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Ahmad N, de la Serna IL, Marathe HG, Fan X, Dube P, Zhang S, Haller ST, Kennedy DJ, Pestov NB, Modyanov NN. Eutherian-Specific Functions of BetaM Acquired through Atp1b4 Gene Co-Option in the Regulation of MyoD Expression. Life (Basel) 2023; 13:414. [PMID: 36836771 PMCID: PMC9962273 DOI: 10.3390/life13020414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Vertebrate ATP1B4 genes represent a rare instance of orthologous gene co-option, resulting in radically different functions of the encoded BetaM proteins. In lower vertebrates, BetaM is a Na, K-ATPase β-subunit that is a component of ion pumps in the plasma membrane. In placental mammals, BetaM lost its ancestral role and, through structural alterations of the N-terminal domain, became a skeletal and cardiac muscle-specific protein of the inner nuclear membrane, highly expressed during late fetal and early postnatal development. We previously determined that BetaM directly interacts with the transcriptional co-regulator SKI-interacting protein (SKIP) and is implicated in the regulation of gene expression. This prompted us to investigate a potential role for BetaM in the regulation of muscle-specific gene expression in neonatal skeletal muscle and cultured C2C12 myoblasts. We found that BetaM can stimulate expression of the muscle regulatory factor (MRF), MyoD, independently of SKIP. BetaM binds to the distal regulatory region (DRR) of MyoD, promotes epigenetic changes associated with activation of transcription, and recruits the SWI/SNF chromatin remodeling subunit, BRG1. These results indicate that eutherian BetaM regulates muscle gene expression by promoting changes in chromatin structure. These evolutionarily acquired new functions of BetaM might be very essential and provide evolutionary advantages to placental mammals.
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Affiliation(s)
- Nisar Ahmad
- Department of Physiology and Pharmacology, Center for Diabetes and Endocrine Research, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Ivana L. de la Serna
- Department of Cell and Cancer Biology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Himangi G. Marathe
- Department of Cell and Cancer Biology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Xiaoming Fan
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Prabhatchandra Dube
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Shungang Zhang
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Steven T. Haller
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - David J. Kennedy
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Nikolay B. Pestov
- Department of Physiology and Pharmacology, Center for Diabetes and Endocrine Research, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Nikolai N. Modyanov
- Department of Physiology and Pharmacology, Center for Diabetes and Endocrine Research, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
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Esteves de Lima J, Blavet C, Bonnin MA, Hirsinger E, Havis E, Relaix F, Duprez D. TMEM8C-mediated fusion is regionalized and regulated by NOTCH signalling during foetal myogenesis. Development 2022; 149:274065. [PMID: 35005776 DOI: 10.1242/dev.199928] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/15/2021] [Indexed: 12/30/2022]
Abstract
The location and regulation of fusion events within skeletal muscles during development remain unknown. Using the fusion marker myomaker (Mymk), named TMEM8C in chicken, as a readout of fusion, we identified a co-segregation of TMEM8C-positive cells and MYOG-positive cells in single-cell RNA-sequencing datasets of limbs from chicken embryos. We found that TMEM8C transcripts, MYOG transcripts and the fusion-competent MYOG-positive cells were preferentially regionalized in central regions of foetal muscles. We also identified a similar regionalization for the gene encoding the NOTCH ligand JAG2 along with an absence of NOTCH activity in TMEM8C+ fusion-competent myocytes. NOTCH function in myoblast fusion had not been addressed so far. We analysed the consequences of NOTCH inhibition for TMEM8C expression and myoblast fusion during foetal myogenesis in chicken embryos. NOTCH inhibition increased myoblast fusion and TMEM8C expression and released the transcriptional repressor HEYL from the TMEM8C regulatory regions. These results identify a regionalization of TMEM8C-dependent fusion and a molecular mechanism underlying the fusion-inhibiting effect of NOTCH in foetal myogenesis. The modulation of NOTCH activity in the fusion zone could regulate the flux of fusion events.
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Affiliation(s)
- Joana Esteves de Lima
- Sorbonne Université, Institut Biologie Paris Seine, CNRS UMR7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France.,Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010 Creteil, France
| | - Cédrine Blavet
- Sorbonne Université, Institut Biologie Paris Seine, CNRS UMR7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France
| | - Marie-Ange Bonnin
- Sorbonne Université, Institut Biologie Paris Seine, CNRS UMR7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France
| | - Estelle Hirsinger
- Sorbonne Université, Institut Biologie Paris Seine, CNRS UMR7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France
| | - Emmanuelle Havis
- Sorbonne Université, Institut Biologie Paris Seine, CNRS UMR7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, F-94010 Creteil, France
| | - Delphine Duprez
- Sorbonne Université, Institut Biologie Paris Seine, CNRS UMR7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France
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3
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Esteves de Lima J, Blavet C, Bonnin MA, Hirsinger E, Comai G, Yvernogeau L, Delfini MC, Bellenger L, Mella S, Nassari S, Robin C, Schweitzer R, Fournier-Thibault C, Jaffredo T, Tajbakhsh S, Relaix F, Duprez D. Unexpected contribution of fibroblasts to muscle lineage as a mechanism for limb muscle patterning. Nat Commun 2021; 12:3851. [PMID: 34158501 PMCID: PMC8219714 DOI: 10.1038/s41467-021-24157-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 06/06/2021] [Indexed: 12/13/2022] Open
Abstract
Positional information driving limb muscle patterning is contained in connective tissue fibroblasts but not in myogenic cells. Limb muscles originate from somites, while connective tissues originate from lateral plate mesoderm. With cell and genetic lineage tracing we challenge this model and identify an unexpected contribution of lateral plate-derived fibroblasts to the myogenic lineage, preferentially at the myotendinous junction. Analysis of single-cell RNA-sequencing data from whole limbs at successive developmental stages identifies a population displaying a dual muscle and connective tissue signature. BMP signalling is active in this dual population and at the tendon/muscle interface. In vivo and in vitro gain- and loss-of-function experiments show that BMP signalling regulates a fibroblast-to-myoblast conversion. These results suggest a scenario in which BMP signalling converts a subset of lateral plate mesoderm-derived cells to a myogenic fate in order to create a boundary of fibroblast-derived myonuclei at the myotendinous junction that controls limb muscle patterning.
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Affiliation(s)
- Joana Esteves de Lima
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, Creteil, France
| | - Cédrine Blavet
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
| | - Marie-Ange Bonnin
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
| | - Estelle Hirsinger
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
| | - Glenda Comai
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Laurent Yvernogeau
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences (KNAW), Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marie-Claire Delfini
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
- Aix Marseille University, CNRS, IBDM, Marseille, France
| | - Léa Bellenger
- Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-FR3631, ARTbio Bioinformatics Platform, Inserm US 037, Paris, France
| | - Sébastien Mella
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Sonya Nassari
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
| | - Catherine Robin
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences (KNAW), Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ronen Schweitzer
- Research Division, Shriners Hospital for Children, Portland, OR, USA
| | - Claire Fournier-Thibault
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
| | - Thierry Jaffredo
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France
- Inserm U1156, Paris, France
| | - Shahragim Tajbakhsh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, Creteil, France
| | - Delphine Duprez
- Developmental Biology Laboratory, Institut Biologie Paris Seine, Sorbonne Université, CNRS, IBPS-UMR 7622, Paris, France.
- Inserm U1156, Paris, France.
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Picaut L, Trichet L, Hélary C, Ducourthial G, Bonnin MA, Haye B, Ronsin O, Schanne-Klein MC, Duprez D, Baumberger T, Mosser G. Core-Shell Pure Collagen Threads Extruded from Highly Concentrated Solutions Promote Colonization and Differentiation of C3H10T1/2 Cells. ACS Biomater Sci Eng 2021; 7:626-635. [PMID: 33400500 DOI: 10.1021/acsbiomaterials.0c01273] [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] [Indexed: 01/11/2023]
Abstract
The elaboration of scaffolds able to efficiently promote cell differentiation toward a given cell type remains challenging. Here, we engineered dense type I collagen threads with the aim of providing scaffolds with specific morphological and mechanical properties for C3H10T1/2 mesenchymal stem cells. Extrusion of pure collagen solutions at different concentrations (15, 30, and 60 mg/mL) in a PBS 5× buffer generated dense fibrillated collagen threads. For the two highest concentrations, threads displayed a core-shell structure with a marked fibril orientation of the outer layer along the longitudinal axis of the threads. Young's modulus and ultimate tensile stress as high as 1 and 0.3 MPa, respectively, were obtained for the most concentrated collagen threads without addition of any cross-linkers. C3H10T1/2 cells oriented themselves with a mean angle of 15-24° with respect to the longitudinal axis of the threads. Cells penetrated the 30 mg/mL scaffolds but remained on the surface of the 60 mg/mL ones. After three weeks of culture, cells displayed strong expression of the tendon differentiation marker Tnmd, especially for the 30 mg/mL threads. These results suggest that both the morphological and mechanical characteristics of collagen threads are key factors in promoting C3H10T1/2 differentiation into tenocytes, offering promising levers to optimize tissue engineering scaffolds for tendon regeneration.
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Affiliation(s)
- Lise Picaut
- Institut des Nanosciences de Paris, Sorbonne-Université, UPMC Univ Paris 6 and CNRS-UMR 7588, F-75005 Paris, France.,Sorbonne-Université, Laboratoire de Chimie de la Matière Condensée de Paris, UPMC Univ Paris 6, CNRS-UMR 7574, F-75005 Paris, France
| | - Léa Trichet
- Sorbonne-Université, Laboratoire de Chimie de la Matière Condensée de Paris, UPMC Univ Paris 6, CNRS-UMR 7574, F-75005 Paris, France
| | - Christophe Hélary
- Sorbonne-Université, Laboratoire de Chimie de la Matière Condensée de Paris, UPMC Univ Paris 6, CNRS-UMR 7574, F-75005 Paris, France
| | - Guillaume Ducourthial
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, F-91128 Palaiseau, France
| | - Marie-Ange Bonnin
- Sorbonne Université, CNRS, Institut Biologie Paris Seine, IBPS-UMR 7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France
| | - Bernard Haye
- Sorbonne-Université, Laboratoire de Chimie de la Matière Condensée de Paris, UPMC Univ Paris 6, CNRS-UMR 7574, F-75005 Paris, France
| | - Olivier Ronsin
- Institut des Nanosciences de Paris, Sorbonne-Université, UPMC Univ Paris 6 and CNRS-UMR 7588, F-75005 Paris, France
| | - Marie-Claire Schanne-Klein
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, F-91128 Palaiseau, France
| | - Delphine Duprez
- Sorbonne Université, CNRS, Institut Biologie Paris Seine, IBPS-UMR 7622, Developmental Biology Laboratory, Inserm U1156, F-75005 Paris, France
| | - Tristan Baumberger
- Institut des Nanosciences de Paris, Sorbonne-Université, UPMC Univ Paris 6 and CNRS-UMR 7588, F-75005 Paris, France
| | - Gervaise Mosser
- Sorbonne-Université, Laboratoire de Chimie de la Matière Condensée de Paris, UPMC Univ Paris 6, CNRS-UMR 7574, F-75005 Paris, France
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5
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Oe M, Ojima K, Muroya S. Difference in potential DNA methylation impact on gene expression between fast- and slow-type myofibers. Physiol Genomics 2021; 53:69-83. [PMID: 33459151 DOI: 10.1152/physiolgenomics.00099.2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscles are comprised of two major types of myofibers, fast and slow. It is hypothesized that once myofiber type is determined, muscle fiber-type specificity is maintained by an epigenetic mechanism, however, this remains poorly understood. To address this, we conducted a comprehensive CpG methylation analysis with a reduced representation of bisulfite sequencing (RRBS). Using GFP-myh7 mouse, we visually distinguished and separately pooled slow-type and myh7-negative fast-type fibers for analyses. A total of 31,967 and 26,274 CpGs were hypermethylated by ≥10% difference in the fast- and slow-type fibers, respectively. Notably, the number of promoter-hypermethylated genes with downregulated expression in the slow-type fibers was 3.5 times higher than that in the fast-type fibers. Gene bodies of the fast-type-specific myofibrillar genes Actn3, Tnnt3, Tnni2, Tnnc2, and Tpm1 were hypermethylated in the slow-type fibers, whereas those of the slow-type-specific genes Myh7, Tnnt1, and Tpm3 were hypermethylated in the fast-type fibers. Each of the instances of gene hypermethylation was associated with the respective downregulated expression. In particular, a relationship between CpG methylation sites and the transcription variant distribution of Tpm1 was observed, suggesting a regulation of Tpm1 alternative promoter usage by gene body CpG methylation. An association of hypermethylation with the regulation of gene expression was also observed in the transcription factors Sim2 and Tbx1. These results suggest not only a myofiber type-specific regulation of gene expression and alternative promoter usage by gene body CpG methylation but also a dominant effect of promoter-hypermethylation on the gene expressions in slow myofibers.
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Affiliation(s)
- Mika Oe
- Muscle Biology Research Unit, Division of Animal Products Research, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Koichi Ojima
- Muscle Biology Research Unit, Division of Animal Products Research, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Susumu Muroya
- Muscle Biology Research Unit, Division of Animal Products Research, NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
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6
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Laan L, Klar J, Sobol M, Hoeber J, Shahsavani M, Kele M, Fatima A, Zakaria M, Annerén G, Falk A, Schuster J, Dahl N. DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors. Clin Epigenetics 2020; 12:9. [PMID: 31915063 PMCID: PMC6950999 DOI: 10.1186/s13148-019-0803-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Background Down syndrome (DS) is characterized by neurodevelopmental abnormalities caused by partial or complete trisomy of human chromosome 21 (T21). Analysis of Down syndrome brain specimens has shown global epigenetic and transcriptional changes but their interplay during early neurogenesis remains largely unknown. We differentiated induced pluripotent stem cells (iPSCs) established from two DS patients with complete T21 and matched euploid donors into two distinct neural stages corresponding to early- and mid-gestational ages. Results Using the Illumina Infinium 450K array, we assessed the DNA methylation pattern of known CpG regions and promoters across the genome in trisomic neural iPSC derivatives, and we identified a total of 500 stably and differentially methylated CpGs that were annotated to CpG islands of 151 genes. The genes were enriched within the DNA binding category, uncovering 37 factors of importance for transcriptional regulation and chromatin structure. In particular, we observed regional epigenetic changes of the transcription factor genes ZNF69, ZNF700 and ZNF763 as well as the HOXA3, HOXB3 and HOXD3 genes. A similar clustering of differential methylation was found in the CpG islands of the HIST1 genes suggesting effects on chromatin remodeling. Conclusions The study shows that early established differential methylation in neural iPSC derivatives with T21 are associated with a set of genes relevant for DS brain development, providing a novel framework for further studies on epigenetic changes and transcriptional dysregulation during T21 neurogenesis.
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Affiliation(s)
- Loora Laan
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Maria Sobol
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | | | - Malin Kele
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Muhammad Zakaria
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jens Schuster
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden.
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Master control: transcriptional regulation of mammalian Myod. J Muscle Res Cell Motil 2019; 40:211-226. [PMID: 31301002 PMCID: PMC6726840 DOI: 10.1007/s10974-019-09538-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/03/2019] [Indexed: 12/22/2022]
Abstract
MYOD is a master regulator of the skeletal myogenic program. But what regulates expression of Myod? More than 20 years ago, studies established that Myod expression is largely controlled by just two enhancer regions located within a region 24 kb upstream of the transcription start site in mammals, which regulate Myod expression in the embryo, fetus and adult. Despite this apparently simple arrangement, Myod regulation is complex, with different combinations of transcription factors acting on these enhancers in different muscle progenitor cells and phases of differentiation. A range of epigenetic modifications in the Myod upstream region also play a part in activating and repressing Myod expression during development and regeneration. Here the evidence for this binding at Myod control regions is summarized, giving an overview of our current understanding of Myod expression regulation in mammals.
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8
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Zhang K, Wang M, Zhao Y, Wang W. Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. SCIENCE ADVANCES 2019; 5:eaav3262. [PMID: 30944857 PMCID: PMC6436936 DOI: 10.1126/sciadv.aav3262] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/30/2019] [Indexed: 05/20/2023]
Abstract
Transcriptional regulation is pivotal to the specification of distinct cell types during embryonic development. However, it still lacks a systematic way to identify key transcription factors (TFs) orchestrating the temporal and tissue specificity of gene expression. Here, we integrated epigenomic and transcriptomic data to reveal key regulators from two cells to postnatal day 0 in mouse embryogenesis. We predicted three-dimensional chromatin interactions in 12 tissues across eight developmental stages, which facilitates linking TFs to their target genes for constructing transcriptional regulatory networks. To identify driver TFs, we developed a new algorithm, dubbed Taiji, to assess the global influence of each TF and systematically uncovered TFs critical for lineage-specific and stage-dependent tissue specification. We have also identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress. Furthermore, lacking stage-specific TF combinations suggests a distributed timing strategy to orchestrate the coordination between tissues during embryonic development.
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Affiliation(s)
- Kai Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Ying Zhao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Corresponding author.
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9
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Esteves de Lima J, Bonnin MA, Birchmeier C, Duprez D. Muscle contraction is required to maintain the pool of muscle progenitors via YAP and NOTCH during fetal myogenesis. eLife 2016; 5. [PMID: 27554485 PMCID: PMC5030091 DOI: 10.7554/elife.15593] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/23/2016] [Indexed: 12/27/2022] Open
Abstract
The importance of mechanical activity in the regulation of muscle progenitors during chick development has not been investigated. We show that immobilization decreases NOTCH activity and mimics a NOTCH loss-of-function phenotype, a reduction in the number of muscle progenitors and increased differentiation. Ligand-induced NOTCH activation prevents the reduction of muscle progenitors and the increase of differentiation upon immobilization. Inhibition of NOTCH ligand activity in muscle fibers suffices to reduce the progenitor pool. Furthermore, immobilization reduces the activity of the transcriptional co-activator YAP and the expression of the NOTCH ligand JAG2 in muscle fibers. YAP forced-activity in muscle fibers prevents the decrease of JAG2 expression and the number of PAX7+ cells in immobilization conditions. Our results identify a novel mechanism acting downstream of muscle contraction, where YAP activates JAG2 expression in muscle fibers, which in turn regulates the pool of fetal muscle progenitors via NOTCH in a non-cell-autonomous manner. DOI:http://dx.doi.org/10.7554/eLife.15593.001 Skeletal muscle is attached to the skeleton and allows the body to move. Making a new muscle, or repairing an existing one, relies on stem cells that are present inside muscles. A major goal of skeletal muscle research is to understand the signals that regulate the abilities of muscle stem cells to divide and give rise to more stem cells or to become muscle cells. Molecular signals are known to regulate the numbers of stem cells in the muscle. Skeletal muscles become larger if they are exercised, but it is not clear if mechanical forces generated by muscle contractions directly affect the number of muscle stem cells. The NOTCH signaling pathway contributes to maintaining the population of stem cells in muscles by forcing the stem cells to divide and preventing them from becoming muscle cells. Here, Esteves de Lima et al. investigated whether muscle contraction regulates NOTCH signaling during muscle formation in chick fetuses. The experiments show that muscle contraction stimulates the activity of a protein called YAP in muscle cells, which in turn, activates a gene in the NOTCH signaling pathway known as JAG2. This increases NOTCH signaling activity in the neighboring stem cells and maintains the number of stem cells in the muscle. The next step following this work will be to establish if this mechanism also operates during muscle formation and regeneration in other animals such as mice and zebrafish. DOI:http://dx.doi.org/10.7554/eLife.15593.002
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Affiliation(s)
- Joana Esteves de Lima
- CNRS UMR 7622, F-75005 Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France.,IBPS-Developmental Biology Laboratory, Paris, France.,Inserm U1156, F-75005, Paris, France
| | - Marie-Ange Bonnin
- CNRS UMR 7622, F-75005 Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France.,IBPS-Developmental Biology Laboratory, Paris, France.,Inserm U1156, F-75005, Paris, France
| | - Carmen Birchmeier
- Developmental Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Delphine Duprez
- CNRS UMR 7622, F-75005 Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France.,IBPS-Developmental Biology Laboratory, Paris, France.,Inserm U1156, F-75005, Paris, France
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10
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11
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Sabillo A, Ramirez J, Domingo CR. Making muscle: Morphogenetic movements and molecular mechanisms of myogenesis in Xenopus laevis. Semin Cell Dev Biol 2016; 51:80-91. [PMID: 26853935 DOI: 10.1016/j.semcdb.2016.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/01/2016] [Indexed: 12/15/2022]
Abstract
Xenopus laevis offers unprecedented access to the intricacies of muscle development. The large, robust embryos make it ideal for manipulations at both the tissue and molecular level. In particular, this model system can be used to fate map early muscle progenitors, visualize cell behaviors associated with somitogenesis, and examine the role of signaling pathways that underlie induction, specification, and differentiation of muscle. Several characteristics that are unique to X. laevis include myogenic waves with distinct gene expression profiles and the late formation of dermomyotome and sclerotome. Furthermore, myogenesis in the metamorphosing frog is biphasic, facilitating regeneration studies. In this review, we describe the morphogenetic movements that shape the somites and discuss signaling and transcriptional regulation during muscle development and regeneration. With recent advances in gene editing tools, X. laevis remains a premier model organism for dissecting the complex mechanisms underlying the specification, cell behaviors, and formation of the musculature system.
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Affiliation(s)
- Armbien Sabillo
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Julio Ramirez
- Department of Biology, San Francisco State University, CA 94132, USA
| | - Carmen R Domingo
- Department of Biology, San Francisco State University, CA 94132, USA.
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12
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Daubas P, Duval N, Bajard L, Langa Vives F, Robert B, Mankoo BS, Buckingham M. Fine-tuning the onset of myogenesis by homeobox proteins that interact with the Myf5 limb enhancer. Biol Open 2015; 4:1614-24. [PMID: 26538636 PMCID: PMC4736032 DOI: 10.1242/bio.014068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Skeletal myogenesis in vertebrates is initiated at different sites of skeletal muscle formation during development, by activation of specific control elements of the myogenic regulatory genes. In the mouse embryo, Myf5 is the first myogenic determination gene to be expressed and its spatiotemporal regulation requires multiple enhancer sequences, extending over 120 kb upstream of the Mrf4-Myf5 locus. An enhancer, located at −57/−58 kb from Myf5, is responsible for its activation in myogenic cells derived from the hypaxial domain of the somite, that will form limb muscles. Pax3 and Six1/4 transcription factors are essential activators of this enhancer, acting on a 145-bp core element. Myogenic progenitor cells that will form the future muscle masses of the limbs express the factors necessary for Myf5 activation when they delaminate from the hypaxial dermomyotome and migrate into the forelimb bud, however they do not activate Myf5 and the myogenic programme until they have populated the prospective muscle masses. We show that Msx1 and Meox2 homeodomain-containing transcription factors bind in vitro and in vivo to specific sites in the 145-bp element, and are implicated in fine-tuning activation of Myf5 in the forelimb. Msx1, when bound between Pax and Six sites, prevents the binding of these key activators, thus inhibiting transcription of Myf5 and consequent premature myogenic differentiation. Meox2 is required for Myf5 activation at the onset of myogenesis via direct binding to other homeodomain sites in this sequence. Thus, these homeodomain factors, acting in addition to Pax3 and Six1/4, fine-tune the entry of progenitor cells into myogenesis at early stages of forelimb development. Summary: Homeodomain factors Msx1 and Meox2, acting in addition to Pax3 and Six1/4, fine-tune the entry of progenitor cells into myogenesis at early stages of forelimb development via modulation of limb enhancer gene Myf5.
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Affiliation(s)
- Philippe Daubas
- CNRS URA 2578, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
| | - Nathalie Duval
- CNRS URA 2578, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
| | - Lola Bajard
- CNRS URA 2578, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
| | | | - Benoît Robert
- CNRS URA 2578, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
| | - Baljinder S Mankoo
- King's College London, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Margaret Buckingham
- CNRS URA 2578, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
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13
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Endo T. Molecular mechanisms of skeletal muscle development, regeneration, and osteogenic conversion. Bone 2015; 80:2-13. [PMID: 26453493 DOI: 10.1016/j.bone.2015.02.028] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 02/18/2015] [Accepted: 02/28/2015] [Indexed: 12/21/2022]
Abstract
Both skeletal muscle and bone are of mesodermal origin and derived from somites during embryonic development. Somites differentiate into the dorsal dermomyotome and the ventral sclerotome, which give rise to skeletal muscle and bone, respectively. Extracellular signaling molecules, such as Wnt and Shh, secreted from the surrounding environment, determine the developmental fate of skeletal muscle. Dermomyotome cells are specified as trunk muscle progenitor cells by transcription factor networks involving Pax3. These progenitor cells delaminate and migrate to form the myotome, where they are determined as myoblasts that differentiate into myotubes or myofibers. The MyoD family of transcription factors plays pivotal roles in myogenic determination and differentiation. Adult skeletal muscle regenerates upon exercise, muscle injury, or degeneration. Satellite cells are muscle-resident stem cells and play essential roles in muscle growth and regeneration. Muscle regeneration recapitulates the process of muscle development in many aspects. In certain muscle diseases, ectopic calcification or heterotopic ossification, as well as fibrosis and adipogenesis, occurs in skeletal muscle. Muscle-resident mesenchymal progenitor cells, which may be derived from vascular endothelial cells, are responsible for the ectopic osteogenesis, fibrogenesis, and adipogenesis. The small GTPase M-Ras is likely to participate in the ectopic calcification and ossification, as well as in osteogenesis during development. This article is part of a Special Issue entitled "Muscle Bone Interactions".
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Affiliation(s)
- Takeshi Endo
- Department of Biology, Graduate School of Science, Chiba University, Yayoicho, Inageku, Chiba, Chiba 263-8522, Japan.
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14
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Bourgeois A, Esteves de Lima J, Charvet B, Kawakami K, Stricker S, Duprez D. Stable and bicistronic expression of two genes in somite- and lateral plate-derived tissues to study chick limb development. BMC DEVELOPMENTAL BIOLOGY 2015; 15:39. [PMID: 26518454 PMCID: PMC4628273 DOI: 10.1186/s12861-015-0088-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/22/2015] [Indexed: 12/02/2022]
Abstract
Background Components of the limb musculoskeletal system have distinct mesoderm origins. Limb skeletal muscles originate from somites, while the skeleton and attachments (tendons and connective tissues) derive from limb lateral plate. Despite distinct mesoderm origins, the development of muscle, skeleton and attachments is highly coordinated both spatially and temporally to ensure complete function of the musculoskeletal system. A system to study molecular interactions between somitic-derived tissues (muscles) and lateral-plate-derived tissues (skeletal components and attachments) during limb development is missing. Results We designed a gene delivery system in chick embryos with the ultimate aim to study the interactions between the components of the musculoskeletal system during limb development. We combined the Tol2 genomic integration system with the viral T2A system and developed new vectors that lead to stable and bicistronic expression of two proteins at comparable levels in chick cells. Combined with limb somite and lateral plate electroporation techniques, two fluorescent reporter proteins were co-expressed in stoichiometric proportion in the muscle lineage (somitic-derived) or in skeleton and their attachments (lateral-plate-derived). In addition, we designed three vectors with different promoters to target muscle cells at different steps of the differentiation process. Conclusion Limb somite electroporation technique using vectors containing these different promoters allowed us to target all myogenic cells, myoblasts or differentiated muscle cells. These stable and promoter-specific vectors lead to bicistronic expression either in somitic-derived myogenic cells or lateral plate-derived cells, depending on the electroporation sites and open new avenues to study the interactions between myogenic cells and tendon or connective tissue cells during limb development.
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Affiliation(s)
- Adeline Bourgeois
- CNRS UMR 7622, IBPS-Developmental Biology Laboratory, F-75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, IBPS-Developmental Biology Laboratory, F-75005, Paris, France. .,Inserm U1156, F-75005, Paris, France.
| | - Joana Esteves de Lima
- CNRS UMR 7622, IBPS-Developmental Biology Laboratory, F-75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, IBPS-Developmental Biology Laboratory, F-75005, Paris, France. .,Inserm U1156, F-75005, Paris, France.
| | - Benjamin Charvet
- CNRS UMR 7622, IBPS-Developmental Biology Laboratory, F-75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, IBPS-Developmental Biology Laboratory, F-75005, Paris, France.
| | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, and Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan.
| | - Sigmar Stricker
- Institue for Chemistry and Biochemistry, Freie Universitaet Berlin, 14195, Berlin, Germany.
| | - Delphine Duprez
- CNRS UMR 7622, IBPS-Developmental Biology Laboratory, F-75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, IBPS-Developmental Biology Laboratory, F-75005, Paris, France. .,Inserm U1156, F-75005, Paris, France.
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15
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Coumailleau P, Kah O. Expression of the cyp19a1 gene in the adult brain of Xenopus is neuronal and not sexually dimorphic. Gen Comp Endocrinol 2015; 221:203-12. [PMID: 26255686 DOI: 10.1016/j.ygcen.2015.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 07/16/2015] [Accepted: 08/04/2015] [Indexed: 01/07/2023]
Abstract
The last step of oestrogen biosynthesis is catalyzed by the enzyme aromatase, the product of the cyp19a1 gene. In vertebrates, cyp19a1 is expressed in the brain resulting in a local oestrogen production that seems important not only for the control of reproduction-related circuits and sexual behaviour, but also for the regulation of neural development, synaptic plasticity and cell survival. In adult amphibians, the precise sites of expression of cyp19a1 in the brain have not been investigated which prevents proper understanding of its potential physiological functions. The present study aimed at examining the precise neuroanatomical distribution of cyp19a1 transcripts in adult brains of both male and female Xenopus. We found that cyp19a1 expression is highly regionalized in the brains of both sexes. The highest expression was found in the anterior part of the preoptic area and in the caudal hypothalamus, but significant levels of cyp19a1 transcripts were also found in the supraoptic paraventricular and suprachiasmatic areas, and in brain regions corresponding to the septum, bed nucleus of the stria terminalis and amygdala. Importantly, no obvious difference between male and female Xenopus was detected at the level of cyp19a1 transcripts. Additionally, in the brain of adult Xenopus, cyp19a1 transcripts were detected in neurons, and not in glial cells. These data and those available in other vertebrates on cyp19a1/aromatase expression suggest that, with the intriguing exception of teleost fishes, cyp19a1 was under strong evolutionary conservation with respect to its sites of expression and the nature of the cells in which it is expressed.
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Affiliation(s)
- Pascal Coumailleau
- Research Institute in Health, Environment and Occupation, INSERM U1085, SFR Biosite, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes cedex, France.
| | - Olivier Kah
- Research Institute in Health, Environment and Occupation, INSERM U1085, SFR Biosite, Université de Rennes 1, Campus de Beaulieu, 35 042 Rennes cedex, France
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Chen KJ, Lizaso A, Lee YH. SIM2 maintains innate host defense of the small intestine. Am J Physiol Gastrointest Liver Physiol 2014; 307:G1044-56. [PMID: 25277798 DOI: 10.1152/ajpgi.00241.2014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The single-minded 2 (SIM2) protein is a basic helix-loop-helix transcription factor regulating central nervous system (CNS) development in Drosophila. In humans, SIM2 is located within the Down syndrome critical region on chromosome 21 and may be involved in the development of mental retardation phenotype in Down syndrome. In this study, knockout of SIM2 expression in mice resulted in a gas distention phenotype in the gastrointestinal tract. We found that SIM2 is required for the expression of all cryptdins and numerous other antimicrobial peptides (AMPs) expressed in the small intestine. The mechanism underlying how SIM2 controls AMP expression involves both direct and indirect regulations. For the cryptdin genes, SIM2 regulates their expression by modulating transcription factor 7-like 2, a crucial regulator in the Wnt/β-catenin signaling pathway, while for other AMP genes, such as RegIIIγ, SIM2 directly activates their promoter activity. Our results establish that SIM2 is a crucial regulator in controlling expression of intestinal AMPs to maintain intestinal innate immunity against microbes.
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Affiliation(s)
- Kuan-Jung Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan; and National Yang-Ming University, Department of Life Sciences and Institute of Genome Sciences, Taipei, Taiwan
| | - Analyn Lizaso
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan; and
| | - Ying-Hue Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan; and
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17
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Grifone R, Xie X, Bourgeois A, Saquet A, Duprez D, Shi DL. The RNA-binding protein Rbm24 is transiently expressed in myoblasts and is required for myogenic differentiation during vertebrate development. Mech Dev 2014; 134:1-15. [PMID: 25217815 DOI: 10.1016/j.mod.2014.08.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/05/2014] [Accepted: 08/22/2014] [Indexed: 12/16/2022]
Abstract
RNA-binding proteins (RBP) contribute to gene regulation through post-transcriptional events. Despite the important roles demonstrated for several RBP in regulating skeletal myogenesis in vitro, very few RBP coding genes have been characterized during skeletal myogenesis in vertebrate embryo. In the present study we report that Rbm24, which encodes the RNA-binding motif protein 24, is required for skeletal muscle differentiation in vivo. We show that Rbm24 transcripts are expressed at all sites of skeletal muscle formation during embryogenesis of different vertebrates, including axial, limb and head muscles. Interestingly, we find that Rbm24 protein starts to accumulate in MyoD-positive myoblasts and is transiently expressed at the onset of muscle cell differentiation. It accumulates in myotomal and limb myogenic cells, but not in Pax3-positive progenitor cells. Rbm24 expression is under the direct regulation by MyoD, as demonstrated by in vivo chromatin immunoprecipitation assay. Using morpholino knockdown approach, we further show that Rbm24 is required for somitic myogenic progenitor cells to differentiate into muscle cells during chick somitic myogenesis. Altogether, these results highlight Rbm24 as a novel key regulator of the myogenic differentiation program during vertebrate development.
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Affiliation(s)
- Raphaëlle Grifone
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France; CNRS, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France
| | - Xin Xie
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France; CNRS, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France
| | - Adeline Bourgeois
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France; CNRS, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France
| | - Audrey Saquet
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France; CNRS, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France
| | - Delphine Duprez
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France; CNRS, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France
| | - De-Li Shi
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France; CNRS, UMR 7622, Laboratory of Developmental Biology, Paris F-75005, France.
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18
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Gene regulatory networks and transcriptional mechanisms that control myogenesis. Dev Cell 2014; 28:225-38. [PMID: 24525185 DOI: 10.1016/j.devcel.2013.12.020] [Citation(s) in RCA: 415] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/24/2013] [Accepted: 12/27/2013] [Indexed: 12/11/2022]
Abstract
We discuss the upstream regulators of myogenesis that lead to the activation of myogenic determination genes and subsequent differentiation, focusing on the mouse model. Key upstream genes, such as Pax3 and Pax7, Six1 and Six4, or Pitx2, participate in gene regulatory networks at different sites of skeletal muscle formation. MicroRNAs also intervene, with emerging evidence for the role of other noncoding RNAs. Myogenic determination and subsequent differentiation depend on members of the MyoD family. We discuss new insights into mechanisms underlying the transcriptional activity of these factors.
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19
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Roberts NA, Woolf AS, Stuart HM, Thuret R, McKenzie EA, Newman WG, Hilton EN. Heparanase 2, mutated in urofacial syndrome, mediates peripheral neural development in Xenopus. Hum Mol Genet 2014; 23:4302-14. [PMID: 24691552 PMCID: PMC4103677 DOI: 10.1093/hmg/ddu147] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Urofacial syndrome (UFS; previously Ochoa syndrome) is an autosomal recessive disease characterized by incomplete bladder emptying during micturition. This is associated with a dyssynergia in which the urethral walls contract at the same time as the detrusor smooth muscle in the body of the bladder. UFS is also characterized by an abnormal facial expression upon smiling, and bilateral weakness in the distribution of the facial nerve has been reported. Biallelic mutations in HPSE2 occur in UFS. This gene encodes heparanase 2, a protein which inhibits the activity of heparanase. Here, we demonstrate, for the first time, an in vivo developmental role for heparanase 2. We identified the Xenopus orthologue of heparanase 2 and showed that the protein is localized to the embryonic ventrolateral neural tube where motor neurons arise. Morpholino-induced loss of heparanase 2 caused embryonic skeletal muscle paralysis, and morphant motor neurons had aberrant morphology including less linear paths and less compactly-bundled axons than normal. Biochemical analyses demonstrated that loss of heparanase 2 led to upregulation of fibroblast growth factor 2/phosphorylated extracellular signal-related kinase signalling and to alterations in levels of transcripts encoding neural- and muscle-associated molecules. Thus, a key role of heparanase 2 is to buffer growth factor signalling in motor neuron development. These results shed light on the pathogenic mechanisms underpinning the clinical features of UFS and support the contention that congenital peripheral neuropathy is a key feature of this disorder.
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Affiliation(s)
- Neil A Roberts
- Centre for Genomic Medicine and Centre for Paediatrics and Child Health, Institute of Human Development, Faculty of Medical and Human Sciences
| | - Adrian S Woolf
- Centre for Paediatrics and Child Health, Institute of Human Development, Faculty of Medical and Human Sciences
| | | | | | - Edward A McKenzie
- Protein Expression Facility, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | | | - Emma N Hilton
- Centre for Genomic Medicine and Centre for Paediatrics and Child Health, Institute of Human Development, Faculty of Medical and Human Sciences,
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20
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Abstract
Mammalian basic HLH (helix-loop-helix)-PER-ARNT-SIM (bHLH-PAS) proteins are heterodimeric transcription factors that sense and respond to environmental signals (such as pollutants) or to physiological signals (for example, hypoxia and circadian rhythms) through their two PAS domains. PAS domains form a generic three-dimensional fold, which commonly contains an internal cavity capable of small-molecule binding and outer surfaces adept at protein-protein interactions. These proteins are important in several pro-tumour and antitumour pathways and their activities can be modulated by both natural metabolites and oncometabolites. Recently determined structures and successful small-molecule screening programmes are now providing new opportunities to discover selective agonists and antagonists directed against this multitasking family of transcription factors.
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Affiliation(s)
- David C Bersten
- School of Molecular and Biomedical Science (Biochemistry) and the Centre for Molecular Pathology, University of Adelaide, South Australia 5005, Australia
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21
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The roles of HLH transcription factors in epithelial mesenchymal transition and multiple molecular mechanisms. Clin Exp Metastasis 2013; 31:367-77. [PMID: 24158354 DOI: 10.1007/s10585-013-9621-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is presently recognized as an important event and the initiating stage for tumor invasion and metastasis. Several EMT inducers have been identified, among which the big family of helix-loop-helix (HLH) transcription factors are rising as a novel and promising family of proteins in EMT mediation, such as Twist1, Twist2, E47, and HIFs, etc. Due to the variety and complexities of HLH members, the pathways and mechanisms they employ to promote EMT are also complex and characteristic. In this review, we will discuss the roles of various HLH proteins in the regulation and sustenance of the EMT and multiple cellular mechanisms, attempting to provide a novel and broadened view towards the link between HLH proteins and EMT.
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22
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Guerquin MJ, Charvet B, Nourissat G, Havis E, Ronsin O, Bonnin MA, Ruggiu M, Olivera-Martinez I, Robert N, Lu Y, Kadler KE, Baumberger T, Doursounian L, Berenbaum F, Duprez D. Transcription factor EGR1 directs tendon differentiation and promotes tendon repair. J Clin Invest 2013; 123:3564-76. [PMID: 23863709 DOI: 10.1172/jci67521] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 05/21/2013] [Indexed: 12/27/2022] Open
Abstract
Tendon formation and repair rely on specific combinations of transcription factors, growth factors, and mechanical parameters that regulate the production and spatial organization of type I collagen. Here, we investigated the function of the zinc finger transcription factor EGR1 in tendon formation, healing, and repair using rodent animal models and mesenchymal stem cells (MSCs). Adult tendons of Egr1-/- mice displayed a deficiency in the expression of tendon genes, including Scx, Col1a1, and Col1a2, and were mechanically weaker compared with their WT littermates. EGR1 was recruited to the Col1a1 and Col2a1 promoters in postnatal mouse tendons in vivo. Egr1 was required for the normal gene response following tendon injury in a mouse model of Achilles tendon healing. Forced Egr1 expression programmed MSCs toward the tendon lineage and promoted the formation of in vitro-engineered tendons from MSCs. The application of EGR1-producing MSCs increased the formation of tendon-like tissues in a rat model of Achilles tendon injury. We provide evidence that the ability of EGR1 to promote tendon differentiation is partially mediated by TGF-β2. This study demonstrates EGR1 involvement in adult tendon formation, healing, and repair and identifies Egr1 as a putative target in tendon repair strategies.
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Six1 regulates MyoD expression in adult muscle progenitor cells. PLoS One 2013; 8:e67762. [PMID: 23840772 PMCID: PMC3695946 DOI: 10.1371/journal.pone.0067762] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 05/22/2013] [Indexed: 12/21/2022] Open
Abstract
Quiescent satellite cells are myogenic progenitors that enable regeneration of skeletal muscle. One of the early events of satellite cell activation following myotrauma is the induction of the myogenic regulatory factor MyoD, which eventually induces terminal differentiation and muscle function gene expression. The purpose of this study was to elucidate the mechanism by which MyoD is induced during activation of satellite cells in mouse muscle undergoing regeneration. We show that Six1, a transcription factor essential for embryonic myogenesis, also regulates MyoD expression in muscle progenitor cells. Six1 knock-down by RNA interference leads to decreased expression of MyoD in myoblasts. Chromatin immunoprecipitation assays reveal that Six1 binds the Core Enhancer Region of MyoD. Further, transcriptional reporter assays demonstrate that Core Enhancer Region reporter gene activity in myoblasts and in regenerating muscle depends on the expression of Six1 and on Six1 binding sites. Finally, we provide evidence indicating that Six1 is required for the proper chromatin structure at the Core Enhancer Region, as well as for MyoD binding at its own enhancer. Together, our results reveal that MyoD expression in satellite cells depends on Six1, supporting the idea that Six1 plays an important role in adult myogenesis, in addition to its role in embryonic muscle formation.
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24
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Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, Lacey M, Ehrlich M. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics 2013; 8:317-32. [PMID: 23417056 PMCID: PMC3669123 DOI: 10.4161/epi.23989] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 12/31/2022] Open
Abstract
Myogenic cell cultures derived from muscle biopsies are excellent models for human cell differentiation. We report the first comprehensive analysis of myogenesis-specific DNA hyper- and hypo-methylation throughout the genome for human muscle progenitor cells (both myoblasts and myotubes) and skeletal muscle tissue vs. 30 non-muscle samples using reduced representation bisulfite sequencing. We also focused on four genes with extensive hyper- or hypo-methylation in the muscle lineage (PAX3, TBX1, MYH7B/MIR499 and OBSCN) to compare DNA methylation, DNaseI hypersensitivity, histone modification, and CTCF binding profiles. We found that myogenic hypermethylation was strongly associated with homeobox or T-box genes and muscle hypomethylation with contractile fiber genes. Nonetheless, there was no simple relationship between differential gene expression and myogenic differential methylation, rather only for subsets of these genes, such as contractile fiber genes. Skeletal muscle retained ~30% of the hypomethylated sites but only ~3% of hypermethylated sites seen in myogenic progenitor cells. By enzymatic assays, skeletal muscle was 2-fold enriched globally in genomic 5-hydroxymethylcytosine (5-hmC) vs. myoblasts or myotubes and was the only sample type enriched in 5-hmC at tested myogenic hypermethylated sites in PAX3/CCDC140 andTBX1. TET1 and TET2 RNAs, which are involved in generation of 5-hmC and DNA demethylation, were strongly upregulated in myoblasts and myotubes. Our findings implicate de novo methylation predominantly before the myoblast stage and demethylation before and after the myotube stage in control of transcription and co-transcriptional RNA processing. They also suggest that, in muscle, TET1 or TET2 are involved in active demethylation and in formation of stable 5-hmC residues.
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MESH Headings
- 5-Methylcytosine/analogs & derivatives
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- CCCTC-Binding Factor
- Cardiac Myosins/genetics
- Cardiac Myosins/metabolism
- Case-Control Studies
- Cell Lineage/genetics
- Child
- Cytosine/analogs & derivatives
- Cytosine/metabolism
- DNA Methylation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Developmental
- Genes, Homeobox
- Genome, Human
- Guanine Nucleotide Exchange Factors/genetics
- Guanine Nucleotide Exchange Factors/metabolism
- Histones/metabolism
- Humans
- Infant, Newborn
- Male
- Middle Aged
- Mixed Function Oxygenases
- Muscle Development/genetics
- Muscle Fibers, Skeletal/metabolism
- Muscle Proteins/genetics
- Muscle Proteins/metabolism
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Myoblasts/metabolism
- Myosin Heavy Chains/genetics
- Myosin Heavy Chains/metabolism
- PAX3 Transcription Factor
- Paired Box Transcription Factors/genetics
- Paired Box Transcription Factors/metabolism
- Protein Serine-Threonine Kinases
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Repressor Proteins/metabolism
- Rho Guanine Nucleotide Exchange Factors
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- Transcription, Genetic
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Affiliation(s)
- Koji Tsumagari
- Program in Human Genetics and Tulane Cancer Center; Tulane Health Sciences Center; New Orleans, LA USA
| | - Carl Baribault
- Tulane Cancer Center and Department of Mathematics; Tulane Health Sciences Center and Tulane University; New Orleans, LA USA
| | | | | | - Jason Gertz
- HudsonAlpha Institute for Biotechnology; Huntsville, AL USA
| | | | - Melody Badoo
- Department of Pathology and Tulane Cancer Center; Tulane Health Sciences Center; New Orleans, LA USA
| | - Charlene M. Crain
- Center for Stem Cell Research and Regenerative Medicine; Tulane Health Sciences Center; New Orleans, LA USA
| | - Lingyun Song
- Institute for Genome Sciences & Policy; Duke University; Durham, NC USA
| | | | | | - Michelle Lacey
- Tulane Cancer Center and Department of Mathematics; Tulane Health Sciences Center and Tulane University; New Orleans, LA USA
| | - Melanie Ehrlich
- Program in Human Genetics; Tulane Cancer Center and Center for Bioinformatics and Genomics; Tulane Health Sciences Center; New Orleans, LA USA
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25
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Anderson C, Williams VC, Moyon B, Daubas P, Tajbakhsh S, Buckingham ME, Shiroishi T, Hughes SM, Borycki AG. Sonic hedgehog acts cell-autonomously on muscle precursor cells to generate limb muscle diversity. Genes Dev 2012; 26:2103-17. [PMID: 22987640 DOI: 10.1101/gad.187807.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
How muscle diversity is generated in the vertebrate body is poorly understood. In the limb, dorsal and ventral muscle masses constitute the first myogenic diversification, as each gives rise to distinct muscles. Myogenesis initiates after muscle precursor cells (MPCs) have migrated from the somites to the limb bud and populated the prospective muscle masses. Here, we show that Sonic hedgehog (Shh) from the zone of polarizing activity (ZPA) drives myogenesis specifically within the ventral muscle mass. Shh directly induces ventral MPCs to initiate Myf5 transcription and myogenesis through essential Gli-binding sites located in the Myf5 limb enhancer. In the absence of Shh signaling, myogenesis is delayed, MPCs fail to migrate distally, and ventral paw muscles fail to form. Thus, Shh production in the limb ZPA is essential for the spatiotemporal control of myogenesis and coordinates muscle and skeletal development by acting directly to regulate the formation of specific ventral muscles.
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Affiliation(s)
- Claire Anderson
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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