sirtuin1 in Lactating and Weaned Rats. Int J Mol Sci 2021; 22:ijms22189666. [PMID: 34575829 PMCID: PMC8467074 DOI: 10.3390/ijms22189666] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 12/28/2022] Open
Abstract
Bisphenol A (BPA) is largely used as a monomer in some types of plastics. It accumulates in tissues and fluids and is able to bypass the placental barrier, affecting various organs and systems. Due to huge developmental processes, children, foetuses, and neonates could be more sensitive to BPA-induced toxicity. To investigate the multi-systemic effects of chronic exposure to a low BPA dose (100 μg/L), pregnant Wistar rats were exposed to BPA in drinking water during gestation and lactation. At weaning, newborn rats received the same treatments as dams until sex maturation. Free and conjugated BPA levels were measured in plasma and adipose tissue; the size of cerebral ventricles was analysed in the brain; morpho-functional and molecular analyses were carried out in the liver with a focus on the expression of inflammatory cytokines and Sirtuin 1 (Sirt1). Higher BPA levels were found in plasma and adipose tissue from BPA treated pups (17 PND) but not in weaned animals. Lateral cerebral ventricles were significantly enlarged in lactating and weaned BPA-exposed animals. In addition, apart from microvesicular steatosis, liver morphology did not exhibit any statistically significant difference for morphological signs of inflammation, hypertrophy, or macrovesicular steatosis, but the expression of inflammatory cytokines, Sirt1, its natural antisense long non-coding RNA (Sirt1-AS LncRNA) and histone deacetylase 1 (Hdac1) were affected in exposed animals. In conclusion, chronic exposure to a low BPA dose could increase the risk for disease in adult life as a consequence of higher BPA circulating levels and accumulation in adipose tissue during the neonatal period.
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Kesharwani D, Kumar A, Poojary M, Scaria V, Datta M. RNA sequencing reveals potential interacting networks between the altered transcriptome and ncRNome in the skeletal muscle of diabetic mice. Biosci Rep 2021; 41:BSR20210495. [PMID: 34190986 PMCID: PMC8276098 DOI: 10.1042/bsr20210495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
For a global epidemic like Type 2 diabetes mellitus (T2DM), while impaired gene regulation is identified as a primary cause of aberrant cellular physiology; in the past few years, non-coding RNAs (ncRNAs) have emerged as important regulators of cellular metabolism. However, there are no reports of comprehensive in-depth cross-talk between these regulatory elements and the potential consequences in the skeletal muscle during diabetes. Here, using RNA sequencing, we identified 465 mRNAs and 12 long non-coding RNAs (lncRNAs), to be differentially regulated in the skeletal muscle of diabetic mice and pathway enrichment analysis of these altered transcripts revealed pathways of insulin, FOXO and AMP-activated protein kinase (AMPK) signaling to be majorly over-represented. Construction of networks showed that these pathways significantly interact with each other that might underlie aberrant skeletal muscle metabolism during diabetes. Gene-gene interaction network depicted strong interactions among several differentially expressed genes (DEGs) namely, Prkab2, Irs1, Pfkfb3, Socs2 etc. Seven altered lncRNAs depicted multiple interactions with the altered transcripts, suggesting possible regulatory roles of these lncRNAs. Inverse patterns of expression were observed between several of the deregulated microRNAs (miRNAs) and the differentially expressed transcripts in the tissues. Towards validation, overexpression of miR-381-3p and miR-539-5p in skeletal muscle C2C12 cells significantly decreased the transcript levels of their targets, Nfkbia, Pik3r1 and Pi3kr1, Cdkn2d, respectively. Collectively, the findings provide a comprehensive understanding of the interactions and cross-talk between the ncRNome and transcriptome in the skeletal muscle during diabetes and put forth potential therapeutic options for improving insulin sensitivity.
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Affiliation(s)
- Devesh Kesharwani
- CSIR-Institute of Genomics and Integrative Biology, Functional and Genomics Unit, Mall Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
| | - Amit Kumar
- CSIR-Institute of Genomics and Integrative Biology, Functional and Genomics Unit, Mall Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
| | - Mukta Poojary
- Academy of Scientific and Innovative Research, CSIR-HRDC, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research, CSIR-HRDC, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
- GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Malabika Datta
- CSIR-Institute of Genomics and Integrative Biology, Functional and Genomics Unit, Mall Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Kamala Nehru Nagar, Ghaziabad 201002, Uttar Pradesh, India
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The Key Lnc (RNA)s in Cardiac and Skeletal Muscle Development, Regeneration, and Disease. J Cardiovasc Dev Dis 2021; 8:jcdd8080084. [PMID: 34436226 PMCID: PMC8397000 DOI: 10.3390/jcdd8080084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/29/2021] [Accepted: 07/15/2021] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play a key role in the regulation of transcriptional and epigenetic activity in mammalian cells. Comprehensive analysis of these ncRNAs has revealed sophisticated gene regulatory mechanisms which finely tune the proper gene output required for cellular homeostasis, proliferation, and differentiation. However, this elaborate circuitry has also made it vulnerable to perturbations that often result in disease. Among the many types of ncRNAs, long non-coding RNAs (lncRNAs) appear to have the most diverse mechanisms of action including competitive binding to miRNA targets, direct binding to mRNA, interactions with transcription factors, and facilitation of epigenetic modifications. Moreover, many lncRNAs display tissue-specific expression patterns suggesting an important regulatory role in organogenesis, yet the molecular mechanisms through which these molecules regulate cardiac and skeletal muscle development remains surprisingly limited. Given the structural and metabolic similarities of cardiac and skeletal muscle, it is likely that several lncRNAs expressed in both of these tissues have conserved functions in establishing the striated muscle phenotype. As many aspects of regeneration recapitulate development, understanding the role lncRNAs play in these processes may provide novel insights to improve regenerative therapeutic interventions in cardiac and skeletal muscle diseases. This review highlights key lncRNAs that function as regulators of development, regeneration, and disease in cardiac and skeletal muscle. Finally, we highlight lncRNAs encoded by imprinted genes in striated muscle and the contributions of these loci on the regulation of gene expression.
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Kanakis I, Alameddine M, Folkes L, Moxon S, Myrtziou I, Ozanne SE, Peffers MJ, Goljanek-Whysall K, Vasilaki A. Small-RNA Sequencing Reveals Altered Skeletal Muscle microRNAs and snoRNAs Signatures in Weanling Male Offspring from Mouse Dams Fed a Low Protein Diet during Lactation. Cells 2021; 10:cells10051166. [PMID: 34064819 PMCID: PMC8150574 DOI: 10.3390/cells10051166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 12/18/2022] Open
Abstract
Maternal diet during gestation and lactation affects the development of skeletal muscles in offspring and determines muscle health in later life. In this paper, we describe the association between maternal low protein diet-induced changes in offspring skeletal muscle and the differential expression (DE) of small non-coding RNAs (sncRNAs). We used a mouse model of maternal protein restriction, where dams were fed either a normal (N, 20%) or a low protein (L, 8%) diet during gestation and newborns were cross-fostered to N or L lactating dams, resulting in the generation of NN, NL and LN offspring groups. Total body and tibialis anterior (TA) weights were decreased in weanling NL male offspring but were not different in the LN group, as compared to NN. However, histological evaluation of TA muscle revealed reduced muscle fibre size in both groups at weaning. Small RNA-sequencing demonstrated DE of multiple miRs, snoRNAs and snRNAs. Bioinformatic analyses of miRs-15a, -34a, -122 and -199a, in combination with known myomiRs, confirmed their implication in key muscle-specific biological processes. This is the first comprehensive report for the DE of sncRNAs in nutrition-associated programming of skeletal muscle development, highlighting the need for further research to unravel the detailed molecular mechanisms.
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Affiliation(s)
- Ioannis Kanakis
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester CH2 1BR, UK;
- Correspondence: or
| | - Moussira Alameddine
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
| | - Leighton Folkes
- School of Biological Sciences, Faculty of Science, University of East Anglia, Norwich NR4 7TJ, UK; (L.F.); (S.M.)
| | - Simon Moxon
- School of Biological Sciences, Faculty of Science, University of East Anglia, Norwich NR4 7TJ, UK; (L.F.); (S.M.)
| | - Ioanna Myrtziou
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester CH2 1BR, UK;
| | - Susan E. Ozanne
- Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK;
| | - Mandy J. Peffers
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
| | - Katarzyna Goljanek-Whysall
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
- Department of Physiology, School of Medicine and REMEDI, CMNHS, NUI Galway, Galway H91 TK33, Ireland
| | - Aphrodite Vasilaki
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
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Zhu R, Feng X, Wei Y, Guo D, Li J, Liu Q, Jiang J, Shi D, Huang J. lncSAMM50 Enhances Adipogenic Differentiation of Buffalo Adipocytes With No Effect on Its Host Gene. Front Genet 2021; 12:626158. [PMID: 33841496 PMCID: PMC8033173 DOI: 10.3389/fgene.2021.626158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022] Open
Abstract
Fat deposition is one of the most important traits that are mediated by a set of complex regulatory factors in meat animals. Several researches have revealed the significant role of long non-coding RNAs (lncRNAs) in fat deposition while the precise regulatory mechanism is still largely elusive. In this study, we investigated the lncRNA profiles of adipose and muscle tissues in buffalo by using the Illumina HiSeq 3000 platform. In total, 43,809 lncRNAs were finally identified based on the computer algorithm. A comparison analysis revealed 241 lncRNAs that are differentially expressed (DE) in adipose and muscle tissues. We focused on lncSAMM50, a DE lncRNA that has a high expression in adipose tissue. Sequence alignment showed that lncSAMM50 is transcribed from the antisense strand of the upstream region of sorting and assembly machinery component 50 homolog (SAMM50), a gene involved in the function of mitochondrion and is subsequently demonstrated to inhibit the adipogenic differentiation of 3T3-L1 adipocyte cells in this study. lncSAMM50 is highly expressed in adipose tissue and upregulated in the mature adipocytes and mainly exists in the nucleus. Gain-of-function experiments demonstrated that lncSAMM50 promotes the adipogenic differentiation by upregulating adipogenic markers but with no effect on its host gene SAMM50 in buffalo adipocytes. These results indicate that lncSAMM50 enhances fat deposition in buffalo and provide a new factor for the regulatory network of adipogenesis.
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Affiliation(s)
- Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yutong Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Duo Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jiaojiao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jianrong Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S. Functional long non-coding and circular RNAs in zebrafish. Brief Funct Genomics 2021:elab014. [PMID: 33755040 DOI: 10.1093/bfgp/elab014] [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: 11/17/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
The utility of model organisms to understand the function of a novel transcript/genes has allowed us to delineate their molecular mechanisms in maintaining cellular homeostasis. Organisms such as zebrafish have contributed a lot in the field of developmental and disease biology. Attributable to advancement and deep transcriptomics, many new transcript isoforms and non-coding RNAs such as long noncoding RNA (lncRNA) and circular RNAs (circRNAs) have been identified and cataloged in multiple databases and many more are yet to be identified. Various methods and tools have been utilized to identify lncRNAs/circRNAs in zebrafish using deep sequencing of transcriptomes as templates. Functional analysis of a few candidates such as tie1-AS, ECAL1 and CDR1as in zebrafish provides a prospective outline to approach other known or novel lncRNA/circRNA. New genetic alteration tools like TALENS and CRISPRs have helped in probing for the molecular function of lncRNA/circRNA in zebrafish. Further latest improvements in experimental and computational techniques offer the identification of lncRNA/circRNA counterparts in humans and zebrafish thereby allowing easy modeling and analysis of function at cellular level.
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LncRNA Sirt1-AS upregulates Sirt1 to attenuate aging related deep venous thrombosis. Aging (Albany NY) 2021; 13:6918-6935. [PMID: 33638947 PMCID: PMC7993686 DOI: 10.18632/aging.202550] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022]
Abstract
Aging is associated with the increased incidence of deep venous thrombosis (DVT), resulting in significant morbidity and mortality in the elderly, but the underlying mechanism is elusive. Silent information regulator 1 (Sirt1) is linked to the senescence, inflammation, oxidative stress and platelet adhesion of endothelial cells. Here we showed that DVT was associated with the senescence of endothelium and lower expression of Sirt1. Furthermore, Sirt1 could inhibit endothelial senescence and reduce the occurrence of DVT. Interestingly, we found antisense long non-coding RNA (lncRNA Sirt1-AS) upregulated Sirt1, decreased the expression of senescence and DVT associated biomarkers in human vascular endothelial cells (HUVECs). In addition, lncRNA Sirt1-AS overexpression alleviated DVT through upregulating Sirt1 and thereby inducing Foxo3a degradation. In conclusion, our findings demonstrate that lncRNA Sirt1-AS may be a potential new biomarker for DVT.
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Braga L, Ali H, Secco I, Giacca M. Non-coding RNA therapeutics for cardiac regeneration. Cardiovasc Res 2021; 117:674-693. [PMID: 32215566 PMCID: PMC7898953 DOI: 10.1093/cvr/cvaa071] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/02/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022] Open
Abstract
A growing body of evidence indicates that cardiac regeneration after myocardial infarction can be achieved by stimulating the endogenous capacity of cardiomyocytes (CMs) to replicate. This process is controlled, both positively and negatively, by a large set of non-coding RNAs (ncRNAs). Some of the microRNAs (miRNAs) that can stimulate CM proliferation is expressed in embryonic stem cells and is required to maintain pluripotency (e.g. the miR-302∼367 cluster). Others also govern the proliferation of different cell types, including cancer cells (e.g. the miR-17∼92 cluster). Additional miRNAs were discovered through systematic screenings (e.g. miR-199a-3p and miR-590-3p). Several miRNAs instead suppress CM proliferation and are involved in the withdrawal of CMs from the cell cycle after birth (e.g. the let-7 and miR-15 families). Similar regulatory roles on CM proliferation are also exerted by a few long ncRNAs. This body of information has obvious therapeutic implications, as miRNAs with activator function or short antisense oligonucleotides against inhibitory miRNAs or lncRNAs can be administered to stimulate cardiac regeneration. Expression of miRNAs can be achieved by gene therapy using adeno-associated vectors, which transduce CMs with high efficiency. More effective and safer for therapeutic purposes, small nucleic acid therapeutics can be obtained as chemically modified, synthetic molecules, which can be administered through lipofection or inclusion in lipid or polymer nanoparticles for efficient cardiac delivery. The notion that it is possible to reprogramme CMs into a regenerative state and that this property can be enhanced by ncRNA therapeutics remains exciting, however extensive experimentation in large mammals and rigorous assessment of safety are required to advance towards clinical application.
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Affiliation(s)
- Luca Braga
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Hashim Ali
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Ilaria Secco
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Mauro Giacca
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
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Zhang S, Li L, Wang J, Zhang T, Ye T, Wang S, Xing D, Chen W. Recent advances in the regulation of ABCA1 and ABCG1 by lncRNAs. Clin Chim Acta 2021; 516:100-110. [PMID: 33545111 DOI: 10.1016/j.cca.2021.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023]
Abstract
Coronary heart disease (CHD) with atherosclerosis is the leading cause of death worldwide. ABCA1 and ABCG1 promote cholesterol efflux to suppress foam cell generation and reduce atherosclerosis development. Long noncoding RNAs (lncRNAs) are emerging as a unique group of RNA transcripts that longer than 200 nucleotides and have no protein-coding potential. Many studies have found that lncRNAs regulate cholesterol efflux to influence atherosclerosis development. ABCA1 is regulated by different lncRNAs, including MeXis, GAS5, TUG1, MEG3, MALAT1, Lnc-HC, RP5-833A20.1, LOXL1-AS1, CHROME, DAPK1-IT1, SIRT1 AS lncRNA, DYNLRB2-2, DANCR, LeXis, LOC286367, and LncOR13C9. ABCG1 is also regulated by different lncRNAs, including TUG1, GAS5, RP5-833A20.1, DYNLRB2-2, ENST00000602558.1, and AC096664.3. Thus, various lncRNAs are associated with the roles of ABCA1 and ABCG1 on cholesterol efflux in atherosclerosis regulation. However, some lncRNAs play dual roles in ABCA1 expression and atherosclerosis, and the functions of some lncRNAs in atherosclerosis have not been investigated in vivo. In this article, we review the roles of lncRNAs in atherosclerosis and focus on new insights into lncRNAs associated with the roles of ABCA1 and ABCG1 on cholesterol efflux and the potential of these lncRNAs as novel therapeutic targets in atherosclerosis.
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Affiliation(s)
- Shun Zhang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China
| | - Lu Li
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China
| | - Jie Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China
| | - Tingting Zhang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China
| | - Ting Ye
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China
| | - Shuai Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China; School of Medical Imaging, Radiotherapy Department of Affiliated Hospital, Weifang Medical University, Weifang, Shandong 261053, China
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Wujun Chen
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong 266071, China.
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Yuan S, Si W, Zhuang K, Li Y, Zhang Y, Liu J, Yang L, Zhang X. LncRNA UCID Promotes Hepatocellular Carcinoma Metastasis via Stabilization of Snail. Onco Targets Ther 2021; 14:725-736. [PMID: 33536764 PMCID: PMC7850577 DOI: 10.2147/ott.s277951] [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: 08/20/2020] [Accepted: 11/27/2020] [Indexed: 01/05/2023] Open
Abstract
Background LncRNAs are functional regulators in tumor progression which act by regulating mRNAs in multiple types of cancer. However, the effect of lnc-UCID on hepatocellular carcinoma (HCC) metastasisremains unclear. Methods Lnc-UCID expression was quantified in HCC tissues and HCC cell lines by qRT-PCR. HCC cell lines with lnc-UCID knockdown were established by lentivirus transduction. The migration and invasion abilities of HCC cells were analyzed by Transwell and wound-healing assays. Protein expression of epithelial–mesenchymal transition (EMT)-related factors was examined by Western blot assay. Dual-luciferase assays and actinomycin D treatment were conducted to explore the relationship between lnc-UCID and Snail mRNA. The direct interaction between lnc-UCID and Snail mRNA was subjected to quantification analysis by biotinylated lnc-UCID pulldown assays. Pearson’s correlation coefficient was used to analyze correlations between lnc-UCID and Snail expression level in clinical samples. Rescue experiments were performed to uncover the role of Snail in the HCC metastasis process. Results Lnc-UCID was upregulated in human HCC tissues and HCC cell lines. Lnc-UCID promoted the cells’ mobility and invasiveness by enhancing the EMT process of HCC cells. The expression of Snail positively correlated with lnc-UCID abundance, and the interaction between lnc-UCID and Snail mRNA prevented miR-122, miR-203, miR-30b, miR-34a or miR-153 binding to the 3ʹ-UTR of Snail. Transfection of Snail greatly rescued the migration and invasion of HCC cells. Conclusion Lnc-UCID was upregulated in clinical HCC samples and directly interacted with Snail mRNA to enhance the stability of Snail mRNA, thus promoting the EMT process to accelerate HCC metastasis.
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Affiliation(s)
- Shanshan Yuan
- Department of Gastroenterology, The Affiliated Xi'an Central Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.,Department of Gastroenterology, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Wangli Si
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Kun Zhuang
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Yijun Li
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Yanting Zhang
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Jiaming Liu
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Li Yang
- Department of Ultrasonography, The Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xin Zhang
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an, Shaanxi, People's Republic of China
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Wang YN, Yang CE, Zhang DD, Chen YY, Yu XY, Zhao YY, Miao H. Long non-coding RNAs: A double-edged sword in aging kidney and renal disease. Chem Biol Interact 2021; 337:109396. [PMID: 33508306 DOI: 10.1016/j.cbi.2021.109396] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/18/2020] [Accepted: 01/22/2021] [Indexed: 01/23/2023]
Abstract
Aging as one of intrinsic biological processes is a risk factor for many chronic diseases. Kidney disease is a global problem and health care burden worldwide. The diagnosis of kidney disease is currently based on serum creatinine and urea levels. Novel biomarkers may improve diagnostic accuracy, thereby allowing early prevention and treatment. Over the past few years, advances in genome analyses have identified an emerging class of noncoding RNAs that play critical roles in the regulation of gene expression and epigenetic reprogramming. Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and could bind DNA, RNA and protein. Emerging evidence has demonstrated that lncRNAs played an important role in all stages of kidney disease. To date, only some lncRNAs were well identified and characterized, but the complexity of multilevel regulation of transcriptional programs involved in these processes remains undefined. In this review, we summarized the lncRNA expression profiling of large-scale identified lncRNAs on kidney diseases including acute kidney injury, chronic kidney disease, diabetic nephropathy and kidney transplantation. We further discussed a number of annotated lncRNAs linking with complex etiology of kidney diseases. Finally, several lncRNAs were highlighted as diagnostic biomarkers and therapeutic targets. Targeting lncRNAs may represent a precise therapeutic strategy for progressive renal fibrosis.
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Affiliation(s)
- Yan-Ni Wang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Chang-E Yang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Dan-Dan Zhang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Yuan-Yuan Chen
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Xiao-Yong Yu
- Department of Nephrology, Shaanxi Traditional Chinese Medicine Hospital, No. 2 Xihuamen, Xi'an, Shaanxi, 710003, China.
| | - Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
| | - Hua Miao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an, Shaanxi, 710069, China.
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Sebastian-delaCruz M, Gonzalez-Moro I, Olazagoitia-Garmendia A, Castellanos-Rubio A, Santin I. The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization. Noncoding RNA 2021; 7:ncrna7010003. [PMID: 33466464 PMCID: PMC7839045 DOI: 10.3390/ncrna7010003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
mRNA stability influences gene expression and translation in almost all living organisms, and the levels of mRNA molecules in the cell are determined by a balance between production and decay. Maintaining an accurate balance is crucial for the correct function of a wide variety of biological processes and to maintain an appropriate cellular homeostasis. Long non-coding RNAs (lncRNAs) have been shown to participate in the regulation of gene expression through different molecular mechanisms, including mRNA stabilization. In this review we provide an overview on the molecular mechanisms by which lncRNAs modulate mRNA stability and decay. We focus on how lncRNAs interact with RNA binding proteins and microRNAs to avoid mRNA degradation, and also on how lncRNAs modulate epitranscriptomic marks that directly impact on mRNA stability.
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Affiliation(s)
- Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Itziar Gonzalez-Moro
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, 48940 Leioa, Spain; (M.S.-d.); (A.O.-G.); (A.C.-R.)
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Izortze Santin
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-94-601-32-09
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Brusa R, Magri F, Bresolin N, Comi GP, Corti S. Noncoding RNAs in Duchenne and Becker muscular dystrophies: role in pathogenesis and future prognostic and therapeutic perspectives. Cell Mol Life Sci 2020; 77:4299-4313. [PMID: 32350552 PMCID: PMC11105074 DOI: 10.1007/s00018-020-03537-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 12/14/2022]
Abstract
Noncoding RNAs (ncRNAs), such as miRNAs and long noncoding RNAs, are key regulators of gene expression at the post-transcriptional level and represent promising therapeutic targets and biomarkers for several human diseases, including Duchenne and Becker muscular dystrophies (DMD/BMD). A role for ncRNAs in the pathogenesis of muscular dystrophies has been suggested, even if it is still incompletely understood. Here, we discuss current progress leading towards the clinical utility of ncRNAs for DMD/BMD. Long and short noncoding RNAs are differentially expressed in DMD/BMD and have a mechanism of action via targeting mRNAs. A subset of muscle-enriched miRNAs, the so-called myomiRs (miR-1, miR-133, and miR-206), are increased in the serum of patients with DMD and in dystrophin-defective animal models. Interestingly, myomiRs might be used as biomarkers, given that their levels can be corrected after dystrophin restoration in dystrophic mice. Remarkably, further evidence demonstrates that ncRNAs also play a role in dystrophin expression; thus, their modulations might represent a potential therapeutic strategy with the aim of upregulating the dystrophin protein in combination with other oligonucleotides/gene therapy approaches.
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Affiliation(s)
- Roberta Brusa
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesca Magri
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Nereo Bresolin
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Giacomo Pietro Comi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
- Neuromuscular and Rare Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy.
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Yuan C, Zhang K, Yue Y, Guo T, Liu J, Niu C, Sun X, Feng R, Wang X, Yang B. Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle. PeerJ 2020; 8:e9957. [PMID: 33024632 PMCID: PMC7518186 DOI: 10.7717/peerj.9957] [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: 11/22/2019] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation.
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Affiliation(s)
- Chao Yuan
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaojing Yue
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Tingting Guo
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Jianbin Liu
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Chune Niu
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaoping Sun
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Ruilin Feng
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bohui Yang
- Sheep Breeding Engineering Technology Research Center, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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43
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Non-coding RNAs: emerging players in cardiomyocyte proliferation and cardiac regeneration. Basic Res Cardiol 2020; 115:52. [PMID: 32748089 PMCID: PMC7398957 DOI: 10.1007/s00395-020-0816-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
Soon after birth, the regenerative capacity of the mammalian heart is lost, cardiomyocytes withdraw from the cell cycle and demonstrate a minimal proliferation rate. Despite improved treatment and reperfusion strategies, the uncompensated cardiomyocyte loss during injury and disease results in cardiac remodeling and subsequent heart failure. The promising field of regenerative medicine aims to restore both the structure and function of damaged tissue through modulation of cellular processes and regulatory mechanisms involved in cardiac cell cycle arrest to boost cardiomyocyte proliferation. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) are functional RNA molecules with no protein-coding function that have been reported to engage in cardiac regeneration and repair. In this review, we summarize the current understanding of both the biological functions and molecular mechanisms of ncRNAs involved in cardiomyocyte proliferation. Furthermore, we discuss their impact on the structure and contractile function of the heart in health and disease and their application for therapeutic interventions.
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lncRNA IGF2 AS Regulates Bovine Myogenesis through Different Pathways. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:874-884. [PMID: 32805490 PMCID: PMC7452115 DOI: 10.1016/j.omtn.2020.07.002] [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: 04/24/2020] [Revised: 05/20/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022]
Abstract
The role of long non-coding RNA (lncRNA) in the regulation of bovine skeletal muscle development remains poorly understood. The present study investigated the function and regulatory mechanism of a novel lncRNA, insulin-like growth factor 2 antisense transcript (IGF2 AS), in bovine myoblast proliferation and differentiation. Gain or loss of IGF2 AS was performed using an expression plasmid or small interfering RNA (siRNA), respectively. Bovine myoblasts were used to investigate the biological function and mechanisms of IGF2 AS in vitro. Results were conjointly analyzed by celluar and molecular biology experiments as well as bioinformatics. Functionally, IGF2 AS could promote proliferation and differentiation of bovine myoblasts. The preliminary mechanism suggests, on the one hand, that IGF2 AS could complement the IGF2 gene intron region and affect the stability and expression of IGF2 mRNA. On the other hand, RNA pull-down and immunoprecipitation assays demonstrated that IGF2 AS could directly bind to the interleukin enhancer binding factor 3 (ILF3) protein and maybe partly though it to regulate myogenesis. In conclusion, the novel identified lncRNA IGF2 AS promoted proliferation and differentiation of bovine myoblasts through various pathways.
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45
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Sirt1 antisense long non-coding RNA attenuates pulmonary fibrosis through sirt1-mediated epithelial-mesenchymal transition. Aging (Albany NY) 2020; 12:4322-4336. [PMID: 32139663 PMCID: PMC7093192 DOI: 10.18632/aging.102882] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/05/2020] [Indexed: 12/20/2022]
Abstract
Long noncoding RNAs sirt1 antisense (sirt1 AS) was reported to play crucial roles in the progression of organ fibrosis. However, the roles of sirt1 AS in idiopathic pulmonary fibrosis (IPF) are still unknown. In addition, we have previously demonstrated that astragaloside IV (ASV), a bioactive saponin extract of the Astragalus root, significantly alleviates IPF by inhibiting transforming growth factor β1 (TGF-β1) induced epithelial-mesenchymal transition (EMT). Further investigations into the influence of ASV on lncRNAs expression will be helpful to delineate the complex regulatory networks underlying the biological function of ASV. Here, we found sirt1 AS expression was significantly decreased in BLM-induced pulmonary fibrosis. We further found that sirt1 AS effectively inhibited TGF-β1-meidated EMT in vitro and alleviated the progression of IPF in vivo. Mechanistically, sirt1 AS was validate to enhance the stability of sirt1 and increased sirt1 expression, thereby to inhibit EMT in IPF. Furthermore, we demonstrated that ASV treatment increased sirt1 AS expression and silencing of sirt1 AS impaired anti-fibrosis effects of ASV on IPF. Collectively, sirt1 AS was critical for ASV-mediated inhibition of IPF progression and targeting of sirt1 AS by ASV could be a potential therapeutic approach for IPF.
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46
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Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs. Int J Mol Sci 2020; 21:ijms21051732. [PMID: 32138348 PMCID: PMC7084294 DOI: 10.3390/ijms21051732] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
Intramuscular fat (IMF) content is closely related to various meat traits, such as tenderness, juiciness, and flavor. The IMF content varies considerably among pig breeds with different genetic backgrounds. Long intergenic non-coding RNAs (lincRNAs) have been widely identified in many species and found to be an important class of regulators that can participate in multiple biological processes. However, the mechanism behind lincRNAs regulation of pig IMF content remains unknown and requires further study. In our study, we identified a total of 156 lincRNAs in the longissimus dorsi muscle of Wei (fat-type) and Yorkshire (lean-type) pigs using previously published data. These identified lincRNAs have shorter transcript length, longer exon length, lower exon number, and lower expression level as compared with protein-coding transcripts. We predicted potential target genes (PTGs) that are potentially regulated by lincRNAs in cis or trans regulation. Gene ontology and pathway analyses indicated that many potential lincRNAs target genes are involved in IMF-related processes or pathways, such as fatty acid catabolic process and adipocytokine signaling pathway. In addition, we analyzed quantitative trait locus (QTL) sites that differentially expressed lincRNAs (DE lincRNAs) between Wei and Yorkshire pigs co-localized. The QTL sites where DE lincRNAs co-localize are mostly related to IMF content. Furthermore, we constructed a co-expressed network between DE lincRNAs and their differentially expressed PTGs (DEPTGs). On the basis of their expression levels, we suggest that many DE lincRNAs can affect IMF development by positively or negatively regulating their PTGs. This study identified and analyzed some lincRNAs- and PTGs-related IMF development of the two pig breeds and provided new insight into research on the roles of lincRNAs in the two types of breeds.
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47
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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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48
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Li H, Huang K, Wang P, Feng T, Shi D, Cui K, Luo C, Shafique L, Qian Q, Ruan J, Liu Q. Comparison of Long Non-Coding RNA Expression Profiles of Cattle and Buffalo Differing in Muscle Characteristics. Front Genet 2020; 11:98. [PMID: 32174968 PMCID: PMC7054449 DOI: 10.3389/fgene.2020.00098] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/29/2020] [Indexed: 02/02/2023] Open
Abstract
Buffalo meat consist good qualitative characteristics as it contains “thined tender” which is favorable for cardavascular system. However, the regulatory mechanisms of long non-coding RNA (lncRNA), differences in meat quality are not well known. The chemical-physical parameters revealed the muscle quality of buffalo that can be equivalent of cattle, but there are significant differences in shearing force and muscle fiber structure. Then, we examined lncRNA expression profiles of buffalo and cattle skeletal muscle that provide first insights into their potential roles in buffalo myogenesis. Here, we profiled the expression of lncRNA in cattle and buffalo skeletal muscle tissues, and 16,236 lncRNA candidates were detected with 865 up-regulated lncRNAs and 1,296 down-regulated lncRNAs when comparing buffalo to cattle muscle tissue. We constructed coexpression and ceRNA networks, and found lncRNA MSTRG.48330.7, MSTRG.30030.4, and MSTRG.203788.46 could be as competitive endogenous RNA (ceRNA) containing potential binding sites for miR-1/206 and miR-133a. Tissue expression analysis showed that MSTRG.48330.7, MSTRG.30030.4, and MSTRG.203788.46 were highly and specifically expressed in muscle tissue. Present study may be used as a reference tool for starting point investigations into the roles played by several of those lncRNAs during buffalo myogenesis.
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Affiliation(s)
- Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Pengcheng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Kuiqing Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Chan Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Laiba Shafique
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Qian Qian
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jue Ruan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Regulatory Mechanisms of Mitochondrial Function and Cardiac Aging. Int J Mol Sci 2020; 21:ijms21041359. [PMID: 32085438 PMCID: PMC7072955 DOI: 10.3390/ijms21041359] [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: 12/30/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 01/10/2023] Open
Abstract
Aging is a major risk factor for cardiovascular diseases (CVDs), the major cause of death worldwide. Cardiac myocytes, which hold the most abundant mitochondrial population, are terminally differentiated cells with diminished regenerative capacity in the adult. Cardiomyocyte mitochondrial dysfunction is a characteristic feature of the aging heart and one out of the nine features of cellular aging. Aging and cardiac pathologies are also associated with increased senescence in the heart. However, the cause and consequences of cardiac senescence during aging or in cardiac pathologies are mostly unrecognized. Further, despite recent advancement in anti-senescence therapy, the targeted cell type and the effect on cardiac structure and function have been largely overlooked. The unique cellular composition of the heart, and especially the functional properties of cardiomyocytes, need to be considered when designing therapeutics to target cardiac aging. Here we review recent findings regarding key factors regulating cell senescence, mitochondrial health as well as cardiomyocyte rejuvenation.
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50
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Chen R, Lei S, Jiang T, Zeng J, Zhou S, She Y. Roles of lncRNAs and circRNAs in regulating skeletal muscle development. Acta Physiol (Oxf) 2020; 228:e13356. [PMID: 31365949 DOI: 10.1111/apha.13356] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 02/06/2023]
Abstract
The multistep biological process of myogenesis is regulated by a variety of myoblast regulators, such as myogenic differentiation antigen, myogenin, myogenic regulatory factor, myocyte enhancer factor2A-D and myosin heavy chain. Proliferation and differentiation during skeletal muscle myogenesis contribute to the physiological function of muscles. Certain non-coding RNAs, including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are involved in the regulation of muscle development, and the aberrant expressions of lncRNAs and circRNAs are associated with muscular diseases. In this review, we summarize the recent advances concerning the roles of lncRNAs and circRNAs in regulating the developmental aspects of myogenesis. These findings have remarkably broadened our understanding of the gene regulation mechanisms governing muscle proliferation and differentiation, which makes it more feasible to design novel preventive, diagnostic and therapeutic strategies 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
| | - Ting Jiang
- Department of Radiology, The Third Affiliated Hospital Sun Yat‐sen University Guangzhou China
| | - Jie Zeng
- Department of Medical Ultrasonics, The Third Affiliated Hospital Sun Yat‐sen University Guangzhou China
| | - Shanyao Zhou
- 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
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