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Xie S, Jiang L, Song W, Zheng J, Liu Y, Chen S, Yan X. Skeletal muscle feature of different populations in large yellow croaker ( Larimichthys crocea): from an epigenetic point of view. Front Mol Biosci 2024; 11:1403861. [PMID: 39015478 PMCID: PMC11249746 DOI: 10.3389/fmolb.2024.1403861] [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: 03/20/2024] [Accepted: 06/04/2024] [Indexed: 07/18/2024] Open
Abstract
Fish skeletal muscle is composed of well-defined fiber types. In order to identify potential candidate genes affecting muscle growth and development under epigenetic regulation. Bisulfite sequencing was utilized to analyze and compare the muscle DNA methylation profiles of Larimichthys crocea inhabiting different environments. The results revealed that DNA methylation in L. crocea was predominantly CG methylation, with 2,396 differentially methylated regions (DMRs) identified through comparisons among different populations. The largest difference in methylation was observed between the ZhouShan and JinMen wild populations, suggesting that L. crocea may have undergone selection and domestication. Additionally, GO and KEGG enrichment analysis of differentially methylated genes (DMGs) revealed 626 enriched GO functional categories, including various muscle-related genes such as myh10, myf5, myf6, ndufv1, klhl31, map3k4, syn2b, sostdc1a, bag4, and hsp90ab. However, significant enrichment in KEGG pathways was observed only in the JinMen and XiangShan populations of L. crocea. Therefore, this study provides a theoretical foundation for a better understanding of the epigenetic regulation of skeletal muscle growth and development in L. crocea under different environmental conditions.
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Affiliation(s)
- Shangwei Xie
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
- Nanji Archipelago National Marine Nature Reserve Administration, Wenzhou, Zhejiang Province, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Weihua Song
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Jialang Zheng
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Yifan Liu
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Shun Chen
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Xiaojun Yan
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
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Núñez-Manchón J, Capó J, Martínez-Piñeiro A, Juanola E, Pesovic J, Mosqueira-Martín L, González-Imaz K, Maestre-Mora P, Odria R, Savic-Pavicevic D, Vallejo-Illarramendi A, Mamchaoui K, Bigot A, Mouly V, Suelves M, Nogales-Gadea G. Immortalized human myotonic dystrophy type 1 muscle cell lines to address patient heterogeneity. iScience 2024; 27:109930. [PMID: 38832025 PMCID: PMC11144749 DOI: 10.1016/j.isci.2024.109930] [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] [Revised: 03/21/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Historically, cellular models have been used as a tool to study myotonic dystrophy type 1 (DM1) and the validation of therapies in said pathology. However, there is a need for in vitro models that represent the clinical heterogeneity observed in patients with DM1 that is lacking in classical models. In this study, we immortalized three DM1 muscle lines derived from patients with different DM1 subtypes and clinical backgrounds and characterized them at the genetic, epigenetic, and molecular levels. All three cell lines display DM1 hallmarks, such as the accumulation of RNA foci, MBNL1 sequestration, splicing alterations, and reduced fusion. In addition, alterations in early myogenic markers, myotube diameter and CTCF1 DNA methylation were also found in DM1 cells. Notably, the new lines show a high level of heterogeneity in both the size of the CTG expansion and the aforementioned molecular alterations. Importantly, these immortalized cells also responded to previously tested therapeutics. Altogether, our results show that these three human DM1 cellular models are suitable to study the pathophysiological heterogeneity of DM1 and to test future therapeutic options.
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Affiliation(s)
- Judit Núñez-Manchón
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Júlia Capó
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Alicia Martínez-Piñeiro
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Eduard Juanola
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Jovan Pesovic
- University of Belgrade - Faculty of Biology, Center for Human Molecular Genetics, Belgrade, Serbia
| | - Laura Mosqueira-Martín
- Group of Neurosciences, Department of Pediatrics, UPV/EHU, Hospital Universitario Donostia - IIS Biodonostia, 20014 San Sebastian, Spain
| | - Klaudia González-Imaz
- Group of Neurosciences, Department of Pediatrics, UPV/EHU, Hospital Universitario Donostia - IIS Biodonostia, 20014 San Sebastian, Spain
| | - Pau Maestre-Mora
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Renato Odria
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Dusanka Savic-Pavicevic
- University of Belgrade - Faculty of Biology, Center for Human Molecular Genetics, Belgrade, Serbia
| | - Ainara Vallejo-Illarramendi
- Group of Neurosciences, Department of Pediatrics, UPV/EHU, Hospital Universitario Donostia - IIS Biodonostia, 20014 San Sebastian, Spain
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France
| | - Anne Bigot
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France
| | - Vincent Mouly
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013 Paris, France
| | - Mònica Suelves
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Gisela Nogales-Gadea
- Grup de REcerca Neuromuscular de BAdalona (GRENBA), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
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Aitken KJ, Schröder A, Haddad A, Sidler M, Penna F, Fernandez N, Ahmed T, Marino V, Bechbache M, Jiang JX, Tolg C, Bägli DJ. Epigenetic insights to pediatric uropathology: Celebrating the fundamental biology vision of Tony Khoury. J Pediatr Urol 2024; 20 Suppl 1:S43-S57. [PMID: 38944627 DOI: 10.1016/j.jpurol.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024]
Abstract
INTRODUCTION Many pediatric urology conditions affect putatively normal tissues or appear too commonly to be based solely on specific DNA mutations. Understanding epigenetic mechanisms in pediatric urology, therefore, has many implications that can impact cell and tissue responses to settings, such as environmental and hormonal influences on urethral development, uropathogenic infections, obstructive stimuli, all of which originate externally or extracellularly. Indeed, the cell's response to external stimuli is often mediated epigenetically. In this commentary, we highlight work on the critical role that epigenetic machinery, such as DNA methyltransferases (DNMTs), Enhancer of Zeste Polycomb Repressive Complex 2 Subunit (EZH2), and others play in regulating gene expression and cellular functions in three urological contexts. DESIGN Animal and cellular constructs were used to model clinical pediatric uropathology. The hypertrophy, trabeculation, and fibrosis of the chronically obstructed bladder was explored using smooth muscle cell models employing disorganised vs. normal extracellular matrix (ECM), as well as a new animal model of chronic obstructive bladder disease (COBD) which retains its pathologic features even after bladder de-obstruction. Cell models from human and murine hypospadias or genital tubercles (GT) were used to illustrate developmental responses and epigenetic dependency of key developmental genes. Finally, using bladder urothelial and organoid culture systems, we examined activity of epigenetic machinery in response to non uropathogenic vs. uropathogenic E.coli (UPEC). DNMT and EZH2 expression and function were interrogated in these model systems. RESULTS Disordered ECM exerted a principal mitogenic and epigenetic role for on bladder smooth muscle both in vitro and in CODB in vivo. Key genes, e.g., BDNF and KCNB2 were under epigenetic regulation in actively evolving obstruction and COBD, though each condition showed distinct epigenetic responses. In models of hypospadias, estrogen strongly dysregulated WNT and Hox expression, which was normalized by epigenetic inhibition. Finally, DNA methylation machinery in the urothelium showed specific activation when challenged by uropathogenic E.coli. Similarly, UPEC induces hypermethylation and downregulation of the growth suppressor p16INK4A. Moreover, host cells exposed to UPEC produced secreted factors inducing epigenetic responses transmissible from one affected cell to another without ongoing bacterial presence. DISCUSSION Microenvironmental influences altered epigenetic activity in the three described urologic contexts. Considering that many obstructed bladders continue to display abnormal architecture and dysfunction despite relief of obstruction similar to after resection of posterior valves or BPH, the epigenetic mechanisms described highlight novel approaches for understanding the underlying smooth muscle myopathy of this crucial clinical problem. Similarly, there is evidence for an epigenetic basis of xenoestrogen on development of hypospadias, and UTI-induced pan-urothelial alteration of epigenetic marks and propensity for subsequent (recurrent) UTI. The impact of mechanical, hormonal, infectious triggers on genitourinary epigenetic machinery activity invite novel avenues for targeting epigenetic modifications associated with these non-cancer diseases in urology. This includes the use of deactivated CRISPR-based technologies for precise epigenome targeting and editing. Overall, we underscore the importance of understanding epigenetic regulation in pediatric urology for the development of innovative therapeutic and management strategies.
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Affiliation(s)
- K J Aitken
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; DIYbio Toronto, 1677 St. Clair West, Toronto, Ontario, Canada.
| | - Annette Schröder
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Urology and Pediatric Urology of the University Medical Center Mainz, Mainz, Rheinland-Pfalz, Germany
| | - Ahmed Haddad
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Martin Sidler
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Frank Penna
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicolas Fernandez
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tabina Ahmed
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Human Biology Programme, University of Toronto, Toronto, Ontario, Canada
| | - Vincent Marino
- DIYbio Toronto, 1677 St. Clair West, Toronto, Ontario, Canada
| | - Matthew Bechbache
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada
| | - Jia-Xin Jiang
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Human Biology Programme, University of Toronto, Toronto, Ontario, Canada; Department of Physiology, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Cornelia Tolg
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada
| | - Darius J Bägli
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, 686 Bay St., Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Physiology, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Division of Urology, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Luo J, Wang W, Li J, Duan H, Xu C, Tian X, Zhang D. Epigenome-wide association study identifies DNA methylation loci associated with handgrip strength in Chinese monozygotic twins. Front Cell Dev Biol 2024; 12:1378680. [PMID: 38633108 PMCID: PMC11021642 DOI: 10.3389/fcell.2024.1378680] [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: 01/30/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Background: The decline in muscle strength and function with aging is well recognized, but remains poorly characterized at the molecular level. Here, we report the epigenetic relationship between genome-wide DNA methylation and handgrip strength (HGS) among Chinese monozygotic (MZ) twins. Methods: DNA methylation (DNAm) profiling was conducted in whole blood samples through Reduced Representation Bisulfite Sequencing method. Generalized estimating equation was applied to regress the DNAm of each CpG with HGS. The Genomic Regions Enrichment of Annotations Tool was used to perform enrichment analysis. Differentially methylated regions (DMRs) were detected using comb-p. Causal inference was performed using Inference about Causation through Examination of Familial Confounding method. Finally, we validated candidate CpGs in community residents. Results: We identified 25 CpGs reaching genome-wide significance level. These CpGs located in 9 genes, especially FBLN1, RXRA, and ABHD14B. Many enriched terms highlighted calcium channels, neuromuscular junctions, and skeletal muscle organ development. We identified 21 DMRs of HGS, with several DMRs within FBLN1, SLC30A8, CST3, and SOCS3. Causal inference indicated that the DNAm of 16 top CpGs within FBLN1, RXRA, ABHD14B, MFSD6, and TYW1B might influence HGS, while HGS influenced DNAm at two CpGs within FBLN1 and RXRA. In validation analysis, methylation levels of six CpGs mapped to FLBN1 and one CpG mapped to ABHD14B were negatively associated with HGS weakness in community population. Conclusion: Our study identified multiple DNAm variants potentially related to HGS, especially CpGs within FBLN1 and ABHD14B. These findings provide new clues to the epigenetic modification underlying muscle strength decline.
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Affiliation(s)
- Jia Luo
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Jingxian Li
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Haiping Duan
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, Shandong, China
- Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Chunsheng Xu
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, Shandong, China
- Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Xiaocao Tian
- Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, Shandong, China
- Qingdao Institute of Preventive Medicine, Qingdao, Shandong, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Qingdao University, Qingdao, Shandong, China
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Wei X, Rigopoulos A, Lienhard M, Pöhle-Kronawitter S, Kotsaris G, Franke J, Berndt N, Mejedo JO, Wu H, Börno S, Timmermann B, Murgai A, Glauben R, Stricker S. Neurofibromin 1 controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors. Nat Commun 2024; 15:1393. [PMID: 38360927 PMCID: PMC10869796 DOI: 10.1038/s41467-024-45618-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Patients affected by neurofibromatosis type 1 (NF1) frequently show muscle weakness with unknown etiology. Here we show that, in mice, Neurofibromin 1 (Nf1) is not required in muscle fibers, but specifically in early postnatal myogenic progenitors (MPs), where Nf1 loss led to cell cycle exit and differentiation blockade, depleting the MP pool resulting in reduced myonuclear accretion as well as reduced muscle stem cell numbers. This was caused by precocious induction of stem cell quiescence coupled to metabolic reprogramming of MPs impinging on glycolytic shutdown, which was conserved in muscle fibers. We show that a Mek/Erk/NOS pathway hypersensitizes Nf1-deficient MPs to Notch signaling, consequently, early postnatal Notch pathway inhibition ameliorated premature quiescence, metabolic reprogramming and muscle growth. This reveals an unexpected role of Ras/Mek/Erk signaling supporting postnatal MP quiescence in concert with Notch signaling, which is controlled by Nf1 safeguarding coordinated muscle growth and muscle stem cell pool establishment. Furthermore, our data suggest transmission of metabolic reprogramming across cellular differentiation, affecting fiber metabolism and function in NF1.
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Affiliation(s)
- Xiaoyan Wei
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Angelos Rigopoulos
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- International Max Planck Research School for Biology and Computation IMPRS-BAC, Berlin, Germany
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Sophie Pöhle-Kronawitter
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Georgios Kotsaris
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Julia Franke
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Nikolaus Berndt
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
- Institute of Computer-assisted Cardiovascular Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Joy Orezimena Mejedo
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Hao Wu
- Division of Gastroenterology, Infectiology and Rheumatology, Medical Department, Charité University Medicine Berlin, 12203, Berlin, Germany
| | - Stefan Börno
- Sequencing Core Unit, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Unit, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Arunima Murgai
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Rainer Glauben
- Division of Gastroenterology, Infectiology and Rheumatology, Medical Department, Charité University Medicine Berlin, 12203, Berlin, Germany
| | - Sigmar Stricker
- Musculoskeletal Development and Regeneration Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
- International Max Planck Research School for Biology and Computation IMPRS-BAC, Berlin, Germany.
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Lu Y, Zhou J, Li F, Cao H, Zhang X, Yu D, He Z, Ji H, Lv K, Wu G, Yu M. The Integration of Genome-Wide DNA Methylation and Transcriptomics Identifies the Potential Genes That Regulate the Development of Skeletal Muscles in Ducks. Int J Mol Sci 2023; 24:15476. [PMID: 37895154 PMCID: PMC10607517 DOI: 10.3390/ijms242015476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
DNA methylation is a pivotal epigenetic regulatory mechanism in the development of skeletal muscles. Nonetheless, the regulators responsible for DNA methylation in the development of embryonic duck skeletal muscles remain unknown. In the present study, whole genome bisulfite sequencing (WGBS) and transcriptome sequencing were conducted on the skeletal muscles of embryonic day 21 (E21) and day 28 (E28) ducks. The DNA methylation pattern was found to fall mainly within the cytosine-guanine (CG) context, with high methylation levels in the intron, exon, and promoter regions. Overall, 7902 differentially methylated regions (DMRs) were identified, which corresponded to 3174 differentially methylated genes (DMGs). By using integrative analysis of both WGBS with transcriptomics, we identified 1072 genes that are DMGs that are negatively associated with differentially expressed genes (DEGs). The gene ontology (GO) analysis revealed significant enrichment in phosphorylation, kinase activity, phosphotransferase activity, alcohol-based receptors, and binding to cytoskeletal proteins. The Kyoto Encyclopedia of Genes and Genomes (KEGGs) analysis showed significant enrichment in MAPK signaling, Wnt signaling, apelin signaling, insulin signaling, and FoxO signaling. The screening of enriched genes showed that hyper-methylation inhibited the expression of Idh3a, Got1, Bcl2, Mylk2, Klf2, Erbin, and Klhl38, and hypo-methylation stimulated the expression of Col22a1, Dnmt3b, Fn1, E2f1, Rprm, and Wfikkn1. Further predictions showed that the CpG islands in the promoters of Klhl38, Klf2, Erbin, Mylk2, and Got1 may play a crucial role in regulating the development of skeletal muscles. This study provides new insights into the epigenetic regulation of the development of duck skeletal muscles.
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Affiliation(s)
- Yinglin Lu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (J.Z.); (F.L.); (H.C.); (X.Z.); (D.Y.)
| | - Jing Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (J.Z.); (F.L.); (H.C.); (X.Z.); (D.Y.)
| | - Fan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (J.Z.); (F.L.); (H.C.); (X.Z.); (D.Y.)
| | - Heng Cao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (J.Z.); (F.L.); (H.C.); (X.Z.); (D.Y.)
| | - Xingyu Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (J.Z.); (F.L.); (H.C.); (X.Z.); (D.Y.)
| | - Debing Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (J.Z.); (F.L.); (H.C.); (X.Z.); (D.Y.)
| | - Zongliang He
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing 210036, China; (Z.H.); (H.J.); (K.L.); (G.W.)
| | - Hongjie Ji
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing 210036, China; (Z.H.); (H.J.); (K.L.); (G.W.)
| | - Kunpeng Lv
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing 210036, China; (Z.H.); (H.J.); (K.L.); (G.W.)
| | - Guansuo Wu
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing 210036, China; (Z.H.); (H.J.); (K.L.); (G.W.)
| | - Minli Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (J.Z.); (F.L.); (H.C.); (X.Z.); (D.Y.)
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7
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Lei S, Li C, She Y, Zhou S, Shi H, Chen R. Roles of super enhancers and enhancer RNAs in skeletal muscle development and disease. Cell Cycle 2023; 22:495-505. [PMID: 36184878 PMCID: PMC9928468 DOI: 10.1080/15384101.2022.2129240] [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: 07/28/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022] Open
Abstract
Skeletal muscle development is a multistep biological process regulated by a variety of myogenic regulatory factors, including MyoG, MyoD, Myf5, and Myf6 (also known as MRF4), as well as members of the FoxO subfamily. Differentiation and regeneration during skeletal muscle myogenesis contribute to the physiological function of muscles. Super enhancers (SEs) and enhancer RNAs (eRNAs) are involved in the regulation of development and diseases. Few studies have identified the roles of SEs and eRNAs in muscle development and pathophysiology. To develop approaches to enhance skeletal muscle mass and function, a more comprehensive understanding of the key processes underlying muscular diseases is needed. In this review, we summarize the roles of SEs and eRNAs in muscle development and disease through affecting of DNA methylation, FoxO subfamily, RAS-MEK signaling, chromatin modifications and accessibility, MyoD and cis regulating target genes. The summary could inform strategies to increase muscle mass and treat muscle-related diseases.
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Affiliation(s)
- Si Lei
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Cheng Li
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Yanling She
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Shanyao Zhou
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Huacai Shi
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Rui Chen
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
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8
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Sahinyan K, Lazure F, Blackburn DM, Soleimani VD. Decline of regenerative potential of old muscle stem cells: contribution to muscle aging. FEBS J 2023; 290:1267-1289. [PMID: 35029021 DOI: 10.1111/febs.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 01/01/2023]
Abstract
Muscle stem cells (MuSCs) are required for life-long muscle regeneration. In general, aging has been linked to a decline in the numbers and the regenerative potential of MuSCs. Muscle regeneration depends on the proper functioning of MuSCs, which is itself dependent on intricate interactions with its niche components. Aging is associated with both cell-intrinsic and niche-mediated changes, which can be the result of transcriptional, posttranscriptional, or posttranslational alterations in MuSCs or in the components of their niche. The interplay between cell intrinsic alterations in MuSCs and changes in the stem cell niche environment during aging and its impact on the number and the function of MuSCs is an important emerging area of research. In this review, we discuss whether the decline in the regenerative potential of MuSCs with age is the cause or the consequence of aging skeletal muscle. Understanding the effect of aging on MuSCs and the individual components of their niche is critical to develop effective therapeutic approaches to diminish or reverse the age-related defects in muscle regeneration.
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Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
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9
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Yazar V, Dawson VL, Dawson TM, Kang SU. DNA Methylation Signature of Aging: Potential Impact on the Pathogenesis of Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2023; 13:145-164. [PMID: 36710687 PMCID: PMC10041453 DOI: 10.3233/jpd-223517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Regulation of gene expression by epigenetic modifications means lasting and heritable changes in the function of genes without alterations in the DNA sequence. Of all epigenetic mechanisms identified thus far, DNA methylation has been of particular interest in both aging and age-related disease research over the last decade given the consistency of site-specific DNA methylation changes during aging that can predict future health and lifespan. An increasing line of evidence has implied the dynamic nature of DNA (de)methylation events that occur throughout the lifespan has a role in the pathophysiology of aging and age-associated neurodegenerative conditions, including Parkinson's disease (PD). In this regard, PD methylome shows, to some extent, similar genome-wide changes observed in the methylome of healthy individuals of matching age. In this review, we start by providing a brief overview of studies outlining global patterns of DNA methylation, then its mechanisms and regulation, within the context of aging and PD. Considering diverging lines of evidence from different experimental and animal models of neurodegeneration and how they combine to shape our current understanding of tissue-specific changes in DNA methylome in health and disease, we report a high-level comparison of the genomic methylation landscapes of brain, with an emphasis on dopaminergic neurons in PD and in natural aging. We believe this will be particularly useful for systematically dissecting overlapping genome-wide alterations in DNA methylation during PD and healthy aging, and for improving our knowledge of PD-specific changes in methylation patterns independent of aging process.
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Affiliation(s)
- Volkan Yazar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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10
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Robinson KG, Marsh AG, Lee SK, Hicks J, Romero B, Batish M, Crowgey EL, Shrader MW, Akins RE. DNA Methylation Analysis Reveals Distinct Patterns in Satellite Cell-Derived Myogenic Progenitor Cells of Subjects with Spastic Cerebral Palsy. J Pers Med 2022; 12:jpm12121978. [PMID: 36556199 PMCID: PMC9780849 DOI: 10.3390/jpm12121978] [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: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Spastic type cerebral palsy (CP) is a complex neuromuscular disorder that involves altered skeletal muscle microanatomy and growth, but little is known about the mechanisms contributing to muscle pathophysiology and dysfunction. Traditional genomic approaches have provided limited insight regarding disease onset and severity, but recent epigenomic studies indicate that DNA methylation patterns can be altered in CP. Here, we examined whether a diagnosis of spastic CP is associated with intrinsic DNA methylation differences in myoblasts and myotubes derived from muscle resident stem cell populations (satellite cells; SCs). Twelve subjects were enrolled (6 CP; 6 control) with informed consent/assent. Skeletal muscle biopsies were obtained during orthopedic surgeries, and SCs were isolated and cultured to establish patient-specific myoblast cell lines capable of proliferation and differentiation in culture. DNA methylation analyses indicated significant differences at 525 individual CpG sites in proliferating SC-derived myoblasts (MB) and 1774 CpG sites in differentiating SC-derived myotubes (MT). Of these, 79 CpG sites were common in both culture types. The distribution of differentially methylated 1 Mbp chromosomal segments indicated distinct regional hypo- and hyper-methylation patterns, and significant enrichment of differentially methylated sites on chromosomes 12, 13, 14, 15, 18, and 20. Average methylation load across 2000 bp regions flanking transcriptional start sites was significantly different in 3 genes in MBs, and 10 genes in MTs. SC derived MBs isolated from study participants with spastic CP exhibited fundamental differences in DNA methylation compared to controls at multiple levels of organization that may reveal new targets for studies of mechanisms contributing to muscle dysregulation in spastic CP.
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Affiliation(s)
- Karyn G. Robinson
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
| | - Adam G. Marsh
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Stephanie K. Lee
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
| | - Jonathan Hicks
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Brigette Romero
- Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Erin L. Crowgey
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
| | - M. Wade Shrader
- Department of Orthopedics, Nemours Children’s Hospital Delaware, Wilmington, DE 19803, USA
| | - Robert E. Akins
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
- Correspondence: ; Tel.: +1-302-651-6779
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11
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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12
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Koehorst E, Odria R, Capó J, Núñez-Manchón J, Arbex A, Almendrote M, Linares-Pardo I, Natera-de Benito D, Saez V, Nascimento A, Ortez C, Rubio MÁ, Díaz-Manera J, Alonso-Pérez J, Lucente G, Rodriguez-Palmero A, Ramos-Fransi A, Martínez-Piñeiro A, Nogales-Gadea G, Suelves M. An Integrative Analysis of DNA Methylation Pattern in Myotonic Dystrophy Type 1 Samples Reveals a Distinct DNA Methylation Profile between Tissues and a Novel Muscle-Associated Epigenetic Dysregulation. Biomedicines 2022; 10:biomedicines10061372. [PMID: 35740394 PMCID: PMC9220235 DOI: 10.3390/biomedicines10061372] [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: 04/22/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a progressive, non-treatable, multi-systemic disorder. To investigate the contribution of epigenetics to the complexity of DM1, we compared DNA methylation profiles of four annotated CpG islands (CpGis) in the DMPK locus and neighbouring genes, in distinct DM1 tissues and derived cells, representing six DM1 subtypes, by bisulphite sequencing. In blood, we found no differences in CpGi 74, 43 and 36 in DNA methylation profile. In contrast, a CTCF1 DNA methylation gradient was found with 100% methylation in congenital cases, 50% in childhood cases and 13% in juvenile cases. CTCF1 methylation correlated to disease severity and CTG expansion size. Notably, 50% of CTCF1 methylated cases showed methylation in the CTCF2 regions. Additionally, methylation was associated with maternal transmission. Interestingly, the evaluation of seven families showed that unmethylated mothers passed on an expansion of the CTG repeat, whereas the methylated mothers transmitted a contraction. The analysis of patient-derived cells showed that DNA methylation profiles were highly preserved, validating their use as faithful DM1 cellular models. Importantly, the comparison of DNA methylation levels of distinct DM1 tissues revealed a novel muscle-specific epigenetic signature with methylation of the CTCF1 region accompanied by demethylation of CpGi 43, a region containing an alternative DMPK promoter, which may decrease the canonical promoter activity. Altogether, our results showed a distinct DNA methylation profile across DM1 tissues and uncovered a novel and dual epigenetic signature in DM1 muscle samples, providing novel insights into the epigenetic changes associated with DM1.
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Affiliation(s)
- Emma Koehorst
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Renato Odria
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Júlia Capó
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Judit Núñez-Manchón
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Andrea Arbex
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Miriam Almendrote
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Ian Linares-Pardo
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Verónica Saez
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Andrés Nascimento
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Neuropediatric Department, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, L'Hospitalet de Llobregat, 08950 Barcelona, Spain
| | - Miguel Ángel Rubio
- Neuromuscular Unit, Department of Neurology, Hospital del Mar, 08003 Barcelona, Spain
| | - Jordi Díaz-Manera
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- John Walton Muscular Dystrophy Research Centre, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK
| | - Jorge Alonso-Pérez
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
| | - Giuseppe Lucente
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Agustín Rodriguez-Palmero
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Pediatric Neurology Unit, Department of Pediatrics, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Alba Ramos-Fransi
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Alicia Martínez-Piñeiro
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
- Neuromuscular Pathology Unit, Neurology Service, Neuroscience Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
| | - Gisela Nogales-Gadea
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Mònica Suelves
- Neuromuscular and Neuropediatric Research Group, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
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13
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Sakai H, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada SI, Ohkawa Y, Kikugawa T, Saika T, Imai Y. Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience 2022; 25:103928. [PMID: 35243267 PMCID: PMC8886052 DOI: 10.1016/j.isci.2022.103928] [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: 04/20/2021] [Revised: 12/06/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is an essential form of epigenetic regulation responsible for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are tightly regulated during differentiation. However, it is unclear how these DNA methylation patterns affect the function of satellite cells. We demonstrate that a key epigenetic regulator, ubiquitin like with PHD and RING finger domains 1 (Uhrf1), is activated in proliferating myogenic cells but not expressed in quiescent satellite cells or differentiated myogenic cells in mice. Ablation of Uhrf1 in mouse satellite cells impairs their proliferation and differentiation, leading to failed muscle regeneration. Uhrf1-deficient myogenic cells exhibited aberrant upregulation of transcripts, including Sox9, with the reduction of DNA methylation level of their promoter and enhancer region. These findings show that Uhrf1 is a critical epigenetic regulator of proliferation and differentiation in satellite cells, by controlling cell-type-specific gene expression via maintenance of DNA methylation. Uhrf1 is activated in proliferating myogenic cells Uhrf1 in satellite cells is required for muscle regeneration Ablation of Uhrf1 in satellite cells impairs their proliferation and differentiation Uhrf1 controls cell-type-specific transcripts via maintenance of DNA methylation
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Affiliation(s)
- Hiroshi Sakai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
- Corresponding author
| | - Yuichiro Sawada
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Naohito Tokunaga
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon, Ehime 791-0295, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-0054, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Iori Sakakibara
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Yusuke Ono
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo, Kumamoto 860-0811, Japan
| | - So-ichiro Fukada
- Project for Muscle Stem Cell Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-0054, Japan
| | - Tadahiko Kikugawa
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Takashi Saika
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
- Corresponding author
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14
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Li Y, Darabi R. Role of epigenetics in cellular reprogramming; from iPSCs to disease modeling and cell therapy. J Cell Biochem 2022; 123:147-154. [PMID: 34668236 PMCID: PMC8860854 DOI: 10.1002/jcb.30164] [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: 08/03/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023]
Abstract
Epigenetics play a fundamental role in induced pluripotent stem cell (iPSC) technology due to their effect on iPSC's reprogramming efficiency and their subsequent role in iPSC differentiation toward a specific lineage. Epigenetics can skew the differentiation course of iPSCs toward a specific lineage based on the epigenetic memory of the source cells, or even lead to acquisition of new cell phenotypes, due to its aberrations during reprogramming. This viewpoint discusses key features of the epigenetic process during iPSC reprogramming/differentiation and outlines important epigenetic factors that need to be considered for successful generation and differentiation of iPSCs for downstream applications.
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Affiliation(s)
- Yong Li
- Department of Orthopaedic Surgery, BioMedical Engineering, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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15
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Agarwal M, Bharadwaj A, Mathew SJ. TLE4 regulates muscle stem cell quiescence and skeletal muscle differentiation. J Cell Sci 2022; 135:274455. [PMID: 35099008 DOI: 10.1242/jcs.256008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/18/2022] [Indexed: 10/19/2022] Open
Abstract
Muscle stem (satellite) cells express Pax7, a key transcription factor essential for satellite cell maintenance and adult muscle regeneration. We identify the corepressor Transducin-Like Enhancer of Split-4 (TLE4) as a Pax7 interaction partner expressed in quiescent satellite cells under homeostasis. A subset of satellite cells transiently downregulate TLE4 during early time points following injury. We identify these to be activated satellite cells where TLE4 downregulation is required for Myf5 activation and myogenic commitment. Our results indicate that TLE4 represses Pax7-mediated Myf5 transcriptional activation by occupying the -111 kb Myf5 enhancer to maintain quiescence. Loss of TLE4 function causes Myf5 upregulation, increase in satellite cell numbers, and altered differentiation dynamics during regeneration. Thus, we have uncovered a novel mechanism to maintain satellite cell quiescence and regulating muscle differentiation mediated by the corepressor TLE4.
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Affiliation(s)
- Megha Agarwal
- Developmental Genetics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India.,Manipal University, Manipal, Karnataka, 576104, India
| | - Anushree Bharadwaj
- Developmental Genetics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Sam J Mathew
- Developmental Genetics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India.,Manipal University, Manipal, Karnataka, 576104, India
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16
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Sibley LA, Broda N, Gross WR, Menezes AF, Embry RB, Swaroop VT, Chambers HG, Schipma MJ, Lieber RL, Domenighetti AA. Differential DNA methylation and transcriptional signatures characterize impairment of muscle stem cells in pediatric human muscle contractures after brain injury. FASEB J 2021; 35:e21928. [PMID: 34559924 DOI: 10.1096/fj.202100649r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 08/11/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
Limb contractures are a debilitating and progressive consequence of a wide range of upper motor neuron injuries that affect skeletal muscle function. One type of perinatal brain injury causes cerebral palsy (CP), which affects a child's ability to move and is often painful. While several rehabilitation therapies are used to treat contractures, their long-term effectiveness is marginal since such therapies do not change muscle biological properties. Therefore, new therapies based on a biological understanding of contracture development are needed. Here, we show that myoblast progenitors from contractured muscle in children with CP are hyperproliferative. This phenotype is associated with DNA hypermethylation and specific gene expression patterns that favor cell proliferation over quiescence. Treatment of CP myoblasts with 5-azacytidine, a DNA hypomethylating agent, reduced this epigenetic imprint to TD levels, promoting exit from mitosis and molecular mechanisms of cellular quiescence. Together with previous studies demonstrating reduction in myoblast differentiation, this suggests a mechanism of contracture formation that is due to epigenetic modifications that alter the myogenic program of muscle-generating stem cells. We suggest that normalization of DNA methylation levels could rescue myogenesis and promote regulated muscle growth in muscle contracture and thus may represent a new nonsurgical approach to treating this devastating neuromuscular condition.
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Affiliation(s)
| | | | | | | | - Ryan B Embry
- NUseq Core, Northwestern University, Chicago, Illinois, USA
| | - Vineeta T Swaroop
- Shirley Ryan AbilityLab, Chicago, Illinois, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Henry G Chambers
- Rady Children's Hospital and Health Center, San Diego, California, USA
| | - Matthew J Schipma
- Rady Children's Hospital and Health Center, San Diego, California, USA
| | - Richard L Lieber
- Shirley Ryan AbilityLab, Chicago, Illinois, USA.,Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, Illinois, USA.,Hines VA Medical Center, Maywood, Illinois, USA
| | - Andrea A Domenighetti
- Shirley Ryan AbilityLab, Chicago, Illinois, USA.,Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, Illinois, USA
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17
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Yagi M, Ji F, Charlton J, Cristea S, Messemer K, Horwitz N, Di Stefano B, Tsopoulidis N, Hoetker MS, Huebner AJ, Bar-Nur O, Almada AE, Yamamoto M, Patelunas A, Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI, Hochedlinger K. Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes Dev 2021; 35:1209-1228. [PMID: 34413137 PMCID: PMC8415322 DOI: 10.1101/gad.348678.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of transcription factor-induced reprogramming. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced myogenic progenitor cells (iMPCs). Here, we dissected the transcriptional and epigenetic dynamics of mouse fibroblasts undergoing reprogramming to either myotubes or iMPCs using a MyoD-inducible transgenic model. Induction of MyoD in fibroblasts combined with small molecules generated Pax7+ iMPCs with high similarity to primary muscle stem cells. Analysis of intermediate stages of iMPC induction revealed that extinction of the fibroblast program preceded induction of the stem cell program. Moreover, key stem cell genes gained chromatin accessibility prior to their transcriptional activation, and these regions exhibited a marked loss of DNA methylation dependent on the Tet enzymes. In contrast, myotube generation was associated with few methylation changes, incomplete and unstable reprogramming, and an insensitivity to Tet depletion. Finally, we showed that MyoD's ability to bind to unique bHLH targets was crucial for generating iMPCs but dispensable for generating myotubes. Collectively, our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity.
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Affiliation(s)
- Masaki Yagi
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Genome Regulation, Max-Planck-Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Simona Cristea
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kathleen Messemer
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Naftali Horwitz
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Joslin Diabetes Center, Boston, Massachusetts 02215, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nikolaos Tsopoulidis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Michael S Hoetker
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aaron J Huebner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ori Bar-Nur
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Albert E Almada
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Joslin Diabetes Center, Boston, Massachusetts 02215, USA
| | - Masakazu Yamamoto
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Anthony Patelunas
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - David J Goldhamer
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Amy J Wagers
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Joslin Diabetes Center, Boston, Massachusetts 02215, USA
| | - Franziska Michor
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,The Ludwig Center at Harvard, Boston, Massachusetts 02115, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Genome Regulation, Max-Planck-Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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18
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Setten RL, Chomchan P, Epps EW, Burnett JC, Rossi JJ. CRED9: A differentially expressed elncRNA regulates expression of transcription factor CEBPA. RNA (NEW YORK, N.Y.) 2021; 27:rna.078752.121. [PMID: 34039742 PMCID: PMC8284328 DOI: 10.1261/rna.078752.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Enhancer RNAs (eRNA) are non-coding transcripts produced from active enhancers and have potential gene regulatory function. CCAAT enhancer-binding protein alpha (CEBPA) is a transcription factor generally involved in metabolism, cell cycle inhibition, hematopoiesis, adipogenesis, hepatogenesis, and is associated with tumorigenesis. In this study, we demonstrate that an enhancer-associated long non-coding RNA (elncRNA), transcribed from an enhancer located 9kb downstream from the transcriptional start site (TSS) of CEBPA, positively regulates the expression of CEBPA. As a result, we named this elncRNA 'CEBPA regulatory elncRNA downstream 9kb' or 'CRED9'. CRED9 expression level positively correlates with CEBPA mRNA expression across multiple cell lines as detected by RT droplet digital PCR. Knockdown of CRED9 resulted in a reduction of CEBPA mRNA expression in Hep3B cells. Additionally, CRED9 knockdown in Hep3B and HepG2 cells resulted in lower CEBPA protein expression. We also found that knockdown of CRED9 in Hep3B cells caused a 57.8% reduction in H3K27ac levels at the +9kb CEBPA enhancer. H3K27ac has previously been described as a marker of active enhancers. Taken together, the evidence presented here supports a previously proposed model whereby, in some contexts, eRNA transcripts are necessary to amplify and maintain H3K27ac levels at a given enhancer. Ultimately, this study adds to the growing body of evidence that elncRNA transcripts have important roles in enhancer function and gene regulation.
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19
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Yang Y, Fan X, Yan J, Chen M, Zhu M, Tang Y, Liu S, Tang Z. A comprehensive epigenome atlas reveals DNA methylation regulating skeletal muscle development. Nucleic Acids Res 2021; 49:1313-1329. [PMID: 33434283 PMCID: PMC7897484 DOI: 10.1093/nar/gkaa1203] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is important for the epigenetic regulation of gene expression and plays a critical role in mammalian development. However, the dynamic regulation of genome-wide DNA methylation in skeletal muscle development remains largely unknown. Here, we generated the first single-base resolution DNA methylome and transcriptome maps of porcine skeletal muscle across 27 developmental stages. The overall methylation level decreased from the embryo to the adult, which was highly correlated with the downregulated expression of DNMT1 and an increase in partially methylated domains. Notably, we identified over 40 000 developmentally differentially methylated CpGs (dDMCs) that reconstitute the developmental trajectory of skeletal muscle and associate with muscle developmental genes and transcription factors (TFs). The dDMCs were significantly under-represented in promoter regulatory regions but strongly enriched as enhancer histone markers and in chromatin-accessible regions. Integrative analysis revealed the negative regulation of both promoter and gene body methylation in genes associated with muscle contraction and insulin signaling during skeletal muscle development. Mechanistically, DNA methylation affected the expression of muscle-related genes by modulating the accessibly of upstream myogenesis TF binding, indicating the involvement of the DNA methylation/SP1/IGF2BP3 axis in skeletal myogenesis. Our results highlight the function and regulation of dynamic DNA methylation in skeletal muscle development.
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Affiliation(s)
- Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Muya Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Min Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yijie Tang
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Siyuan Liu
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama 547500, China
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20
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Núñez-Álvarez Y, Hurtado E, Muñoz M, García-Tuñon I, Rech GE, Pluvinet R, Sumoy L, Pendás AM, Peinado MA, Suelves M. Loss of HDAC11 accelerates skeletal muscle regeneration in mice. FEBS J 2021; 288:1201-1223. [PMID: 32602219 DOI: 10.1111/febs.15468] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/29/2020] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
Histone deacetylase 11 (HDAC11) is the latest identified member of the histone deacetylase family of enzymes. It is highly expressed in brain, heart, testis, kidney, and skeletal muscle, although its role in these tissues is poorly understood. Here, we investigate for the first time the consequences of HDAC11 genetic impairment on skeletal muscle regeneration, a process principally dependent on its resident stem cells (satellite cells) in coordination with infiltrating immune cells and stromal cells. Our results show that HDAC11 is dispensable for adult muscle growth and establishment of the satellite cell population, while HDAC11 deficiency advances the regeneration process in response to muscle injury. This effect is not caused by differences in satellite cell activation or proliferation upon injury, but rather by an enhanced capacity of satellite cells to differentiate at early regeneration stages in the absence of HDAC11. Infiltrating HDAC11-deficient macrophages could also contribute to this accelerated muscle regenerative process by prematurely producing high levels of IL-10, a cytokine known to promote myoblast differentiation. Altogether, our results show that HDAC11 depletion advances skeletal muscle regeneration and this finding may have potential implications for designing new strategies for muscle pathologies coursing with chronic damage. DATABASE: Data were deposited in NCBI's Gene Expression Omnibus accessible through GEO Series accession number GSE147423.
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Affiliation(s)
- Yaiza Núñez-Álvarez
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Erica Hurtado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Mar Muñoz
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Ignacio García-Tuñon
- Institute of Cellular and Molecular Biology of Cancer (CSIC-USAL), Salamanca, Spain
| | - Gabriel E Rech
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Raquel Pluvinet
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Lauro Sumoy
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Alberto M Pendás
- Institute of Cellular and Molecular Biology of Cancer (CSIC-USAL), Salamanca, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
| | - Mònica Suelves
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Can Ruti Campus, Badalona, Spain
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21
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Koganti P, Yao J, Cleveland BM. Molecular Mechanisms Regulating Muscle Plasticity in Fish. Animals (Basel) 2020; 11:ani11010061. [PMID: 33396941 PMCID: PMC7824542 DOI: 10.3390/ani11010061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 12/12/2022] Open
Abstract
Growth rates in fish are largely dependent on genetic and environmental factors, of which the latter can be highly variable throughout development. For this reason, muscle growth in fish is particularly dynamic as muscle structure and function can be altered by environmental conditions, a concept referred to as muscle plasticity. Myogenic regulatory factors (MRFs) like Myogenin, MyoD, and Pax7 control the myogenic mechanisms regulating quiescent muscle cell maintenance, proliferation, and differentiation, critical processes central for muscle plasticity. This review focuses on recent advancements in molecular mechanisms involving microRNAs (miRNAs) and DNA methylation that regulate the expression and activity of MRFs in fish. Findings provide overwhelming support that these mechanisms are significant regulators of muscle plasticity, particularly in response to environmental factors like temperature and nutritional challenges. Genetic variation in DNA methylation and miRNA expression also correlate with variation in body weight and growth, suggesting that genetic markers related to these mechanisms may be useful for genomic selection strategies. Collectively, this knowledge improves the understanding of mechanisms regulating muscle plasticity and can contribute to the development of husbandry and breeding strategies that improve growth performance and the ability of the fish to respond to environmental challenges.
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Affiliation(s)
- Prasanthi Koganti
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108, USA; (P.K.); (J.Y.)
| | - Jianbo Yao
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506-6108, USA; (P.K.); (J.Y.)
| | - Beth M. Cleveland
- USDA ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
- Correspondence: ; Tel.: +1-304-724-8340 (ext. 2133)
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22
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Zhang X, Sun W, He L, Wang L, Qiu K, Yin J. Global DNA methylation pattern involved in the modulation of differentiation potential of adipogenic and myogenic precursors in skeletal muscle of pigs. Stem Cell Res Ther 2020; 11:536. [PMID: 33308295 PMCID: PMC7731745 DOI: 10.1186/s13287-020-02053-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background Skeletal muscle is a complex and heterogeneous tissue accounting for approximately 40% of body weight. Excessive ectopic lipid accumulation in the muscle fascicle would undermine the integrity of skeletal muscle in humans but endow muscle with marbling-related characteristics in farm animals. Therefore, the balance of myogenesis and adipogenesis is of great significance for skeletal muscle homeostasis. Significant DNA methylation occurs during myogenesis and adipogenesis; however, DNA methylation pattern of myogenic and adipogenic precursors derived from skeletal muscle remains unknown yet. Methods In this study, reduced representation bisulfite sequencing was performed to analyze genome-wide DNA methylation of adipogenic and myogenic precursors derived from the skeletal muscle of neonatal pigs. Integrated analysis of DNA methylation and transcription profiles was further conducted. Based on the results of pathway enrichment analysis, myogenic precursors were transfected with CACNA2D2-overexpression plasmids to explore the function of CACNA2D2 in myogenic differentiation. Results As a result, 11,361 differentially methylated regions mainly located in intergenic region and introns were identified. Furthermore, 153 genes with different DNA methylation and gene expression level between adipogenic and myogenic precursors were characterized. Subsequently, pathway enrichment analysis revealed that DNA methylation programing was involved in the regulation of adipogenic and myogenic differentiation potential through mediating the crosstalk among pathways including focal adhesion, regulation of actin cytoskeleton, MAPK signaling pathway, and calcium signaling pathway. In particular, we characterized a new role of CACNA2D2 in inhibiting myogenic differentiation by suppressing JNK/MAPK signaling pathway. Conclusions This study depicted a comprehensive landmark of DNA methylome of skeletal muscle-derived myogenic and adipogenic precursors, highlighted the critical role of CACNA2D2 in regulating myogenic differentiation, and illustrated the possible regulatory ways of DNA methylation on cell fate commitment and skeletal muscle homeostasis. Supplementary information The online version contains supplementary material available at 10.1186/s13287-020-02053-3.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenjuan Sun
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Linjuan He
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Liqi Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kai Qiu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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23
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Shi K, Lu Y, Chen X, Li D, Du W, Yu M. Effects of Ten-Eleven Translocation-2 (Tet2) on myogenic differentiation of chicken myoblasts. Comp Biochem Physiol B Biochem Mol Biol 2020; 252:110540. [PMID: 33242661 DOI: 10.1016/j.cbpb.2020.110540] [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: 08/27/2020] [Revised: 10/29/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
Skeletal muscle development is an orchestrated progress that is primarily regulated by temporospatial expression of myogenic regulatory factors (MRFs). Recent studies demonstrated that DNA demethylation also exerted a critical role in myogenesis. However, the function of Tet2 in the regulation of chicken myogenesis still remains unknown. In the present study, the role of Tet2 in regulating myogenic differentiation was determined by using a model of primary myoblasts from chickens. The expression of Tet2 was significantly elevated during myoblast differentiation. Meanwhile, the level of 5hmC in genomic DNA was increased, but H3K9me2 and H3K27me3 were markedly reduced following differentiation. Knockdown of Tet2 significantly inhibited the formation of multinucleated myotubes, which was accompanied by a reduction of relevant pivotal MRFs. Moreover, the level of 5hmC decreased sharply in Tet2 knockdown myoblasts. Attenuated differentiated myoblasts that resulted from reduced Tet2 also demonstrated an increased level of H3K9me2 and H3K27me3. Collectively, these results indicated that Tet2 played an essential role during myogenesis, which affected demethylation of genomic DNA and histone to regulate expression of MRFs and therefore, contributed to myoblast differentiation.
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Affiliation(s)
- Kai Shi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Yingling Lu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Xiaolu Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Dongfeng Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Wenxing Du
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China
| | - Minli Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, PR China.
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24
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Evano B, Gill D, Hernando-Herraez I, Comai G, Stubbs TM, Commere PH, Reik W, Tajbakhsh S. Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation. PLoS Genet 2020; 16:e1009022. [PMID: 33125370 PMCID: PMC7657492 DOI: 10.1371/journal.pgen.1009022] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 11/11/2020] [Accepted: 08/02/2020] [Indexed: 12/14/2022] Open
Abstract
Adult skeletal muscles are maintained during homeostasis and regenerated upon injury by muscle stem cells (MuSCs). A heterogeneity in self-renewal, differentiation and regeneration properties has been reported for MuSCs based on their anatomical location. Although MuSCs derived from extraocular muscles (EOM) have a higher regenerative capacity than those derived from limb muscles, the molecular determinants that govern these differences remain undefined. Here we show that EOM and limb MuSCs have distinct DNA methylation signatures associated with enhancers of location-specific genes, and that the EOM transcriptome is reprogrammed following transplantation into a limb muscle environment. Notably, EOM MuSCs expressed host-site specific positional Hox codes after engraftment and self-renewal within the host muscle. However, about 10% of EOM-specific genes showed engraftment-resistant expression, pointing to cell-intrinsic molecular determinants of the higher engraftment potential of EOM MuSCs. Our results underscore the molecular diversity of distinct MuSC populations and molecularly define their plasticity in response to microenvironmental cues. These findings provide insights into strategies designed to improve the functional capacity of MuSCs in the context of regenerative medicine.
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Affiliation(s)
- Brendan Evano
- Stem Cells & Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr. Roux, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
| | - Diljeet Gill
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Glenda Comai
- Stem Cells & Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr. Roux, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
| | - Thomas M. Stubbs
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Pierre-Henri Commere
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, 28 rue du Dr. Roux, Paris, France
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Shahragim Tajbakhsh
- Stem Cells & Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr. Roux, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
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25
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nat Commun 2020; 11:1189. [PMID: 32132541 PMCID: PMC7055320 DOI: 10.1038/s41467-020-15020-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Lily Agranat-Tamir
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Swapan Mallick
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Heng Li
- Broad Institute, Cambridge, MA, 02138, USA
| | | | - Mario Novak
- Institute for Anthropological Research, 10000, Zagreb, Croatia
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | | | - Jason M Osinski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | | | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Iddi Lipende
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Deus Mjungu
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Ivanela Kondova
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ottmar Kullmer
- Department of Palaeoanthropology and Messel Research, Senckenberg Center of Human Evolution and Paleoecology, Frankfurt am Main, Germany
| | - Gerhard Weber
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Tal Shahar
- Department of Neurosurgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Mona Dvir-Ginzberg
- Laboratory of Cartilage Biology, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Marina Faerman
- Laboratory of Bioanthropology and Ancient DNA, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 85287, USA
| | - Alexander Meissner
- Broad Institute, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yonatan Lahav
- Otolaryngology - Head & Neck Surgery Department, Laryngeal Surgery Unit, Kaplan Medical Center, Rehovot, Israel
- The Hebrew University Medical School, Jerusalem, Israel
| | - Leonid Kandel
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Meir Liebergall
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - María E Prada
- I.E.S.O. 'Los Salados'. Junta de Castilla y León, León, Spain
| | - Julio M Vidal
- Junta de Castilla y León, Servicio de Cultura de León, León, Spain
| | - Richard M Gronostajski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
- Genetics, Genomics and Bioinformatics Program, New York State Center of Excellence in Bioinformatics and Life Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Benjamin Yakir
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - David Reich
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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Gao L, Yang M, Wei Z, Gu M, Yang L, Bai C, Wu Y, Li G. MSTN Mutant Promotes Myogenic Differentiation by Increasing Demethylase TET1 Expression via the SMAD2/SMAD3 Pathway. Int J Biol Sci 2020; 16:1324-1334. [PMID: 32210722 PMCID: PMC7085230 DOI: 10.7150/ijbs.40551] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/31/2020] [Indexed: 12/20/2022] Open
Abstract
Myostatin (MSTN) is mostly expressed in skeletal muscle and plays crucial roles in the negative regulation of muscle mass development. The methylation and demethylation of myogenesis-specific genes are major regulatory factors in muscle satellite cell differentiation. The present study was designed to investigate the mechanism of myogenic differentiation regulated by MSTN mutation (MT) and the methylation/demethylation state of downstream genes. The results showed that, in the MSTN-/+ satellite cells, a higher myotube fusion index and a larger myotube length were observed compared to the wild type controls; the genes associated with myogenesis were all up-regulated compared to the WT controls. The methylation of the promoters and gene bodies of PAX3, PAX7, MyoD, and MyoG were all down-regulated, while the expression of the key demethylase TET1 was significantly promoted. ChIP-qPCR was used to demonstrate that the SMAD2/SMAD3 complex combined with the promoter of TET1 to inhibit the activity of TET1 promoter, indicating that MSTN may regulate TET1 via SMAD2/SMAD3. The overexpression of TET1 in wild type cells promoted myogenic differentiation, increased the myotube index, and reduced the methylation of the associated genes. On the contrary, the knockdown of TET1 in the MSTN mutant cells resulted in the opposite phenomena as in the overexpressed cells. In conclusion, the myostatin mutant showed an increased transcriptional activity of TET1, inducing higher levels of demethylation and improving the transcriptional activity levels of myogenic differentiation-associated genes. The binding of SMAD2/SMAD3 directly to the TET1 promoter region indicated that the MSTN mutant demethylated the myogenesis-specific genes by up-regulating TET1, which is directly controlled by SMAD2/SMAD3.
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Affiliation(s)
- Li Gao
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China
| | - Miaomiao Yang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China
| | - Zhuying Wei
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.,School of Life Science, Inner Mongolia University, Hohhot, 010070, China
| | - Mingjuan Gu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Yang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.,School of Life Science, Inner Mongolia University, Hohhot, 010070, China
| | - Yunxi Wu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.,School of Life Science, Inner Mongolia University, Hohhot, 010070, China
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.,School of Life Science, Inner Mongolia University, Hohhot, 010070, China
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28
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Ehrlich KC, Lacey M, Ehrlich M. Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families. EPIGENOMES 2020; 4:1. [PMID: 34968235 PMCID: PMC8594701 DOI: 10.3390/epigenomes4010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Much remains to be discovered about the intersection of tissue-specific transcription control and the epigenetics of skeletal muscle (SkM), a very complex and dynamic organ. From four gene families, Leucine-Rich Repeat Containing (LRRC), Oxysterol Binding Protein Like (OSBPL), Ankyrin Repeat and Socs Box (ASB), and Transmembrane Protein (TMEM), we chose 21 genes that are preferentially expressed in human SkM relative to 52 other tissue types and analyzed relationships between their tissue-specific epigenetics and expression. We also compared their genetics, proteomics, and descriptions in the literature. For this study, we identified genes with little or no previous descriptions of SkM functionality (ASB4, ASB8, ASB10, ASB12, ASB16, LRRC14B, LRRC20, LRRC30, TMEM52, TMEM233, OSBPL6/ORP6, and OSBPL11/ORP11) and included genes whose SkM functions had been previously addressed (ASB2, ASB5, ASB11, ASB15, LRRC2, LRRC38, LRRC39, TMEM38A/TRIC-A, and TMEM38B/TRIC-B). Some of these genes have associations with SkM or heart disease, cancer, bone disease, or other diseases. Among the transcription-related SkM epigenetic features that we identified were: super-enhancers, promoter DNA hypomethylation, lengthening of constitutive low-methylated promoter regions, and SkM-related enhancers for one gene embedded in a neighboring gene (e.g., ASB8-PFKM, LRRC39-DBT, and LRRC14B-PLEKHG4B gene-pairs). In addition, highly or lowly co-expressed long non-coding RNA (lncRNA) genes probably regulate several of these genes. Our findings give insights into tissue-specific epigenetic patterns and functionality of related genes in a gene family and can elucidate normal and disease-related regulation of gene expression in SkM.
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Affiliation(s)
- Kenneth C. Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA;
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA;
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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29
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Lin X, Li L, Liu X, Tian J, Zheng W, Li J, Wang L. Genome-wide analysis of aberrant methylation of enhancer DNA in human osteoarthritis. BMC Med Genomics 2020; 13:1. [PMID: 31900157 PMCID: PMC6942377 DOI: 10.1186/s12920-019-0646-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/15/2019] [Indexed: 12/17/2022] Open
Abstract
Background Osteoarthritis is a chronic musculoskeletal disease characterized by age-related gradual thinning and a high risk in females. Recent studies have shown that DNA methylation plays important roles in osteoarthritis. However, the genome-wide pattern of methylation in enhancers in osteoarthritis remains unclear. Methods To explore the function of enhancers in osteoarthritis, we quantified CpG methylation in human enhancers based on a public dataset that included methylation profiles of 470,870 CpG probes in 108 samples from patients with hip and knee osteoarthritis and hip tissues from healthy individuals. Combining various bioinformatics analysis tools, we systematically analyzed aberrant DNA methylation of the enhancers throughout the genome in knee osteoarthritis and hip osteoarthritis. Results We identified 16,816 differentially methylated CpGs, and nearly half (8111) of them were from enhancers, suggesting major DNA methylation changes in both types of osteoarthritis in the enhancer regions. A detailed analysis of hip osteoarthritis identified 2426 differentially methylated CpGs in enhancers between male and female patients, and 84.5% of them were hypomethylated in female patients and enriched in phenotypes related to hip osteoarthritis in females. Next, we explored the enhancer methylation dynamics among patients with knee osteoarthritis and identified 280 differentially methylated enhancer CpGs that were enriched in the human phenotypes and disease ontologies related to osteoarthritis. Finally, a comparison of enhancer methylation between knee osteoarthritis and hip osteoarthritis revealed organ source-dependent differences in enhancer methylation. Conclusion Our findings indicate that aberrant methylation of enhancers is related to osteoarthritis phenotypes, and a comprehensive atlas of enhancer methylation is useful for further analysis of the epigenetic regulation of osteoarthritis and the development of clinical drugs for treatment of osteoarthritis.
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Affiliation(s)
- Xiaozong Lin
- Department of Orthopedics, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Li Li
- Department of Nuclear Medicine, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
| | - Xiaojuan Liu
- Department of Rehabilitation, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Jun Tian
- Department of Orthopedics, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Weizhuo Zheng
- Department of Orthopedics, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Jin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Limei Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China. .,College of Automation, Harbin Engineering University, Harbin, 150001, China.
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30
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Liu Z, Han S, Shen X, Wang Y, Cui C, He H, Chen Y, Zhao J, Li D, Zhu Q, Yin H. The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken. Int J Biol Sci 2019; 15:1404-1418. [PMID: 31337971 PMCID: PMC6643139 DOI: 10.7150/ijbs.35073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/26/2019] [Indexed: 12/27/2022] Open
Abstract
Scope: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported. Methods: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of broilers and layers in different embryonic development points (E10, E13, E16 and E19) to explore the genetic basis of embryonic muscle development in chicken. The differential methylated regions and novel lncRNAs were identified for association analyses. Through genomic position and correlation analysis between DMRs and lncRNAs, the target lncRNAs were detected to participate in the embryonic muscle formation and the results were then verified in vitro experiments. Results: Comparison of methylome profiles between two chicken lines revealed that lower methylation in broilers might contribute to muscle development in embryonic period. Differential methylated region analysis showed that the majority of differential methylated regions were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, we identified a long non-coding RNA MyH1-AS that potentially regulated embryonic muscle development, proved by the regulatory network construction and further in vitro experiments. Conclusion: Our study revealed an integrative landscape of middle- to late-stage of embryonic myogenesis in chicken, gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in muscle development. Moreover, we provided a reliable data resource for further embryonic muscle development studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
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31
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Breuls N, Giacomazzi G, Sampaolesi M. (Epi)genetic Modifications in Myogenic Stem Cells: From Novel Insights to Therapeutic Perspectives. Cells 2019; 8:cells8050429. [PMID: 31075875 PMCID: PMC6562881 DOI: 10.3390/cells8050429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
The skeletal muscle is considered to be an ideal target for stem cell therapy as it has an inherent regenerative capacity. Upon injury, the satellite cells, muscle stem cells that reside under the basal lamina of the myofibres, start to differentiate in order to reconstitute the myofibres while maintaining the initial stem cell pool. In recent years, it has become more and more evident that epigenetic mechanisms such as histon modifications, DNA methylations and microRNA modulations play a pivatol role in this differentiation process. By understanding the mechanisms behind myogenesis, researchers are able to use this knowledge to enhance the differentiation and engraftment potential of different muscle stem cells. Besides manipulation on an epigenetic level, recent advances in the field of genome-engineering allow site-specific modifications in the genome of these stem cells. Combining epigenetic control of the stem cell fate with the ability to site-specifically correct mutations or add genes for further cell control, can increase the use of stem cells as treatment of muscular dystrophies drastically. In this review, we will discuss the advances that have been made in genome-engineering and the epigenetic regulation of muscle stem cells and how this knowledge can help to get stem cell therapy to its full potential.
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Affiliation(s)
- Natacha Breuls
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
| | - Giorgia Giacomazzi
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
| | - Maurilio Sampaolesi
- Translational Cardiomyology Lab, Department of Development and Regeneration, Stem Cell Institute Leuven, 3000 KU Leuven, Belgium.
- Human Anatomy Unit, Department of Public Health, Experimental and Forensic Medicine, and Interuniversity Institute of Myology, University of Pavia, 27100 Pavia, Italy.
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32
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Jiang K, Wong L, Chen Y, Xing X, Li D, Wang T, Jarvis JN. Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. J Reprod Immunol 2018; 128:2-8. [PMID: 29800761 PMCID: PMC6086739 DOI: 10.1016/j.jri.2018.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 04/27/2018] [Accepted: 05/10/2018] [Indexed: 11/23/2022]
Abstract
The studies proposed here were undertaken to test the hypothesis that, under specific circumstances (e.g., a strong enough inflammatory stimulus), genes that are repressed at the maternal-fetal interface via DNA methylation might be de-methylated, allowing either a maternal immune response to the semi-allogenic fetus or the onset of early labor. Chorionic trophoblasts (CT) were isolated from fetal membranes, followed by incubation with medium from LPS-activated PBMC or resting PBMC medium for 2 h. RNA and DNA were isolated from the cells for RNA-seq and DNA methylation studies. Two hrs after being exposed to conditioned medium from LPS-activated PBMC, CT showed differential expression of 114 genes, all but 2 of which showed higher expression in the stimulated cells than is the unstimulated cells. We also identified 318 differentially methylated regions (DMRs) that associated with 306 genes (155 protein coding genes) in the two groups, but the observed methylation changes had negligible impact on the observed transcriptional changes in CT. CT display complex patterns of transcription in response to inflammation. DNA methylation does not appear to be an important regulator of the observed transcriptional changes.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Laiping Wong
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Yanmin Chen
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Ave, St. Louis, MO, 63108, USA
| | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Ave, St. Louis, MO, 63108, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Ave, St. Louis, MO, 63108, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA; Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
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33
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Domenighetti AA, Mathewson MA, Pichika R, Sibley LA, Zhao L, Chambers HG, Lieber RL. Loss of myogenic potential and fusion capacity of muscle stem cells isolated from contractured muscle in children with cerebral palsy. Am J Physiol Cell Physiol 2018; 315:C247-C257. [PMID: 29694232 DOI: 10.1152/ajpcell.00351.2017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cerebral palsy (CP) is the most common cause of pediatric neurodevelopmental and physical disability in the United States. It is defined as a group of motor disorders caused by a nonprogressive perinatal insult to the brain. Although the brain lesion is nonprogressive, there is a progressive, lifelong impact on skeletal muscles, which are shorter, spastic, and may develop debilitating contractures. Satellite cells are resident muscle stem cells that are indispensable for postnatal growth and regeneration of skeletal muscles. Here we measured the myogenic potential of satellite cells isolated from contractured muscles in children with CP. When compared with typically developing (TD) children, satellite cell-derived myoblasts from CP differentiated more slowly (slope: 0.013 (SD 0.013) CP vs. 0.091 (SD 0.024) TD over 24 h, P < 0.001) and fused less (fusion index: 21.3 (SD 8.6) CP vs. 81.3 (SD 7.7) TD after 48 h, P < 0.001) after exposure to low-serum conditions that stimulated myotube formation. This impairment was associated with downregulation of several markers important for myoblast fusion and myotube formation, including DNA methylation-dependent inhibition of promyogenic integrin-β 1D (ITGB1D) protein expression levels (-50% at 42 h), and ~25% loss of integrin-mediated focal adhesion kinase phosphorylation. The cytidine analog 5-Azacytidine (5-AZA), a demethylating agent, restored ITGB1D levels and promoted myogenesis in CP cultures. Our data demonstrate that muscle contractures in CP are associated with loss of satellite cell myogenic potential that is dependent on DNA methylation patterns affecting expression of genetic programs associated with muscle stem cell differentiation and muscle fiber formation.
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Affiliation(s)
- Andrea A Domenighetti
- The Shirley Ryan AbilityLab, Chicago, Illinois.,Department of Physical Medicine & Rehabilitation, Northwestern University , Chicago, Illinois.,Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Margie A Mathewson
- Bioengineering Department, University of California, San Diego, La Jolla, California
| | | | | | - Leyna Zhao
- ACEA Biosciences Incorporated, San Diego, California
| | | | - Richard L Lieber
- The Shirley Ryan AbilityLab, Chicago, Illinois.,Department of Physical Medicine & Rehabilitation, Northwestern University , Chicago, Illinois.,Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
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34
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Abstract
Skeletal muscle regeneration is an efficient stem cell-based repair system that ensures healthy musculature. For this repair system to function continuously throughout life, muscle stem cells must contribute to the process of myofiber repair as well as repopulation of the stem cell niche. The decision made by the muscle stem cells to commit to the muscle repair or to remain a stem cell depends upon patterns of gene expression, a process regulated at the epigenetic level. Indeed, it is well accepted that dynamic changes in epigenetic landscapes to control DNA accessibility and expression is a critical component during myogenesis for the effective repair of damaged muscle. Changes in the epigenetic landscape are governed by various posttranslational histone tail modifications, nucleosome repositioning, and DNA methylation events which collectively allow the control of changes in transcription networks during transitions of satellite cells from a dormant quiescent state toward terminal differentiation. This chapter focuses upon the specific epigenetic changes that occur during muscle stem cell-mediated regeneration to ensure myofiber repair and continuity of the stem cell compartment. Furthermore, we explore open questions in the field that are expected to be important areas of exploration as we move toward a more thorough understanding of the epigenetic mechanism regulating muscle regeneration.
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Affiliation(s)
- Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada
| | - Francis J Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada.
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Ten-Eleven Translocation-2 (Tet2) Is Involved in Myogenic Differentiation of Skeletal Myoblast Cells in Vitro. Sci Rep 2017; 7:43539. [PMID: 28272491 PMCID: PMC5341099 DOI: 10.1038/srep43539] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/25/2017] [Indexed: 12/20/2022] Open
Abstract
Muscle cell differentiation is a complex process that is principally governed by related myogenic regulatory factors (MRFs). DNA methylation is considered to play an important role on the expression of MRF genes and on muscle cell differentiation. However, the roles of enzymes specifically in myogenesis are not fully understood. Here, we demonstrate that Tet2, a ten-eleven translocation (Tet) methylcytosine dioxygenase, exerts a role during skeletal myoblast differentiation. By using an immunostaining method, we found that the levels of 5-hydroxymethylcytosine (5-hmC) were much higher in differentiated myotubes than in undifferentiated C2C12 myoblasts. Both Tet1 and Tet2 expression were upregulated after differentiation induction of C2C12 myoblasts. Knockdown of Tet2, but not Tet1, significantly reduced the expression of myogenin as well as Myf6 and myomaker, and impaired myoblast differentiation. DNA demethylation of myogenin and myomaker promoters was negatively influenced by Tet2 knockdown as detected by bisulfite sequencing analysis. Furthermore, although vitamin C could promote genomic 5hmC generation, myogenic gene expression and myoblast differentiation, its effect was significantly attenuated by Tet2 knockdown. Taken together, these results indicate that Tet2 is involved in myoblast differentiation through promoting DNA demethylation and myogenic gene expression.
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Segalés J, Perdiguero E, Muñoz-Cánoves P. Regulation of Muscle Stem Cell Functions: A Focus on the p38 MAPK Signaling Pathway. Front Cell Dev Biol 2016; 4:91. [PMID: 27626031 PMCID: PMC5003838 DOI: 10.3389/fcell.2016.00091] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/17/2016] [Indexed: 12/17/2022] Open
Abstract
Formation of skeletal muscle fibers (myogenesis) during development and after tissue injury in the adult constitutes an excellent paradigm to investigate the mechanisms whereby environmental cues control gene expression programs in muscle stem cells (satellite cells) by acting on transcriptional and epigenetic effectors. Here we will review the molecular mechanisms implicated in the transition of satellite cells throughout the distinct myogenic stages (i.e., activation from quiescence, proliferation, differentiation, and self-renewal). We will also discuss recent findings on the causes underlying satellite cell functional decline with aging. In particular, our review will focus on the epigenetic changes underlying fate decisions and on how the p38 MAPK signaling pathway integrates the environmental signals at the chromatin to build up satellite cell adaptive responses during the process of muscle regeneration, and how these responses are altered in aging. A better comprehension of the signaling pathways connecting external and intrinsic factors will illuminate the path for improving muscle regeneration in the aged.
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Affiliation(s)
- Jessica Segalés
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra University Barcelona, Spain
| | - Eusebio Perdiguero
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra University Barcelona, Spain
| | - Pura Muñoz-Cánoves
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra UniversityBarcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain; Tissue Regeneration Laboratory, Centro Nacional de Investigaciones CardiovascularesMadrid, Spain
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Liu H, Li S, Wang X, Zhu J, Wei Y, Wang Y, Wen Y, Wang L, Huang Y, Zhang B, Shang S, Zhang Y. DNA methylation dynamics: identification and functional annotation. Brief Funct Genomics 2016; 15:470-484. [PMID: 27515490 DOI: 10.1093/bfgp/elw029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic modification of cytosines that undergoes dynamic changes in a temporal, spatial and cell-type-specific manner. Recent advances in technology have permitted the profiling of high-throughput methylomes in large numbers of biological samples. Various computational tools have been developed to identify and analyze DNA methylation dynamics in a variety of critical biological processes. As DNA methylation is becoming increasingly viewed as a dynamic process, the mechanisms governing DNA methylation dynamics and its roles in the transcriptional regulatory network are of great interest. It has been reported that DNA methylation dynamics plays essential roles in multiple biological processes, including development and cancer. As a functional event, the dynamics of DNA methylation have become increasingly relevant to many researchers. Here, we review state-of-the-art advances at three levels (genome-wide identification, regulatory mechanism investigation and the functional annotation) in the field of DNA methylation dynamics, as well as the future perspective of DNA methylation dynamics.
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Morrison J, Simon N, Witten D. Simultaneous detection and estimation of trait associations with genomic phenotypes. Biostatistics 2016; 18:147-164. [PMID: 27496912 DOI: 10.1093/biostatistics/kxw033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/17/2016] [Accepted: 06/08/2016] [Indexed: 01/09/2023] Open
Abstract
Genomic phenotypes, such as DNA methylation and chromatin accessibility, can be used to characterize the transcriptional and regulatory activity of DNA within a cell. Recent technological advances have made it possible to measure such phenotypes very densely. This density often results in spatial structure, in the sense that measurements at nearby sites are very similar. In this article, we consider the task of comparing genomic phenotypes across experimental conditions, cell types, or disease subgroups. We propose a new method, Joint Adaptive Differential Estimation (JADE), which leverages the spatial structure inherent to genomic phenotypes. JADE simultaneously estimates smooth underlying group average genomic phenotype profiles and detects regions in which the average profile differs between groups. We evaluate JADE's performance in several biologically plausible simulation settings. We also consider an application to the detection of regions with differential methylation between mature skeletal muscle cells, myotubes, and myoblasts.
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Affiliation(s)
- Jean Morrison
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Daniela Witten
- Department of Statistics, University of Washington, Seattle, WA, 98195, USA and Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
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Abstract
Mammalian embryonic development is a tightly regulated process that, from a single zygote, produces a large number of cell types with hugely divergent functions. Distinct cellular differentiation programmes are facilitated by tight transcriptional and epigenetic regulation. However, the contribution of epigenetic regulation to tissue homeostasis after the completion of development is less well understood. In this Review, we explore the effects of epigenetic dysregulation on adult stem cell function. We conclude that, depending on the tissue type and the epigenetic regulator affected, the consequences range from negligible to stem cell malfunction and disruption of tissue homeostasis, which may predispose to diseases such as cancer.
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Suelves M, Carrió E, Núñez-Álvarez Y, Peinado MA. DNA methylation dynamics in cellular commitment and differentiation. Brief Funct Genomics 2016; 15:443-453. [PMID: 27416614 DOI: 10.1093/bfgp/elw017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts, revealing a more dynamic regulation than originally thought, as active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. Recent data provide insights into the contribution of different epigenetic factors, and DNA methylation in particular, to the establishment of cellular memory during embryonic development and the modulation of cell type-specific gene regulation programs to ensure proper differentiation. This review summarizes published data regarding DNA methylation changes along lineage specification and differentiation programs. We also discuss the current knowledge about DNA methylation alterations occurring in physiological and pathological conditions such as aging and cancer.
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Carrió E, Magli A, Muñoz M, Peinado MA, Perlingeiro R, Suelves M. Muscle cell identity requires Pax7-mediated lineage-specific DNA demethylation. BMC Biol 2016; 14:30. [PMID: 27075038 PMCID: PMC4831197 DOI: 10.1186/s12915-016-0250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/23/2016] [Indexed: 12/01/2022] Open
Abstract
Background Skeletal muscle stem cells enable the formation, growth, maintenance, and regeneration of skeletal muscle throughout life. The regeneration process is compromised in several pathological conditions, and muscle progenitors derived from pluripotent stem cells have been suggested as a potential therapeutic source for tissue replacement. DNA methylation is an important epigenetic mechanism in the setting and maintenance of cellular identity, but its role in stem cell determination towards the myogenic lineage is unknown. Here we addressed the DNA methylation dynamics of the major genes orchestrating the myogenic determination and differentiation programs in embryonic stem (ES) cells, their Pax7-induced myogenic derivatives, and muscle stem cells in proliferating and differentiating conditions. Results Our data showed a common muscle-specific DNA demethylation signature required to acquire and maintain the muscle-cell identity. This specific-DNA demethylation is Pax7-mediated, and it is a prime event in muscle stem cells gene activation. Notably, downregulation of the demethylation-related enzyme Apobec2 in ES-derived myogenic precursors reduced myogenin-associated DNA demethylation and dramatically impaired the expression of differentiation markers and, ultimately, muscle differentiation. Conclusions Our results underscore DNA demethylation as a key mechanism driving myogenesis and identify specific Pax7-mediated DNA demethylation signatures to acquire and maintain the muscle-cell identity. Additionally, we provide a panel of epigenetic markers for the efficient and safe generation of ES- and induced pluripotent stem cell (iPS)-derived myogenic progenitors for therapeutic applications. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0250-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elvira Carrió
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Alessandro Magli
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, 55455, USA
| | - Mar Muñoz
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Miguel A Peinado
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Rita Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, 55455, USA
| | - Mònica Suelves
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain.
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Sincennes MC, Brun CE, Rudnicki MA. Concise Review: Epigenetic Regulation of Myogenesis in Health and Disease. Stem Cells Transl Med 2016; 5:282-90. [PMID: 26798058 PMCID: PMC4807671 DOI: 10.5966/sctm.2015-0266] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023] Open
Abstract
This review describes the recent findings on epigenetic regulation in satellite stem cells and committed myoblasts. It also addresses the potential of epigenetic drugs, such as histone deacetylase inhibitors, and their molecular mechanism of action in muscle cells. Skeletal muscle regeneration is initiated by satellite cells, a population of adult stem cells that reside in the muscle tissue. The ability of satellite cells to self-renew and to differentiate into the muscle lineage is under transcriptional and epigenetic control. Satellite cells are characterized by an open and permissive chromatin state. The transcription factor Pax7 is necessary for satellite cell function. Pax7 is a nodal factor regulating the expression of genes associated with satellite cell growth and proliferation, while preventing differentiation. Pax7 recruits chromatin modifiers to DNA to induce expression of specific target genes involved in myogenic commitment following asymmetric division of muscle stem cells. Emerging evidence suggests that replacement of canonical histones with histone variants is an important regulatory mechanism controlling the ability of satellite cells and myoblasts to differentiate. Differentiation into the muscle lineage is associated with a global gene repression characterized by a decrease in histone acetylation with an increase in repressive histone marks. However, genes important for differentiation are upregulated by the specific action of histone acetyltransferases and other chromatin modifiers, in combination with several transcription factors, including MyoD and Mef2. Treatment with histone deacetylase (HDAC) inhibitors enhances muscle regeneration and is considered as a therapeutic approach in the treatment of muscular dystrophy. This review describes the recent findings on epigenetic regulation in satellite stem cells and committed myoblasts. The potential of epigenetic drugs, such as HDAC inhibitors, as well as their molecular mechanism of action in muscle cells, will be addressed. Significance This review summarizes recent findings concerning the epigenetic regulation of satellite cells in skeletal muscle.
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Affiliation(s)
- Marie-Claude Sincennes
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Caroline E Brun
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael A Rudnicki
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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DNA Methylation in Skeletal Muscle Stem Cell Specification, Proliferation, and Differentiation. Stem Cells Int 2016; 2016:5725927. [PMID: 26880971 PMCID: PMC4736426 DOI: 10.1155/2016/5725927] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/07/2015] [Indexed: 12/15/2022] Open
Abstract
An unresolved and critically important question in skeletal muscle biology is how muscle stem cells initiate and regulate the genetic program during muscle development. Epigenetic dynamics are essential for cellular development and organogenesis in early life and it is becoming increasingly clear that epigenetic remodeling may also be responsible for the cellular adaptations that occur in later life. DNA methylation of cytosine bases within CpG dinucleotide pairs is an important epigenetic modification that reduces gene expression when located within a promoter or enhancer region. Recent advances in the field suggest that epigenetic regulation is essential for skeletal muscle stem cell identity and subsequent cell development. This review summarizes what is currently known about how skeletal muscle stem cells regulate the myogenic program through DNA methylation, discusses a novel role for metabolism in this process, and addresses DNA methylation dynamics in adult skeletal muscle in response to physical activity.
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44
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Liu H, Liu X, Zhang S, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q, Zhang Y. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. Nucleic Acids Res 2015; 44:75-94. [PMID: 26635396 PMCID: PMC4705665 DOI: 10.1093/nar/gkv1332] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 11/17/2015] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is a key epigenetic mark that is critical for gene regulation in multicellular eukaryotes. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understand the complex regulatory network for cell fate determination. In this study, we proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757 887 genome segments. Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, we identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through H3K27ac and transcription factor binding sites in cell type-specific manner. In particular, we observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation.
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Affiliation(s)
- Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaojuan Liu
- Department of Rehabilitation, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Shumei Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Song Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shanshan Jia
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jianzhong Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Abstract
Regenerative capacity of skeletal muscles resides in satellite cells, a self-renewing population of muscle cells. Several studies are investigating epigenetic mechanisms that control myogenic proliferation and differentiation to find new approaches that could boost regeneration of endogenous myogenic progenitor populations. In recent years, a lot of effort has been applied to purify, expand and manipulate adult stem cells from muscle tissue. However, this population of endogenous myogenic progenitors in adults is limited and their access is difficult and invasive. Therefore, other sources of stem cells with potential to regenerate muscles need to be examined. An excellent candidate could be a population of adult stromal cells within fat characterized by mesenchymal properties, which have been termed adipose-derived stem cells (ASCs). These progenitor adult stem cells have been successfully differentiated in vitro to osteogenic, chondrogenic, neurogenic and myogenic lineages. Autologous ASCs are multipotent and can be harvested with low morbidity; thus, they hold promise for a range of therapeutic applications. This review will summarize the use of ASCs in muscle regenerative approaches.
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Affiliation(s)
- Sonia-V Forcales
- Genetics and Epigenetics of Cancer, Institute of Predictive and Personalized Medicine of Cancer Barcelona, Spain
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46
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Forn M, Díez-Villanueva A, Merlos-Suárez A, Muñoz M, Lois S, Carriò E, Jordà M, Bigas A, Batlle E, Peinado MA. Overlapping DNA methylation dynamics in mouse intestinal cell differentiation and early stages of malignant progression. PLoS One 2015; 10:e0123263. [PMID: 25933092 PMCID: PMC4416816 DOI: 10.1371/journal.pone.0123263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
Mouse models of intestinal crypt cell differentiation and tumorigenesis have been used to characterize the molecular mechanisms underlying both processes. DNA methylation is a key epigenetic mark and plays an important role in cell identity and differentiation programs and cancer. To get insights into the dynamics of cell differentiation and malignant transformation we have compared the DNA methylation profiles along the mouse small intestine crypt and early stages of tumorigenesis. Genome-scale analysis of DNA methylation together with microarray gene expression have been applied to compare intestinal crypt stem cells (EphB2high), differentiated cells (EphB2negative), ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26. Compared with late stages, small intestine crypt differentiation and early stages of tumorigenesis display few and relatively small changes in DNA methylation. Hypermethylated loci are largely shared by the two processes and affect the proximities of promoter and enhancer regions, with enrichment in genes associated with the intestinal stem cell signature and the PRC2 complex. The hypermethylation is progressive, with minute levels in differentiated cells, as compared with intestinal stem cells, and reaching full methylation in advanced stages. Hypomethylation shows different signatures in differentiation and cancer and is already present in the non-tumor tissue adjacent to the adenomas in ApcMin/+ mice, but at lower levels than advanced cancers. This study provides a reference framework to decipher the mechanisms driving mouse intestinal tumorigenesis and also the human counterpart.
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Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Merlos-Suárez
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
| | - Mar Muñoz
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Sergi Lois
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Elvira Carriò
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Mireia Jordà
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Bigas
- Institut Hospital del Mar d’Investigació Mèdica (IMIM) 08003 Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
- * E-mail:
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