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Lukowicz-Bedford RM, Eisen JS, Miller AC. Gap-junction-mediated bioelectric signaling required for slow muscle development and function in zebrafish. Curr Biol 2024:S0960-9822(24)00759-0. [PMID: 38936363 DOI: 10.1016/j.cub.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/11/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Bioelectric signaling, intercellular communication facilitated by membrane potential and electrochemical coupling, is emerging as a key regulator of animal development. Gap junction (GJ) channels can mediate bioelectric signaling by creating a fast, direct pathway between cells for the movement of ions and other small molecules. In vertebrates, GJ channels are formed by a highly conserved transmembrane protein family called the connexins. The connexin gene family is large and complex, creating challenges in identifying specific connexins that create channels within developing and mature tissues. Using the embryonic zebrafish neuromuscular system as a model, we identify a connexin conserved across vertebrate lineages, gjd4, which encodes the Cx46.8 protein, that mediates bioelectric signaling required for slow muscle development and function. Through mutant analysis and in vivo imaging, we show that gjd4/Cx46.8 creates GJ channels specifically in developing slow muscle cells. Using genetics, pharmacology, and calcium imaging, we find that spinal-cord-generated neural activity is transmitted to developing slow muscle cells, and synchronized activity spreads via gjd4/Cx46.8 GJ channels. Finally, we show that bioelectrical signal propagation within the developing neuromuscular system is required for appropriate myofiber organization and that disruption leads to defects in behavior. Our work reveals a molecular basis for GJ communication among developing muscle cells and reveals how perturbations to bioelectric signaling in the neuromuscular system may contribute to developmental myopathies. Moreover, this work underscores a critical motif of signal propagation between organ systems and highlights the pivotal role of GJ communication in coordinating bioelectric signaling during development.
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Affiliation(s)
| | - Judith S Eisen
- University of Oregon, Institute of Neuroscience, Eugene, OR 97405, USA
| | - Adam C Miller
- University of Oregon, Institute of Neuroscience, Eugene, OR 97405, USA.
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2
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Aranda-Martínez P, Sayed RKA, Fernández-Martínez J, Ramírez-Casas Y, Yang Y, Escames G, Acuña-Castroviejo D. Zebrafish as a Human Muscle Model for Studying Age-Dependent Sarcopenia and Frailty. Int J Mol Sci 2024; 25:6166. [PMID: 38892357 PMCID: PMC11172448 DOI: 10.3390/ijms25116166] [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: 05/14/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Currently, there is an increase in the aging of the population, which represents a risk factor for many diseases, including sarcopenia. Sarcopenia involves progressive loss of mass, strength, and function of the skeletal muscle. Some mechanisms include alterations in muscle structure, reduced regenerative capacity, oxidative stress, mitochondrial dysfunction, and inflammation. The zebrafish has emerged as a new model for studying skeletal muscle aging because of its numerous advantages, including histological and molecular similarity to human skeletal muscle. In this study, we used fish of 2, 10, 30, and 60 months of age. The older fish showed a higher frailty index with a value of 0.250 ± 0.000 because of reduced locomotor activity and alterations in biometric measurements. We observed changes in muscle structure with a decreased number of myocytes (0.031 myocytes/μm2 ± 0.004 at 60 months) and an increase in collagen with aging up to 15% ± 1.639 in the 60-month group, corresponding to alterations in the synthesis, degradation, and differentiation pathways. These changes were accompanied by mitochondrial alterations, such as a nearly 50% reduction in the number of intermyofibrillar mitochondria, 100% mitochondrial damage, and reduced mitochondrial dynamics. Overall, we demonstrated a similarity in the aging processes of muscle aging between zebrafish and mammals.
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Affiliation(s)
- Paula Aranda-Martínez
- Centro de Investigación Biomédica, Facultad de Medicina, Departamento de Fisiología, Universidad de Granada, 18016 Granada, Spain; (P.A.-M.); (J.F.-M.); (Y.R.-C.); (G.E.)
- Instituto de Biotecnología, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (Ibs. Granada), Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Ramy K. A. Sayed
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Sohag University, Sohag 82524, Egypt;
| | - José Fernández-Martínez
- Centro de Investigación Biomédica, Facultad de Medicina, Departamento de Fisiología, Universidad de Granada, 18016 Granada, Spain; (P.A.-M.); (J.F.-M.); (Y.R.-C.); (G.E.)
- Instituto de Biotecnología, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (Ibs. Granada), Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Yolanda Ramírez-Casas
- Centro de Investigación Biomédica, Facultad de Medicina, Departamento de Fisiología, Universidad de Granada, 18016 Granada, Spain; (P.A.-M.); (J.F.-M.); (Y.R.-C.); (G.E.)
- Instituto de Biotecnología, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (Ibs. Granada), Hospital Universitario San Cecilio, 18016 Granada, Spain
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences and Medicine, Northwest University, Xi’an 710069, China;
| | - Germaine Escames
- Centro de Investigación Biomédica, Facultad de Medicina, Departamento de Fisiología, Universidad de Granada, 18016 Granada, Spain; (P.A.-M.); (J.F.-M.); (Y.R.-C.); (G.E.)
- Instituto de Biotecnología, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (Ibs. Granada), Hospital Universitario San Cecilio, 18016 Granada, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Darío Acuña-Castroviejo
- Centro de Investigación Biomédica, Facultad de Medicina, Departamento de Fisiología, Universidad de Granada, 18016 Granada, Spain; (P.A.-M.); (J.F.-M.); (Y.R.-C.); (G.E.)
- Instituto de Biotecnología, Parque Tecnológico de Ciencias de la Salud, Universidad de Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria (Ibs. Granada), Hospital Universitario San Cecilio, 18016 Granada, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- UGC de Laboratorios Clínicos, Hospital Universitario San Cecilio, 18016 Granada, Spain
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Lukowicz-Bedford RM, Eisen JS, Miller AC. Gap junction mediated bioelectric coordination is required for slow muscle development, organization, and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572619. [PMID: 38187655 PMCID: PMC10769300 DOI: 10.1101/2023.12.20.572619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Bioelectrical signaling, intercellular communication facilitated by membrane potential and electrochemical coupling, is emerging as a key regulator of animal development. Gap junction (GJ) channels can mediate bioelectric signaling by creating a fast, direct pathway between cells for the movement of ions and other small molecules. In vertebrates, GJ channels are formed by a highly conserved transmembrane protein family called the Connexins. The connexin gene family is large and complex, presenting a challenge in identifying the specific Connexins that create channels within developing and mature tissues. Using the embryonic zebrafish neuromuscular system as a model, we identify a connexin conserved across vertebrate lineages, gjd4, which encodes the Cx46.8 protein, that mediates bioelectric signaling required for appropriate slow muscle development and function. Through a combination of mutant analysis and in vivo imaging we show that gjd4/Cx46.8 creates GJ channels specifically in developing slow muscle cells. Using genetics, pharmacology, and calcium imaging we find that spinal cord generated neural activity is transmitted to developing slow muscle cells and synchronized activity spreads via gjd4/Cx46.8 GJ channels. Finally, we show that bioelectrical signal propagation within the developing neuromuscular system is required for appropriate myofiber organization, and that disruption leads to defects in behavior. Our work reveals the molecular basis for GJ communication among developing muscle cells and reveals how perturbations to bioelectric signaling in the neuromuscular system_may contribute to developmental myopathies. Moreover, this work underscores a critical motif of signal propagation between organ systems and highlights the pivotal role played by GJ communication in coordinating bioelectric signaling during development.
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4
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Lambert MR, Gussoni E. Tropomyosin 3 (TPM3) function in skeletal muscle and in myopathy. Skelet Muscle 2023; 13:18. [PMID: 37936227 PMCID: PMC10629095 DOI: 10.1186/s13395-023-00327-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
The tropomyosin genes (TPM1-4) contribute to the functional diversity of skeletal muscle fibers. Since its discovery in 1988, the TPM3 gene has been recognized as an indispensable regulator of muscle contraction in slow muscle fibers. Recent advances suggest that TPM3 isoforms hold more extensive functions during skeletal muscle development and in postnatal muscle. Additionally, mutations in the TPM3 gene have been associated with the features of congenital myopathies. The use of different in vitro and in vivo model systems has leveraged the discovery of several disease mechanisms associated with TPM3-related myopathy. Yet, the precise mechanisms by which TPM3 mutations lead to muscle dysfunction remain unclear. This review consolidates over three decades of research about the role of TPM3 in skeletal muscle. Overall, the progress made has led to a better understanding of the phenotypic spectrum in patients affected by mutations in this gene. The comprehensive body of work generated over these decades has also laid robust groundwork for capturing the multiple functions this protein plays in muscle fibers.
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Affiliation(s)
- Matthias R Lambert
- Division of Genetics and Genomics, Boston Children's Hospital, 300 Longwood Ave., Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Emanuela Gussoni
- Division of Genetics and Genomics, Boston Children's Hospital, 300 Longwood Ave., Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- The Stem Cell Program, Boston Children's Hospital, Boston, MA, 02115, USA
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Oprescu SN, Baumann N, Chen X, Sun Q, Zhao Y, Yue F, Wang H, Kuang S. Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of the skeletal muscle. Skelet Muscle 2023; 13:15. [PMID: 37705115 PMCID: PMC10498607 DOI: 10.1186/s13395-023-00324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Transcription factors (TFs) play key roles in regulating differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associating domains. Unexpectedly, Myod1Cre-driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7CreER- or Rosa26CreER- driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remains to be elucidated.
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Affiliation(s)
- Stephanie N Oprescu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Nick Baumann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiyue Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Qiang Sun
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Yu Zhao
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Feng Yue
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Huating Wang
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Hong Kong, China
| | - Shihuan Kuang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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Tesoriero C, Greco F, Cannone E, Ghirotto F, Facchinello N, Schiavone M, Vettori A. Modeling Human Muscular Dystrophies in Zebrafish: Mutant Lines, Transgenic Fluorescent Biosensors, and Phenotyping Assays. Int J Mol Sci 2023; 24:8314. [PMID: 37176020 PMCID: PMC10179009 DOI: 10.3390/ijms24098314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Muscular dystrophies (MDs) are a heterogeneous group of myopathies characterized by progressive muscle weakness leading to death from heart or respiratory failure. MDs are caused by mutations in genes involved in both the development and organization of muscle fibers. Several animal models harboring mutations in MD-associated genes have been developed so far. Together with rodents, the zebrafish is one of the most popular animal models used to reproduce MDs because of the high level of sequence homology with the human genome and its genetic manipulability. This review describes the most important zebrafish mutant models of MD and the most advanced tools used to generate and characterize all these valuable transgenic lines. Zebrafish models of MDs have been generated by introducing mutations to muscle-specific genes with different genetic techniques, such as (i) N-ethyl-N-nitrosourea (ENU) treatment, (ii) the injection of specific morpholino, (iii) tol2-based transgenesis, (iv) TALEN, (v) and CRISPR/Cas9 technology. All these models are extensively used either to study muscle development and function or understand the pathogenetic mechanisms of MDs. Several tools have also been developed to characterize these zebrafish models by checking (i) motor behavior, (ii) muscle fiber structure, (iii) oxidative stress, and (iv) mitochondrial function and dynamics. Further, living biosensor models, based on the expression of fluorescent reporter proteins under the control of muscle-specific promoters or responsive elements, have been revealed to be powerful tools to follow molecular dynamics at the level of a single muscle fiber. Thus, zebrafish models of MDs can also be a powerful tool to search for new drugs or gene therapies able to block or slow down disease progression.
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Affiliation(s)
- Chiara Tesoriero
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
| | - Francesca Greco
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
| | - Elena Cannone
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy;
| | - Francesco Ghirotto
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
| | - Nicola Facchinello
- Neuroscience Institute, Italian National Research Council (CNR), 35131 Padua, Italy
| | - Marco Schiavone
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy;
| | - Andrea Vettori
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (C.T.); (F.G.); (F.G.); (A.V.)
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Oprescu SN, Baumann N, Chen X, Sun Q, Zhao Y, Yue F, Wang H, Kuang S. Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of skeletal muscle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534956. [PMID: 37034612 PMCID: PMC10081271 DOI: 10.1101/2023.03.30.534956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Transcription factors (TFs) play key roles in regulating the differentiation and function of stem cells, including muscle satellite cells (MuSCs), a resident stem cell population responsible for postnatal regeneration of the skeletal muscle. Sox11 belongs to the Sry-related HMG-box (SOX) family of TFs that play diverse roles in stem cell behavior and tissue specification. Analysis of single-cell RNA-sequencing (scRNA-seq) datasets identify a specific enrichment of Sox11 mRNA in differentiating but not quiescent MuSCs. Consistent with the scRNA-seq data, Sox11 levels increase during differentiation of murine primary myoblasts in vitro. scRNA-seq data comparing muscle regeneration in young and old mice further demonstrate that Sox11 expression is reduced in aged MuSCs. Age-related decline of Sox11 expression is associated with reduced chromatin contacts within the topologically associated domains. Unexpectedly, Myod1 Cre -driven deletion of Sox11 in embryonic myoblasts has no effects on muscle development and growth, resulting in apparently healthy muscles that regenerate normally. Pax7 CreER or Rosa26 CreER driven (MuSC-specific or global) deletion of Sox11 in adult mice similarly has no effects on MuSC differentiation or muscle regeneration. These results identify Sox11 as a novel myogenic differentiation marker with reduced expression in quiescent and aged MuSCs, but the specific function of Sox11 in myogenesis remain to be elucidated.
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Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak. Animals (Basel) 2022; 12:ani12223074. [PMID: 36428302 PMCID: PMC9686495 DOI: 10.3390/ani12223074] [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: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks (p < 0.05) and 30-months yaks (p < 0.05), and withers height of 6 months yaks (p < 0.05) and 18-months yaks (p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. In conclusion, SOX6 might be prominently involved in promoting growth and development of yaks, suggesting that the SOX6 gene can be used in breeding yaks by molecular marker-assisted selection (MAS). The study also offered some important insights into the references and clues for the genetic breeding of yaks.
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Wu P, Yong P, Zhang Z, Xu R, Shang R, Shi J, Zhang J, Bi P, Chen E, Du S. Loss of Myomixer Results in Defective Myoblast Fusion, Impaired Muscle Growth, and Severe Myopathy in Zebrafish. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1023-1038. [PMID: 36083384 PMCID: PMC10112271 DOI: 10.1007/s10126-022-10159-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
The development and growth of fish skeletal muscles require myoblast fusion to generate multinucleated myofibers. While zebrafish fast-twitch muscle can fuse to generate multinucleated fibers, the slow-twitch muscle fibers remain mononucleated in zebrafish embryos and larvae. The mechanism underlying the fiber-type-specific control of fusion remains elusive. Recent genetic studies using mice identified a long-sought fusion factor named Myomixer. To understand whether Myomixer is involved in the fiber-type specific fusion, we analyzed the transcriptional regulation of myomixer expression and characterized the muscle growth phenotype upon genetic deletion of myomixer in zebrafish. The data revealed that overexpression of Sonic Hedgehog (Shh) drastically inhibited myomixer expression and blocked myoblast fusion, recapitulating the phenotype upon direct genetic deletion of myomixer from zebrafish. The fusion defect in myomixer mutant embryos could be faithfully rescued upon re-expression of zebrafish myomixer gene or its orthologs from shark or human. Interestingly, myomixer mutant fish survived to adult stage though were notably smaller than wildtype siblings. Severe myopathy accompanied by the uncontrolled adipose infiltration was observed in both fast and slow muscle tissues of adult myomixer mutants. Collectively, our data highlight an indispensable role of myomixer gene for cell fusion during both embryonic muscle development and post-larval muscle growth.
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Affiliation(s)
- Ping Wu
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, USA
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, China
| | - Pengzheng Yong
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, USA
| | - Zhanxiong Zhang
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, USA
| | - Rui Xu
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, USA
| | - Renjie Shang
- Center for Molecular Medicine & Department of Genetics, University of Georgia, Athens, USA
| | - Jun Shi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, USA
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jianshe Zhang
- Department of Bioengineering and Environmental Science, Changsha University, Changsha, China
| | - Pengpeng Bi
- Center for Molecular Medicine & Department of Genetics, University of Georgia, Athens, USA
| | - Elizabeth Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, USA
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, USA.
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Liu YF, Zhang M, Shan YJ, Pang LC, Ji GG, Ju XJ, Tu YJ, Shi SY, Bai H, Zou JM, Shu JT. Transcriptome sequencing analysis of the role of miR-499-5p and SOX6 in chicken skeletal myofiber specification. Front Genet 2022; 13:1008649. [PMID: 36186474 PMCID: PMC9521549 DOI: 10.3389/fgene.2022.1008649] [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: 08/01/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) might play critical roles in skeletal myofiber specification. In a previous study, we found that chicken miR-499-5p is specifically expressed in slow-twitch muscle and that its potential target gene is SOX6. In this study, we performed RNA sequencing to investigate the effects of SOX6 and miR-499-5p on the modulation and regulation of chicken muscle fiber type and its regulatory mechanism. The expression levels of miR-499-5p and SOX6 demonstrated opposing trends in different skeletal muscles and were associated with muscle fiber type composition. Differential expression analysis revealed that miR-499-5p overexpression led to significant changes in the expression of 297 genes in chicken primary myoblasts (CPMs). Myofiber type-related genes, including MYH7B and CSRP3, showed expression patterns similar to those in slow-twitch muscle. According to functional enrichment analysis, differentially expressed genes were mostly associated with muscle development and muscle fiber-related processes. SOX6 was identified as the target gene of miR-499-5p in CPM using target gene mining and luciferase reporter assays. SOX6 knockdown resulted in upregulation of the slow myosin genes and downregulation of fast myosin genes. Furthermore, protein-protein interaction network analysis revealed that MYH7B and RUNX2 may be the direct targets of SOX6. These results indicated that chicken miR-499-5p may promote slow-twitch muscle fiber formation by repressing SOX6 expression. Our study provides a dataset that can be used as a reference for animal meat quality and human muscle disease studies.
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Affiliation(s)
- Yi-Fan Liu
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Ming Zhang
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Yan-Ju Shan
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Li-Chuan Pang
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Gai-Ge Ji
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Xiao-Jun Ju
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Yun-Jie Tu
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Shi-Ying Shi
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of China, Yangzhou University, Yangzhou, China
| | - Jian-Min Zou
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Jing-Ting Shu
- Jiangsu Institute of Poultry Science Innovation Co., Yangzhou, China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou, China
- *Correspondence: Jing-Ting Shu,
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Fast and slow myofiber-specific expression profiles are affected by noncoding RNAs in Mongolian horses. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100942. [PMID: 34823143 DOI: 10.1016/j.cbd.2021.100942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
The heterogeneity and plasticity of muscle fibers are essential for the athletic performance of horses, mainly at the adaption of exercises and the effect on muscle diseases. Skeletal muscle fibers can be generally distinguished by their characteristics of contraction as slow and fast type myofibers. The diversity of contractile properties and metabolism enable skeletal muscles to respond to the variable functional requirements. We investigated the muscle fiber composition and metabolic enzyme activities of splenius muscle and gluteus medius muscle from Mongolian horses. The deep RNA-seq analysis of detecting differentially expressed mRNAs, lncRNAs, circRNAs and their correlation analysis from two muscles were performed. Splenius muscle and gluteus medius muscle from Mongolian horses showed a high divergence of myofiber compositions and metabolic enzyme activities. Corresponding to their phenotypic characteristics, 57 differentially expressed long noncoding RNAs and 12 differentially expressed circle RNAs were found between two muscles. The analysis results indicate multiple binding sites were detected in lncRNAs and circRNAs with myofiber-specific expressed miRNAs. Among which we found significant correlations between the above noncoding RNAs, miRNAs, their target genes, myofiber-specific developmental transcript factors, and sarcomere genes. We suggest that the ceRNA mechanism of differentially expressed noncoding RNAs by acting as miRNA sponges could be fine tuners in regulating skeletal muscle fiber composition and transition in horses, which will operate new protective measures of muscle disease and locomotor adaption for racehorses.
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12
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Sox6, A Potential Target for MicroRNAs in Cardiometabolic Disease. Curr Hypertens Rep 2022; 24:145-156. [DOI: 10.1007/s11906-022-01175-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 12/25/2022]
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13
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Girgis J, Yang D, Chakroun I, Liu Y, Blais A. Six1 promotes skeletal muscle thyroid hormone response through regulation of the MCT10 transporter. Skelet Muscle 2021; 11:26. [PMID: 34809717 PMCID: PMC8607597 DOI: 10.1186/s13395-021-00281-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Six1 transcription factor is implicated in controlling the development of several tissue types, notably skeletal muscle. Six1 also contributes to muscle metabolism and its activity is associated with the fast-twitch, glycolytic phenotype. Six1 regulates the expression of certain genes of the fast muscle program by directly stimulating their transcription or indirectly acting through a long non-coding RNA. We hypothesized that additional mechanisms of action of Six1 might be at play. METHODS A combined analysis of gene expression profiling and genome-wide location analysis data was performed. Results were validated using in vivo RNA interference loss-of-function assays followed by measurement of gene expression by RT-PCR and transcriptional reporter assays. RESULTS The Slc16a10 gene, encoding the thyroid hormone transmembrane transporter MCT10, was identified as a gene with a transcriptional enhancer directly bound by Six1 and requiring Six1 activity for full expression in adult mouse tibialis anterior, a predominantly fast-twitch muscle. Of the various thyroid hormone transporters, MCT10 mRNA was found to be the most abundant in skeletal muscle, and to have a stronger expression in fast-twitch compared to slow-twitch muscle groups. Loss-of-function of MCT10 in the tibialis anterior recapitulated the effect of Six1 on the expression of fast-twitch muscle genes and led to lower activity of a thyroid hormone receptor-dependent reporter gene. CONCLUSIONS These results shed light on the molecular mechanisms controlling the tissue expression profile of MCT10 and identify modulation of the thyroid hormone signaling pathway as an additional mechanism by which Six1 influences skeletal muscle metabolism.
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Affiliation(s)
- John Girgis
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Dabo Yang
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Imane Chakroun
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Yubing Liu
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Alexandre Blais
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada. .,Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada. .,University of Ottawa Centre for Inflammation, Immunity and Infection (CI3), Ottawa, Ontario, Canada.
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14
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Yin YH, Zhang XH, Wang XA, Li RH, Zhang YW, Shan XX, You XX, Huang XD, Wu AL, Wang M, Pan XF, Bian C, Jiang WS, Shi Q, Yang JX. Construction of a chromosome-level genome assembly for genome-wide identification of growth-related quantitative trait loci in Sinocyclocheilus grahami (Cypriniformes, Cyprinidae). Zool Res 2021; 42:262-266. [PMID: 33764016 PMCID: PMC8175956 DOI: 10.24272/j.issn.2095-8137.2020.321] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Dianchi golden-line barbel, Sinocyclocheilus grahami (Regan, 1904), is one of the “Four Famous Fishes” of Yunnan Province, China. Given its economic value, this species has been artificially bred successfully since 2007, with a nationally selected breed (“S. grahami, Bayou No. 1”) certified in 2018. For the future utilization of this species, its growth rate, disease resistance, and wild adaptability need to be improved, which could be achieved with the help of molecular marker-assisted selection (MAS). In the current study, we constructed the first chromosome-level genome of S. grahami, assembled 48 pseudo-chromosomes, and obtained a genome assembly of 1.49 Gb. We also performed QTL-seq analysis of S. grahami using the highest and lowest bulks (i.e., largest and smallest size) in both a sibling and random population. We screened two quantitative trait loci (QTLs) (Chr3, 14.9–39.1 Mb and Chr17, 4.1–27.4 Mb) as the major growth-related locations. Several candidate genes (e.g., map2k5, stat1, phf21a, sox6, and smad6) were also identified, with functions related to growth, such as cell differentiation, neuronal development, skeletal muscle development, chondrogenesis, and immunity. These results built a solid foundation for in-depth MAS studies on the growth traits of S. grahami.
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Affiliation(s)
- Yan-Hui Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Hui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xiao-Ai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China
| | - Rui-Han Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Yuan-Wei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China
| | - Xin-Xin Shan
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xin-Xin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xin-Di Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - An-Li Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China
| | - Mo Wang
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Xiao-Fu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Wan-Sheng Jiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest and Chemical Industry Engineering, Jishou University, Zhangjiajie, Hunan 427000, China. E-mail:
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Jun-Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650224, China. E-mail:
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15
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Zafar I, Iftikhar R, Ahmad SU, Rather MA. Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp ( Cyprinus carpio). ACTA ACUST UNITED AC 2021; 30:e00607. [PMID: 33936955 PMCID: PMC8076717 DOI: 10.1016/j.btre.2021.e00607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/20/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
27 SOX (high-mobility group HMG-box) genes were identified in the C. carp genome. SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative protein series from 307 to 509 amino acids. Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %. Chromosomal location and synteny analysis display all SOX gene are located on different chromosomes.
Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. In our results, a total of 27 SOX (high-mobility group HMG-box) domain genes were identified in the C. carp genome. The full length sequences of SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative proteins series from 307 to 509 amino acids and all gene having exon number expect SOX9 and SOX13. All the SOX proteins contained at least one conserved DNA-binding HMG-box domain and two (SOX7 and SOX18) were found C terminal. The Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %, average in biological regulation 45.188 %, biosynthetic process (19.992 %), regulation of cellular process 39.68, 45.508 % organic substance metabolic process, multicellular organismal process 23.23 %,developmental process 21.74 %, system development 16.59 %, gene expression 16.05 % and 14.337 % of RNA metabolic process. Chromosomal location and syntanic analysis show all SOX gene are located on different chromosomes and apparently does not fallow the unique pattern. The maximum linkage of chromosome is (2) on Unplaced Scaffold region. Finally, our results provide important genomic suggestion for upcoming studies of biochemical, physiological, and phylogenetic understanding on SOX genes among teleost.
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Affiliation(s)
- Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University Pakistan, Punjab, Pakistan
| | - Rida Iftikhar
- Department of Bioinformatics and Computational Biology, Virtual University Pakistan, Punjab, Pakistan
| | - Syed Umair Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Fauclty of Fisheries Rangil, Ganderbal, SKUAST-Kashmir, India
- Corresponding author.
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16
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Li B, Tian Y, Wen H, Qi X, Wang L, Zhang J, Li J, Dong X, Zhang K, Li Y. Systematic identification and expression analysis of the Sox gene family in spotted sea bass (Lateolabrax maculatus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100817. [PMID: 33677158 DOI: 10.1016/j.cbd.2021.100817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
The Sox gene family encodes a set of transcription factors characterized by a conserved Sry-related high mobility group (HMG)-box domain, which performs a series of essential biological functions in diverse tissues and developmental processes. In this study, the Sox gene family was systematically characterized in spotted sea bass (Lateolabrax maculatus). A total of 26 Sox genes were identified and classified into eight subfamilies, namely, SoxB1, SoxB2, SoxC, SoxD, SoxE, SoxF, SoxH and SoxK. The phylogenetic relationship, exon-intron and domain structure analyses supported their annotation and classification. Comparison of gene copy numbers and chromosome locations among different species indicated that except tandem duplicated paralogs of Sox17/Sox32, duplicated Sox genes in spotted sea bass were generated from teleost-specific whole genome duplication during evolution. In addition, qRT-PCR was performed to detect the expression profiles of Sox genes during development and adulthood. The results showed that the expression of 16 out of 26 Sox genes was induced dramatically at different starting points after the multicellular stage, which is consistent with embryogenesis. At the early stage of sex differentiation, 9 Sox genes exhibited sexually dimorphic expression patterns, among which Sox3, Sox19 and Sox6b showed the most significant ovary-biased expression. Moreover, the distinct expression pattern of Sox genes was observed in different adult tissues. Our results provide a fundamental resource for further investigating the functions of Sox genes in embryonic processes, sex determination and differentiation as well as controlling the homeostasis of adult tissues in spotted sea bass.
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Affiliation(s)
- Bingyu Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Yuan Tian
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Haishen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Xin Qi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Lingyu Wang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Jingru Zhang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Jinku Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Ximeng Dong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Kaiqiang Zhang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Yun Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China.
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17
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Feng GJ, Wei XT, Zhang H, Yang XL, Shen H, Tian Q, Deng HW, Zhang L, Pei YF. Identification of pleiotropic loci underlying hip bone mineral density and trunk lean mass. J Hum Genet 2021; 66:251-260. [PMID: 32929176 PMCID: PMC7880826 DOI: 10.1038/s10038-020-00835-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/15/2020] [Accepted: 08/24/2020] [Indexed: 11/09/2022]
Abstract
Bone mineral density (BMD) and lean body mass (LBM) not only have a considerable heritability each, but also are genetically correlated. However, common genetic determinants shared by both traits are largely unknown. In the present study, we performed a bivariate genome-wide association study (GWAS) meta-analysis of hip BMD and trunk lean mass (TLM) in 11,335 subjects from 6 samples, and performed replication in estimated heel BMD and TLM in 215,234 UK Biobank (UKB) participants. We identified 2 loci that nearly attained the genome-wide significance (GWS, p < 5.0 × 10-8) level in the discovery GWAS meta-analysis and that were successfully replicated in the UKB sample: 11p15.2 (lead SNP rs12800228, discovery p = 2.88 × 10-7, replication p = 1.95 × 10-4) and 18q21.32 (rs489693, discovery p = 1.67 × 10-7, replication p = 1.17 × 10-3). The above 2 pleiotropic loci may play a pleiotropic role for hip BMD and TLM development. So our findings provide useful insights that further enhance our understanding of genetic interplay between BMD and LBM.
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Affiliation(s)
- Gui-Juan Feng
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, People's Republic of China
| | - Xin-Tong Wei
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, People's Republic of China
| | - Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, People's Republic of China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
| | - Xiao-Lin Yang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, People's Republic of China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China
| | - Hui Shen
- Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Qing Tian
- Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.
| | - Lei Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, People's Republic of China.
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China.
| | - Yu-Fang Pei
- Department of Epidemiology and Health Statistics, School of Public Health, Medical College of Soochow University, Jiangsu, People's Republic of China.
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Jiangsu, People's Republic of China.
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18
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Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep. Sci Rep 2021; 11:2466. [PMID: 33510350 PMCID: PMC7844035 DOI: 10.1038/s41598-021-81932-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
The identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.
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19
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Narumi R, Liu S, Ikeda N, Morita O, Tasaki J. Chemical-Induced Cleft Palate Is Caused and Rescued by Pharmacological Modulation of the Canonical Wnt Signaling Pathway in a Zebrafish Model. Front Cell Dev Biol 2020; 8:592967. [PMID: 33381503 PMCID: PMC7767894 DOI: 10.3389/fcell.2020.592967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/02/2020] [Indexed: 11/13/2022] Open
Abstract
Cleft palate is one of the most frequent birth defects worldwide. It causes severe problems regarding eating and speaking and requires long-term treatment. Effective prenatal treatment would contribute to reducing the risk of cleft palate. The canonical Wnt signaling pathway is critically involved in palatogenesis, and genetic or chemical disturbance of this signaling pathway leads to cleft palate. Presently, preventative treatment for cleft palate during prenatal development has limited efficacy, but we expect that zebrafish will provide a useful high-throughput chemical screening model for effective prevention. To achieve this, the zebrafish model should recapitulate cleft palate development and its rescue by chemical modulation of the Wnt pathway. Here, we provide proof of concept for a zebrafish chemical screening model. Zebrafish embryos were treated with 12 chemical reagents known to induce cleft palate in mammals, and all 12 chemicals induced cleft palate characterized by decreased proliferation and increased apoptosis of palatal cells. The cleft phenotype was enhanced by combinatorial treatment with Wnt inhibitor and teratogens. Furthermore, the expression of tcf7 and lef1 as a readout of the pathway was decreased. Conversely, cleft palate was prevented by Wnt agonist and the cellular defects were also prevented. In conclusion, we provide evidence that chemical-induced cleft palate is caused by inhibition of the canonical Wnt pathway. Our results indicate that this zebrafish model is promising for chemical screening for prevention of cleft palate as well as modulation of the Wnt pathway as a therapeutic target.
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Affiliation(s)
- Rika Narumi
- R&D, Safety Science Research, Kao Corporation, Kawasaki, Japan
| | - Shujie Liu
- R&D, Safety Science Research, Kao Corporation, Ichikai-machi, Japan
| | - Naohiro Ikeda
- R&D, Safety Science Research, Kao Corporation, Kawasaki, Japan
| | - Osamu Morita
- R&D, Safety Science Research, Kao Corporation, Ichikai-machi, Japan
| | - Junichi Tasaki
- R&D, Safety Science Research, Kao Corporation, Kawasaki, Japan
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20
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Li J, Yang T, Tang H, Sha Z, Chen R, Chen L, Yu Y, Rowe GC, Das S, Xiao J. Inhibition of lncRNA MAAT Controls Multiple Types of Muscle Atrophy by cis- and trans-Regulatory Actions. Mol Ther 2020; 29:1102-1119. [PMID: 33279721 DOI: 10.1016/j.ymthe.2020.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/09/2020] [Accepted: 11/29/2020] [Indexed: 12/18/2022] Open
Abstract
Muscle atrophy is associated with negative outcomes in a variety of diseases. Identification of a common therapeutic target would address a significant unmet clinical need. Here, we identify a long non-coding RNA (lncRNA) (muscle-atrophy-associated transcript, lncMAAT) as a common regulator of skeletal muscle atrophy. lncMAAT is downregulated in multiple types of muscle-atrophy models both in vivo (denervation, Angiotensin II [AngII], fasting, immobilization, and aging-induced muscle atrophy) and in vitro (AngII, H2O2, and tumor necrosis factor alpha [TNF-α]-induced muscle atrophy). Gain- and loss-of-function analysis both in vitro and in vivo reveals that downregulation of lncMAAT is sufficient to induce muscle atrophy, while overexpression of lncMAAT can ameliorate multiple types of muscle atrophy. Mechanistically, lncMAAT negatively regulates the transcription of miR-29b through SOX6 by a trans-regulatory module and increases the expression of the neighboring gene Mbnl1 by a cis-regulatory module. Therefore, overexpression of lncMAAT may represent a promising therapy for muscle atrophy induced by different stimuli.
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Affiliation(s)
- Jin Li
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Sciences, Shanghai University, Shanghai 200444, China; School of Medicine, Shanghai University, Shanghai 200444, China
| | - Tingting Yang
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Haifei Tang
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Zhao Sha
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Rui Chen
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- Department of Spine Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Yan Yu
- Department of Spine Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Glenn C Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02214, USA
| | - Junjie Xiao
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Sciences, Shanghai University, Shanghai 200444, China; School of Medicine, Shanghai University, Shanghai 200444, China.
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21
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miRNA-mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome. Sci Rep 2020; 10:10619. [PMID: 32606372 PMCID: PMC7326969 DOI: 10.1038/s41598-020-67482-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/08/2020] [Indexed: 12/23/2022] Open
Abstract
Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. However, the molecular mechanism for determining muscle fiber types in chickens was hardly understood. In this study, we used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. Among the 44,705 identified mRNAs in the two types of muscles, 3,457 exhibited significantly different expression patterns, including 2,364 up-regulated and 1,093 down-regulated mRNAs in the SART. A total of 698 chicken miRNAs were identified, including 189 novel miRNAs, among which 67 differentially expressed miRNAs containing 42 up-regulated and 25 down-regulated miRNAs in the SART were identified. Furthermore, function enrichment showed that the differentially expressed mRNAs and miRNAs were involved in energy metabolism, muscle contraction, and calcium, peroxisome proliferator-activated receptor (PPAR), insulin and adipocytokine signaling. Using miRNA-mRNA integrated analysis, we identified several candidate miRNA-gene pairs that might affect muscle fiber performance, viz, gga-miR-499-5p/SOX6 and gga-miR-196-5p/CALM1, which were supported by target validation using the dual-luciferase reporter system. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens.
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22
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Hromowyk KJ, Talbot JC, Martin BL, Janssen PML, Amacher SL. Cell fusion is differentially regulated in zebrafish post-embryonic slow and fast muscle. Dev Biol 2020; 462:85-100. [PMID: 32165147 PMCID: PMC7225055 DOI: 10.1016/j.ydbio.2020.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 02/08/2020] [Accepted: 03/03/2020] [Indexed: 12/13/2022]
Abstract
Skeletal muscle fusion occurs during development, growth, and regeneration. To investigate how muscle fusion compares among different muscle cell types and developmental stages, we studied muscle cell fusion over time in wild-type, myomaker (mymk), and jam2a mutant zebrafish. Using live imaging, we show that embryonic myoblast elongation and fusion correlate tightly with slow muscle cell migration. In wild-type embryos, only fast muscle fibers are multinucleate, consistent with previous work showing that the cell fusion regulator gene mymk is specifically expressed throughout the embryonic fast muscle domain. However, by 3 weeks post-fertilization, slow muscle fibers also become multinucleate. At this late-larval stage, mymk is not expressed in muscle fibers, but is expressed in small cells near muscle fibers. Although previous work showed that both mymk and jam2a are required for embryonic fast muscle cell fusion, we observe that muscle force and function is almost normal in mymk and jam2a mutant embryos, despite the lack of fast muscle multinucleation. We show that genetic requirements change post-embryonically, with jam2a becoming much less important by late-larval stages and mymk now required for muscle fusion and growth in both fast and slow muscle cell types. Correspondingly, adult mymk mutants perform poorly in sprint and endurance tests compared to wild-type and jam2a mutants. We show that adult mymk mutant muscle contains small mononucleate myofibers with average myonuclear domain size equivalent to that in wild type adults. The mymk mutant fibers have decreased Laminin expression and increased numbers of Pax7-positive cells, suggesting that impaired fiber growth and active regeneration contribute to the muscle phenotype. Our findings identify several aspects of muscle fusion that change with time in slow and fast fibers as zebrafish develop beyond embryonic stages.
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Affiliation(s)
- Kimberly J Hromowyk
- Department of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH, 43210, USA; Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Jared C Talbot
- Department of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH, 43210, USA.
| | - Brit L Martin
- Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH, 43210, USA; Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, 43210, USA; Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Paul M L Janssen
- Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH, 43210, USA; Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210, USA; Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
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23
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Pellerin D, Aykanat A, Ellezam B, Troiano EC, Karamchandani J, Dicaire MJ, Petitclerc M, Robertson R, Allard-Chamard X, Brunet D, Konersman CG, Mathieu J, Warman Chardon J, Gupta VA, Beggs AH, Brais B, Chrestian N. Novel Recessive TNNT1 Congenital Core-Rod Myopathy in French Canadians. Ann Neurol 2020; 87:568-583. [PMID: 31970803 DOI: 10.1002/ana.25685] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 01/06/2020] [Accepted: 01/19/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Recessive null variants of the slow skeletal muscle troponin T1 (TNNT1) gene are a rare cause of nemaline myopathy that is fatal in infancy due to respiratory insufficiency. Muscle biopsy shows rods and fiber type disproportion. We report on 4 French Canadians with a novel form of recessive congenital TNNT1 core-rod myopathy. METHODS Patients underwent full clinical characterization, lower limb magnetic resonance imaging (MRI), muscle biopsy, and genetic testing. A zebrafish loss-of-function model using morpholinos was created to assess the pathogenicity of the identified variant. Wild-type or mutated human TNNT1 mRNAs were coinjected with morpholinos to assess their abilities to rescue the morphant phenotype. RESULTS Three adults and 1 child shared a novel missense homozygous variant in the TNNT1 gene (NM_003283.6: c.287T > C; p.Leu96Pro). They developed from childhood very slowly progressive limb-girdle weakness with rigid spine and disabling contractures. They suffered from restrictive lung disease requiring noninvasive mechanical ventilation in 3 patients, as well as recurrent episodes of rhabdomyolysis triggered by infections, which were relieved by dantrolene in 1 patient. Older patients remained ambulatory into their 60s. MRI of the leg muscles showed fibrofatty infiltration predominating in the posterior thigh and the deep posterior leg compartments. Muscle biopsies showed multiminicores and lobulated fibers, rods in half the patients, and no fiber type disproportion. Wild-type TNNT1 mRNA rescued the zebrafish morphants, but mutant transcripts failed to do so. INTERPRETATION This study expands the phenotypic spectrum of TNNT1 myopathy and provides functional evidence for the pathogenicity of the newly identified missense mutation. ANN NEUROL 2020;87:568-583.
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Affiliation(s)
- David Pellerin
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
| | - Asli Aykanat
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, Quebec, Canada
| | - Emily C Troiano
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Jason Karamchandani
- Department of Pathology, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
| | - Marie-Josée Dicaire
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
| | - Marc Petitclerc
- Department of Neurology, Hôpital Hôtel-Dieu de Lévis, Lévis, Quebec, Canada
| | - Rebecca Robertson
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
| | - Xavier Allard-Chamard
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada
| | - Denis Brunet
- Department of Neurology, Hôpital de l'Enfant Jésus, Université Laval, Quebec City, Quebec, Canada
| | | | - Jean Mathieu
- Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.,Neuromuscular Disease Clinic, Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Jonquière, Quebec, Canada
| | - Jodi Warman Chardon
- Department of Neurosciences, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Vandana A Gupta
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, Quebec, Canada.,Neuromuscular Disease Clinic, Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Jonquière, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Nicolas Chrestian
- Department of Child Neurology, Centre Hospitalier de l'Université Laval et Centre Mère-Enfant Soleil, Université Laval, Quebec City, Quebec, Canada
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24
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Abstract
The zebrafish (Danio rerio) has emerged as a widely used model system during the last four decades. The fact that the zebrafish larva is transparent enables sophisticated in vivo imaging, including calcium imaging of intracellular transients in many different tissues. While being a vertebrate, the reduced complexity of its nervous system and small size make it possible to follow large-scale activity in the whole brain. Its genome is sequenced and many genetic and molecular tools have been developed that simplify the study of gene function in health and disease. Since the mid 90's, the development and neuronal function of the embryonic, larval, and later, adult zebrafish have been studied using calcium imaging methods. This updated chapter is reviewing the advances in methods and research findings of zebrafish calcium imaging during the last decade. The choice of calcium indicator depends on the desired number of cells to study and cell accessibility. Synthetic calcium indicators, conjugated to dextrans and acetoxymethyl (AM) esters, are still used to label specific neuronal cell types in the hindbrain and the olfactory system. However, genetically encoded calcium indicators, such as aequorin and the GCaMP family of indicators, expressed in various tissues by the use of cell-specific promoters, are now the choice for most applications, including brain-wide imaging. Calcium imaging in the zebrafish has contributed greatly to our understanding of basic biological principles during development and adulthood, and the function of disease-related genes in a vertebrate system.
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25
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Madelaine R, Notwell JH, Skariah G, Halluin C, Chen CC, Bejerano G, Mourrain P. A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human. Nucleic Acids Res 2019. [PMID: 29518216 PMCID: PMC5909433 DOI: 10.1093/nar/gky166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thousands of human disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding genome, but only a handful have been demonstrated to affect gene expression and human biology. We computationally identified risk-associated SNPs in deeply conserved non-exonic elements (CNEs) potentially contributing to 45 human diseases. We further demonstrated that human CNE1/rs17421627 associated with retinal vasculature defects showed transcriptional activity in the zebrafish retina, while introducing the risk-associated allele completely abolished CNE1 enhancer activity. Furthermore, deletion of CNE1 led to retinal vasculature defects and to a specific downregulation of microRNA-9, rather than MEF2C as predicted by the original genome-wide association studies. Consistent with these results, miR-9 depletion affects retinal vasculature formation, demonstrating MIR-9-2 as a critical gene underpinning the associated trait. Importantly, we validated that other CNEs act as transcriptional enhancers that can be disrupted by conserved non-coding SNPs. This study uncovers disease-associated non-coding mutations that are deeply conserved, providing a path for in vivo testing to reveal their cis-regulated genes and biological roles.
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Affiliation(s)
- Romain Madelaine
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA
| | | | - Gemini Skariah
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA
| | - Caroline Halluin
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA
| | | | - Gill Bejerano
- Department of Computer Science, Stanford, CA 94305, USA.,Department of Developmental Biology, Stanford, CA 94305, USA.,Division of Medical Genetics, Department of Pediatrics, Stanford, CA 94305, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA.,INSERM 1024, Ecole Normale Supérieure Paris, 75005, France
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26
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Khanshour AM, Kou I, Fan Y, Einarsdottir E, Makki N, Kidane YH, Kere J, Grauers A, Johnson TA, Paria N, Patel C, Singhania R, Kamiya N, Takeda K, Otomo N, Watanabe K, Luk KDK, Cheung KMC, Herring JA, Rios JJ, Ahituv N, Gerdhem P, Gurnett CA, Song YQ, Ikegawa S, Wise CA. Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci. Hum Mol Genet 2019; 27:3986-3998. [PMID: 30395268 DOI: 10.1093/hmg/ddy306] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common musculoskeletal disorder of childhood development. The genetic architecture of AIS is complex, and the great majority of risk factors are undiscovered. To identify new AIS susceptibility loci, we conducted the first genome-wide meta-analysis of AIS genome-wide association studies, including 7956 cases and 88 459 controls from 3 ancestral groups. Three novel loci that surpassed genome-wide significance were uncovered in intragenic regions of the CDH13 (P-value_rs4513093 = 1.7E-15), ABO (P-value_ rs687621 = 7.3E-10) and SOX6 (P-value_rs1455114 = 2.98E-08) genes. Restricting the analysis to females improved the associations at multiple loci, most notably with variants within CDH13 despite the reduction in sample size. Genome-wide gene-functional enrichment analysis identified significant perturbation of pathways involving cartilage and connective tissue development. Expression of both SOX6 and CDH13 was detected in cartilage chondrocytes and chromatin immunoprecipitation sequencing experiments in that tissue revealed multiple HeK27ac-positive peaks overlapping associated loci. Our results further define the genetic architecture of AIS and highlight the importance of vertebral cartilage development in its pathogenesis.
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Affiliation(s)
- Anas M Khanshour
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Ikuyo Kou
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Biosciences & Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nadja Makki
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yared H Kidane
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, 00014 University of Helsinki, Finland.,Molecular Neurology Research Program, University of Helsinki, 00014 University of Helsinki, Finland.,Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London SE1 9RT, UK.,Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden
| | - Anna Grauers
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Sundsvall and Härnösand County Hospital, Sundsvall, Sweden
| | - Todd A Johnson
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nandina Paria
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | - Chandreshkumar Patel
- McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Richa Singhania
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA
| | | | - Kazuki Takeda
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Nao Otomo
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.,Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Keith D K Luk
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - Kenneth M C Cheung
- Department of Orthopaedics & Traumatology, The University of Hong Kong, Hong Kong, China
| | - John A Herring
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan J Rios
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nadav Ahituv
- Department of Bioengineering & Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Gerdhem
- Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, K54 Huddinge, Stockholm, Sweden.,Department of Orthopedics, Karolinska University Hospital, K54 Huddinge, Stockholm, Sweden
| | - Christina A Gurnett
- Department of Neurology, School of Medicine, Washington University, St. Louis, MO, USA
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Shiro Ikegawa
- Laboratory of Bone & Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Carol A Wise
- Sarah M. & Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, TX, USA.,McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Orthopaedic Surgery, Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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27
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Kelu JJ, Webb SE, Galione A, Miller AL. Characterization of ADP-ribosyl cyclase 1-like (ARC1-like) activity and NAADP signaling during slow muscle cell development in zebrafish embryos. Dev Biol 2018; 445:211-225. [PMID: 30447180 DOI: 10.1016/j.ydbio.2018.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
We recently demonstrated the requirement of two-pore channel type 2 (TPC2)-mediated Ca2+ release during slow muscle cell differentiation and motor circuit maturation in intact zebrafish embryos. However, the upstream trigger(s) of TPC2/Ca2+ signaling during these developmental processes remains unclear. Nicotinic acid adenine dinucleotide phosphate (NAADP) is a potent Ca2+ mobilizing messenger, which is suggested to target TPC2 in mediating the release of Ca2+ from acidic vesicles. Here, we report the molecular cloning of the zebrafish ADP ribosyl cyclase (ARC) homolog (i.e., ARC1-like), which is a putative enzyme for generating NAADP. We characterized the expression of the arc1-like transcript and the NAADP levels between ~ 16 h post-fertilization (hpf) and ~ 48 hpf in whole zebrafish embryos. We showed that if ARC1-like (when fused with either EGFP or tdTomato) was overexpressed it localized in the plasma membrane, and associated with intracellular organelles, such as the acidic vesicles, Golgi complex and sarcoplasmic reticulum, in primary muscle cell cultures. Morpholino (MO)-mediated knockdown of arc1-like or pharmacological inhibition of ARC1-like (via treatment with nicotinamide), led to an attenuation of Ca2+ signaling and disruption of slow muscle cell development. In addition, the injection of arc1-like mRNA into ARC1-like morphants partially rescued the Ca2+ signals and slow muscle cell development. Together, our data might suggest a link between ARC1-like, NAADP, TPC2 and Ca2+ signaling during zebrafish myogenesis.
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Affiliation(s)
- Jeffrey J Kelu
- Division of Life Science&State Key Laboratory of Molecular Neuroscience, HKUST, Hong Kong
| | - Sarah E Webb
- Division of Life Science&State Key Laboratory of Molecular Neuroscience, HKUST, Hong Kong
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Andrew L Miller
- Division of Life Science&State Key Laboratory of Molecular Neuroscience, HKUST, Hong Kong.
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28
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Wang X, Chen X, Huang Z, Chen D, Yu B, Chen H, He J, Zheng P, Luo J, Yu J, Luo Y. Effects of active immunization against porcine Sox6 on meat quality and myosin heavy chain isoform expression in growing-finishing pigs. Anim Biotechnol 2018; 30:260-266. [PMID: 30264664 DOI: 10.1080/10495398.2018.1481416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A feeding trial for 91 days was conducted to investigate effects of active immunization against porcine Sox6 (pSox6) on meat quality and myosin heavy chain (MyHC) isoform expression in growing-finishing pigs. Twenty-four castrated Duroc × Landrace × Yarkshire pigs were randomly divided into three groups: (1) Control group; (2) 1 mg/head pSox6 active immunity group; (3) 4 mg/head pSox6 active immunity group (4 mg/head group). The results showed that pigs in 4 mg/head group had a greater a* (Redness) and a higher marbling score, while no significant effect was observed in L* (Lightness), b* (Yellowness), intramuscular fat and cooking loss. Muscle succinic dehydrogenase activity in pSox6 active immunization groups was significantly increased, and muscle lactate dehydrogenase activity was significantly reduced. Meanwhile, active immunization against pSox6 upregulated the mRNA expression of MyHC I, while no effect was observed on the mRNA expressions of MyHC IIa, MyHC IIx, MyHC IIb. In addition, pigs in the 4 mg/head group exhibited lower Sox6 mRNA level and higher MyHC I protein level, while no significant influence was observed on MyHC IIb protein level. Together, our data imply that active immunization against pSox6 could improve the pork quality and promote the MyHC I expression in growing-finishing pigs.
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Affiliation(s)
- Xiaoqin Wang
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Xiaoling Chen
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Zhiqing Huang
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Daiwen Chen
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Bing Yu
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Hong Chen
- b College of Food Science , Sichuan Agricultural University , Yaan , Sichuan , PR China
| | - Jun He
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Ping Zheng
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Junqiu Luo
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Jie Yu
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
| | - Yuheng Luo
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , PR China
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29
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Lin S, Lin X, Zhang Z, Jiang M, Rao Y, Nie Q, Zhang X. Copy Number Variation in SOX6 Contributes to Chicken Muscle Development. Genes (Basel) 2018; 9:genes9010042. [PMID: 29342086 PMCID: PMC5793193 DOI: 10.3390/genes9010042] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 11/16/2022] Open
Abstract
Copy number variations (CNVs), which cover many functional genes, are associated with complex diseases, phenotypic diversity and traits that are economically important to raising chickens. The sex-determining region Y-box 6 (Sox6) plays a key role in fast-twitch muscle fiber differentiation of zebrafish and mice, but it is still unknown whether SOX6 plays a role in chicken skeletal muscle development. We identified two copy number polymorphisms (CNPs) which were significantly related to different traits on the genome level in chickens by AccuCopy® and CNVplex® analyses. Notably, five white recessive rock (CN = 1, CN = 3) variant individuals and two Xinghua (CN = 3) variant individuals contain a CNP13 (chromosome5: 10,500,294-10,675,531) which overlaps with SOX6. There is a disordered region in SOX6 proteins 265-579 aa coded by a partial CNV overlapping region. A quantitative real-time polymerase chain reaction showed that the expression level of SOX6 mRNA was positively associated with CNV and highly expressed during the skeletal muscle cell differentiation in chickens. After the knockdown of the SOX6, the expression levels of IGFIR1, MYF6, SOX9, SHOX and CCND1 were significantly down-regulated. All of them directly linked to muscle development. These results suggest that the number of CNVs in the CNP13 is positively associated with the expression level of SOX6, which promotes the proliferation and differentiation of skeletal muscle cells by up-regulating the expression levels of the muscle-growth-related genes in chickens as in other animal species.
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Affiliation(s)
- Shudai Lin
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Xiran Lin
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Zihao Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Mingya Jiang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Yousheng Rao
- Department of Biological Technology, Nanchang Normal University, Nanchang 330029, China.
| | - Qinghua Nie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science of South China Agricultural University, Guangzhou 510642, China.
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30
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Taglietti V, Maroli G, Cermenati S, Monteverde S, Ferrante A, Rossi G, Cossu G, Beltrame M, Messina G. Nfix Induces a Switch in Sox6 Transcriptional Activity to Regulate MyHC-I Expression in Fetal Muscle. Cell Rep 2017; 17:2354-2366. [PMID: 27880909 PMCID: PMC5149531 DOI: 10.1016/j.celrep.2016.10.082] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/08/2016] [Accepted: 10/24/2016] [Indexed: 02/01/2023] Open
Abstract
Sox6 belongs to the Sox gene family and plays a pivotal role in fiber type differentiation, suppressing transcription of slow-fiber-specific genes during fetal development. Here, we show that Sox6 plays opposite roles in MyHC-I regulation, acting as a positive and negative regulator of MyHC-I expression during embryonic and fetal myogenesis, respectively. During embryonic myogenesis, Sox6 positively regulates MyHC-I via transcriptional activation of Mef2C, whereas during fetal myogenesis, Sox6 requires and cooperates with the transcription factor Nfix in repressing MyHC-I expression. Mechanistically, Nfix is necessary for Sox6 binding to the MyHC-I promoter and thus for Sox6 repressive function, revealing a key role for Nfix in driving Sox6 activity. This feature is evolutionarily conserved, since the orthologs Nfixa and Sox6 contribute to repression of the slow-twitch phenotype in zebrafish embryos. These data demonstrate functional cooperation between Sox6 and Nfix in regulating MyHC-I expression during prenatal muscle development. Sox6 has opposite roles in MyHC-I regulation during embryonic and fetal myogenesis In embryonic muscle, Sox6 enhances MyHC-I expression via regulation of Mef2C In fetal muscle, Nfix is required for Sox6-mediated repression of MyHC-I The Sox6 and Nfixa orthologs cooperate in repressing smyhc1 in zebrafish
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Affiliation(s)
| | - Giovanni Maroli
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Solei Cermenati
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | | | - Andrea Ferrante
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Giuliana Rossi
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Giulio Cossu
- Department of Biosciences, University of Milan, Milan 20133, Italy; Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Oxford Road, M13 9PL Manchester, UK
| | - Monica Beltrame
- Department of Biosciences, University of Milan, Milan 20133, Italy
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Berberoglu MA, Gallagher TL, Morrow ZT, Talbot JC, Hromowyk KJ, Tenente IM, Langenau DM, Amacher SL. Satellite-like cells contribute to pax7-dependent skeletal muscle repair in adult zebrafish. Dev Biol 2017; 424:162-180. [PMID: 28279710 DOI: 10.1016/j.ydbio.2017.03.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/02/2017] [Accepted: 03/05/2017] [Indexed: 12/24/2022]
Abstract
Satellite cells, also known as muscle stem cells, are responsible for skeletal muscle growth and repair in mammals. Pax7 and Pax3 transcription factors are established satellite cell markers required for muscle development and regeneration, and there is great interest in identifying additional factors that regulate satellite cell proliferation, differentiation, and/or skeletal muscle regeneration. Due to the powerful regenerative capacity of many zebrafish tissues, even in adults, we are exploring the regenerative potential of adult zebrafish skeletal muscle. Here, we show that adult zebrafish skeletal muscle contains cells similar to mammalian satellite cells. Adult zebrafish satellite-like cells have dense heterochromatin, express Pax7 and Pax3, proliferate in response to injury, and show peak myogenic responses 4-5 days post-injury (dpi). Furthermore, using a pax7a-driven GFP reporter, we present evidence implicating satellite-like cells as a possible source of new muscle. In lieu of central nucleation, which distinguishes regenerating myofibers in mammals, we describe several characteristics that robustly identify newly-forming myofibers from surrounding fibers in injured adult zebrafish muscle. These characteristics include partially overlapping expression in satellite-like cells and regenerating myofibers of two RNA-binding proteins Rbfox2 and Rbfoxl1, known to regulate embryonic muscle development and function. Finally, by analyzing pax7a; pax7b double mutant zebrafish, we show that Pax7 is required for adult skeletal muscle repair, as it is in the mouse.
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Affiliation(s)
- Michael A Berberoglu
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Thomas L Gallagher
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Zachary T Morrow
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Jared C Talbot
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Kimberly J Hromowyk
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA
| | - Inês M Tenente
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Molecular Pathology and Regenerative Medicine, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David M Langenau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Molecular Pathology and Regenerative Medicine, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sharon L Amacher
- Departments of Molecular Genetics and Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children's Hospital, Columbus, OH 43210, USA.
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Abstract
Skeletal muscle performs an essential function in human physiology with defects in genes encoding a variety of cellular components resulting in various types of inherited muscle disorders. Muscular dystrophies (MDs) are a severe and heterogeneous type of human muscle disease, manifested by progressive muscle wasting and degeneration. The disease pathogenesis and therapeutic options for MDs have been investigated for decades using rodent models, and considerable knowledge has been accumulated on the cause and pathogenetic mechanisms of this group of human disorders. However, due to some differences between disease severity and progression, what is learned in mammalian models does not always transfer to humans, prompting the desire for additional and alternative models. More recently, zebrafish have emerged as a novel and robust animal model for the study of human muscle disease. Zebrafish MD models possess a number of distinct advantages for modeling human muscle disorders, including the availability and ease of generating mutations in homologous disease-causing genes, the ability to image living muscle tissue in an intact animal, and the suitability of zebrafish larvae for large-scale chemical screens. In this chapter, we review the current understanding of molecular and cellular mechanisms involved in MDs, the process of myogenesis in zebrafish, and the structural and functional characteristics of zebrafish larval muscles. We further discuss the insights gained from the key zebrafish MD models that have been so far generated, and we summarize the attempts that have been made to screen for small molecules inhibitors of the dystrophic phenotypes using these models. Overall, these studies demonstrate that zebrafish is a useful in vivo system for modeling aspects of human skeletal muscle disorders. Studies using these models have contributed both to the understanding of the pathogenesis of muscle wasting disorders and demonstrated their utility as highly relevant models to implement therapeutic screening regimens.
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Affiliation(s)
- M Li
- Monash University, Clayton, VIC, Australia
| | - K J Hromowyk
- The Ohio State University, Columbus, OH, United States
| | - S L Amacher
- The Ohio State University, Columbus, OH, United States
| | - P D Currie
- Monash University, Clayton, VIC, Australia
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Identification of novel MYO18A interaction partners required for myoblast adhesion and muscle integrity. Sci Rep 2016; 6:36768. [PMID: 27824130 PMCID: PMC5099880 DOI: 10.1038/srep36768] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/20/2016] [Indexed: 01/02/2023] Open
Abstract
The unconventional myosin MYO18A that contains a PDZ domain is required for muscle integrity during zebrafish development. However, the mechanism by which it functions in myofibers is not clear. The presence of a PDZ domain suggests that MYO18A may interact with other partners to perform muscle-specific functions. Here we performed double-hybrid screening and co-immunoprecipitation to identify MYO18A-interacting proteins, and have identified p190RhoGEF and Golgin45 as novel partners for the MYO18A PDZ domain. We have also identified Lurap1, which was previously shown to bind MYO18A. Functional analyses indicate that, similarly as myo18a, knockdown of lurap1, p190RhoGEF and Golgin45 by morpholino oligonucleotides disrupts dystrophin localization at the sarcolemma and produces muscle lesions. Simultaneous knockdown of myo18a with either of these genes severely disrupts myofiber integrity and dystrophin localization, suggesting that they may function similarly to maintain myofiber integrity. We further show that MYO18A and its interaction partners are required for adhesion of myoblasts to extracellular matrix, and for the formation of the Golgi apparatus and organization of F-actin bundles in myoblast cells. These findings suggest that MYO18A has the potential to form a multiprotein complex that links the Golgi apparatus to F-actin, which regulates muscle integrity and function during early development.
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34
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Leow SC, Poschmann J, Too PG, Yin J, Joseph R, McFarlane C, Dogra S, Shabbir A, Ingham PW, Prabhakar S, Leow MKS, Lee YS, Ng KL, Chong YS, Gluckman PD, Stünkel W. The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis. Development 2016; 143:950-61. [PMID: 26893351 DOI: 10.1242/dev.131573] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/05/2016] [Indexed: 12/21/2022]
Abstract
An association between impaired fetal growth and the postnatal development of obesity has been established. Here, by comparing adipocytes differentiated from mesenchymal stem cells (MSCs) taken from the umbilical cord and derived from normal and growth-restricted neonates, we identified the transcription factor SOX6 as highly expressed only in growth-restricted individuals. We found that SOX6 regulates adipogenesis in vertebrate species by activating adipogenic regulators including PPARγ, C/EBPα and MEST. We further show that SOX6 interacts with β-catenin in adipocytes, suggesting an inhibition of WNT/β-catenin signaling, thereby promoting adipogenesis. The upstream regulatory region of the MEST gene in MSCs from growth-restricted subjects harbors hypomethylated CpGs next to SOX6 binding motifs, and we found that SOX6 binding is impaired by adjacent CpG methylation. In summary, we report that SOX6 is a novel regulator of adipogenesis synergizing with epigenetic mechanisms.
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Affiliation(s)
- Shi Chi Leow
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609
| | - Jeremie Poschmann
- Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), Singapore, Singapore 138672
| | - Peh Gek Too
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609
| | - Juan Yin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore 636921
| | - Roy Joseph
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609
| | - Craig McFarlane
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609
| | - Shaillay Dogra
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609
| | - Asim Shabbir
- Department of Surgery, National University Hospital, National University of Singapore, Singapore 119074
| | - Philip W Ingham
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore 636921 Developmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Singapore, Singapore 138673
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), Singapore, Singapore 138672
| | - Melvin K S Leow
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609 Department of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore 308433
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609 Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Kai Lyn Ng
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609 Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609 Liggins Institute, University of Auckland, Auckland 1142, New Zealand
| | - Walter Stünkel
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Singapore, Singapore 117609
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Muscle fiber type specific activation of the slow myosin heavy chain 2 promoter by a non-canonical E-box. Biochem Biophys Res Commun 2016; 469:842-7. [PMID: 26707643 DOI: 10.1016/j.bbrc.2015.12.013] [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: 11/23/2015] [Accepted: 12/02/2015] [Indexed: 11/21/2022]
Abstract
Different mechanisms control skeletal muscle fiber type gene expression at specific times in vertebrate development. Embryonic myogenesis leading to formation of primary muscle fibers in avian species is largely directed by myoblast cell commitment to the formation of diverse fiber types. In contrast, development of different secondary fiber types during fetal myogenesis is partly determined by neural influences. In both primary and secondary chicken muscle fibers, differential expression of the slow myosin heavy chain 2 (MyHC2) gene distinguishes fast from fast/slow muscle fibers. This study focused on the transcriptional regulation of the slow MyHC2 gene in primary myotubes formed from distinct fast/slow and fast myogenic cell lineages. Promoter deletion analyses identified a discrete 86 bp promoter segment that conferred fiber type, lineage-specific gene expression in fast/slow versus fast myoblast derived primary myotubes. Sequence analysis and promoter activity assays determined that this segment contains two functional cis-regulatory elements. One element is a non-canonical E-box, and electromobility shift assays demonstrated that both cis-elements interacted with the E-protein, E47. The results indicate that primary muscle fiber type specific expression of the slow MyHC2 gene is controlled by a novel mechanism involving a transcriptional complex that includes E47 at a non-canonical E-box.
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36
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Adaxial cell migration in the zebrafish embryo is an active cell autonomous property that requires the Prdm1a transcription factor. Differentiation 2015; 89:77-86. [DOI: 10.1016/j.diff.2015.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/17/2015] [Accepted: 03/17/2015] [Indexed: 02/06/2023]
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