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Chen G, Chen J, Qi L, Yin Y, Lin Z, Wen H, Zhang S, Xiao C, Bello SF, Zhang X, Nie Q, Luo W. Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation. Cell Prolif 2024; 57:e13545. [PMID: 37705195 PMCID: PMC10849790 DOI: 10.1111/cpr.13545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/08/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative splicing (AS) disruption has been linked to disorders of muscle development, as well as muscular atrophy. However, the precise changes in AS patterns that occur during myogenesis are not well understood. Here, we employed isoform long-reads RNA-seq (Iso-seq) and single-cell RNA-seq (scRNA-seq) to investigate the AS landscape during myogenesis. Our Iso-seq data identified 61,146 full-length isoforms representing 11,682 expressed genes, of which over 52% were novel. We identified 38,022 AS events, with most of these events altering coding sequences and exhibiting stage-specific splicing patterns. We identified AS dynamics in different types of muscle cells through scRNA-seq analysis, revealing genes essential for the contractile muscle system and cytoskeleton that undergo differential splicing across cell types. Gene-splicing analysis demonstrated that AS acts as a regulator, independent of changes in overall gene expression. Two isoforms of splicing factor TRA2B play distinct roles in myogenic differentiation by triggering AS of TGFBR2 to regulate canonical TGF-β signalling cascades differently. Our study provides a valuable transcriptome resource for myogenesis and reveals the complexity of AS and its regulation during myogenesis.
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Affiliation(s)
- Genghua Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lin Qi
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Yunqian Yin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Zetong Lin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Huaqiang Wen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Shuai Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Chuanyun Xiao
- Human and Animal PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Semiu Folaniyi Bello
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Xiquan Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Qinghua Nie
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Wen Luo
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
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Berkholz J, Schmitt A, Fragasso A, Schmid AC, Munz B. Smyd1: Implications for novel approaches in rhabdomyosarcoma therapy. Exp Cell Res 2024; 434:113863. [PMID: 38097153 DOI: 10.1016/j.yexcr.2023.113863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
Rhabdomyosarcoma (RMS), a tumor that consists of poorly differentiated skeletal muscle cells, is the most common soft-tissue sarcoma in children. Despite considerable progress within the last decades, therapeutic options are still limited, warranting the need for novel approaches. Recent data suggest deregulation of the Smyd1 protein, a sumoylation target as well as H3K4me2/3 methyltransferase and transcriptional regulator in myogenesis, and its binding partner skNAC, in RMS cells. Here, we show that despite the fact that most RMS cells express at least low levels of Smyd1 and skNAC, failure to upregulate expression of these genes in reaction to differentiation-promoting signals can always be observed. While overexpression of the Smyd1 gene enhances many aspects of RMS cell differentiation and inhibits proliferation rate and metastatic potential of these cells, functional integrity of the putative Smyd1 sumoylation motif and its SET domain, the latter being crucial for HMT activity, appear to be prerequisites for most of these effects. Based on these findings, we explored the potential for novel RMS therapeutic strategies, employing small-molecule compounds to enhance Smyd1 activity. In particular, we tested manipulation of (a) Smyd1 sumoylation, (b) stability of H3K4me2/3 marks, and (c) calpain activity, with calpains being important targets of Smyd1 in myogenesis. We found that specifically the last strategy might represent a promising approach, given that suitable small-molecule compounds will be available for clinical use in the future.
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Affiliation(s)
- Janine Berkholz
- Charité - University Medicine Berlin, Institute of Physiology, Charitéplatz 1, D-10117, Berlin, Germany
| | - Angelika Schmitt
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Annunziata Fragasso
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Anna-Celina Schmid
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Barbara Munz
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany; Interfaculty Research Institute for Sport and Physical Activity, Eberhard Karls University of Tübingen, D-72074 / D-72076, Tübingen, Germany.
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3
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Differential plasma protein expression after ingestion of essential amino acid-based dietary supplement verses whey protein in low physical functioning older adults. GeroScience 2023:10.1007/s11357-023-00725-5. [PMID: 36720768 PMCID: PMC10400527 DOI: 10.1007/s11357-023-00725-5] [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: 06/24/2022] [Accepted: 01/02/2023] [Indexed: 02/02/2023] Open
Abstract
In a recent randomized, double-blind, placebo-controlled trial, we were able to demonstrate the superiority of a dietary supplement composed of essential amino acids (EAAs) over whey protein, in older adults with low physical function. In this paper, we describe the comparative plasma protein expression in the same subject groups of EAAs vs whey. The plasma proteomics data was generated using SOMA scan assay. A total of twenty proteins were found to be differentially expressed in both groups with a 1.5-fold change. Notably, five proteins showed a significantly higher fold change expression in the EAA group which included adenylate kinase isoenzyme 1, casein kinase II 2-alpha, Nascent polypeptide-associated complex subunit alpha, peroxiredoxin-1, and peroxiredoxin-6. These five proteins might have played a significant role in providing energy for the improved cardiac and muscle strength of older adults with LPF. On the other hand, fifteen proteins showed slightly lower fold change expression in the EAA group. Some of these 15 proteins regulate metabolism and were found to be associated with inflammation or other comorbidities. Gene Ontology (GO) enrichment analysis showed the association of these proteins with several biological processes. Furthermore, protein-protein interaction network analysis also showed distinct networks between upregulated and downregulated proteins. In conclusion, the important biological roles of the upregulated proteins plus better physical function of participants in the EAAs vs whey group demonstrated that EAAs have the potential to improve muscle strength and physical function in older adults. This study was registered with ClinicalTrials.gov: NCT03424265 "Nutritional interventions in heart failure."
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Welch N, Singh SS, Musich R, Mansuri MS, Bellar A, Mishra S, Chelluboyina AK, Sekar J, Attaway AH, Li L, Willard B, Hornberger TA, Dasarathy S. Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes. iScience 2022; 25:105325. [PMID: 36345342 PMCID: PMC9636548 DOI: 10.1016/j.isci.2022.105325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Skeletal muscle generation of ammonia, an endogenous cytotoxin, is increased during exercise. Perturbations in ammonia metabolism consistently occur in chronic diseases, and may blunt beneficial skeletal muscle molecular responses and protein homeostasis with exercise. Phosphorylation of skeletal muscle proteins mediates cellular signaling responses to hyperammonemia and exercise. Comparative bioinformatics and machine learning-based analyses of published and experimentally derived phosphoproteomics data identified differentially expressed phosphoproteins that were unique and shared between hyperammonemic murine myotubes and skeletal muscle from exercise models. Enriched processes identified in both hyperammonemic myotubes and muscle from exercise models with selected experimental validation included protein kinase A (PKA), calcium signaling, mitogen-activated protein kinase (MAPK) signaling, and protein homeostasis. Our approach of feature extraction from comparative untargeted "omics" data allows for selection of preclinical models that recapitulate specific human exercise responses and potentially optimize functional capacity and skeletal muscle protein homeostasis with exercise in chronic diseases.
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Affiliation(s)
- Nicole Welch
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shashi Shekhar Singh
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan Musich
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - M. Shahid Mansuri
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Annette Bellar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Saurabh Mishra
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Jinendiran Sekar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amy H. Attaway
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ling Li
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Belinda Willard
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Troy A. Hornberger
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
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Schroeder AM, Nielsen T, Lynott M, Vogler G, Colas AR, Bodmer R. Nascent polypeptide-Associated Complex and Signal Recognition Particle have cardiac-specific roles in heart development and remodeling. PLoS Genet 2022; 18:e1010448. [PMID: 36240221 PMCID: PMC9604979 DOI: 10.1371/journal.pgen.1010448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/26/2022] [Accepted: 09/27/2022] [Indexed: 11/25/2022] Open
Abstract
Establishing a catalog of Congenital Heart Disease (CHD) genes and identifying functional networks would improve our understanding of its oligogenic underpinnings. Our studies identified protein biogenesis cofactors Nascent polypeptide-Associated Complex (NAC) and Signal-Recognition-Particle (SRP) as disease candidates and novel regulators of cardiac differentiation and morphogenesis. Knockdown (KD) of the alpha- (Nacα) or beta-subunit (bicaudal, bic) of NAC in the developing Drosophila heart disrupted cardiac developmental remodeling resulting in a fly with no heart. Heart loss was rescued by combined KD of Nacα with the posterior patterning Hox gene Abd-B. Consistent with a central role for this interaction in cardiogenesis, KD of Nacα in cardiac progenitors derived from human iPSCs impaired cardiac differentiation while co-KD with human HOXC12 and HOXD12 rescued this phenotype. Our data suggest that Nacα KD preprograms cardioblasts in the embryo for abortive remodeling later during metamorphosis, as Nacα KD during translation-intensive larval growth or pupal remodeling only causes moderate heart defects. KD of SRP subunits in the developing fly heart produced phenotypes that targeted specific segments and cell types, again suggesting cardiac-specific and spatially regulated activities. Together, we demonstrated directed function for NAC and SRP in heart development, and that regulation of NAC function depends on Hox genes.
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Affiliation(s)
- Analyne M. Schroeder
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- * E-mail: (AMS); (RB)
| | - Tanja Nielsen
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Michaela Lynott
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Georg Vogler
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Alexandre R. Colas
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- * E-mail: (AMS); (RB)
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6
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Müller T, Boileau E, Talyan S, Kehr D, Varadi K, Busch M, Most P, Krijgsveld J, Dieterich C. Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics. J Mol Cell Cardiol 2020; 150:23-31. [PMID: 33049256 DOI: 10.1016/j.yjmcc.2020.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
Clinically translatable large animal models have become indispensable for cardiovascular research, clinically relevant proof of concept studies and for novel therapeutic interventions. In particular, the pig has emerged as an essential cardiovascular disease model, because its heart, circulatory system, and blood supply are anatomically and functionally similar to that of humans. Currently, molecular and omics-based studies in the pig are hampered by the incompleteness of the genome and the lack of diversity of the corresponding transcriptome annotation. Here, we employed Nanopore long-read sequencing and in-depth proteomics on top of Illumina RNA-seq to enhance the pig cardiac transcriptome annotation. We assembled 15,926 transcripts, stratified into coding and non-coding, and validated our results by complementary mass spectrometry. A manual review of several gene loci, which are associated with cardiac function, corroborated the utility of our enhanced annotation. All our data are available for download and are provided as tracks for integration in genome browsers. We deem this resource as highly valuable for molecular research in an increasingly relevant large animal model.
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Affiliation(s)
- Torsten Müller
- German Cancer Research Center (DKFZ), Functional and Structural Genomics, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Heidelberg University, Medical Faculty, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
| | - Etienne Boileau
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Sweta Talyan
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Dorothea Kehr
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Division of Molecular and Translational Cardiology, Department of Internal Medicine III, Heidelberg University Hospital, INF 410, 69120 Heidelberg, Germany
| | - Karl Varadi
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Division of Molecular and Translational Cardiology, Department of Internal Medicine III, Heidelberg University Hospital, INF 410, 69120 Heidelberg, Germany
| | - Martin Busch
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Division of Molecular and Translational Cardiology, Department of Internal Medicine III, Heidelberg University Hospital, INF 410, 69120 Heidelberg, Germany
| | - Patrick Most
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany; Division of Molecular and Translational Cardiology, Department of Internal Medicine III, Heidelberg University Hospital, INF 410, 69120 Heidelberg, Germany; Center for Translational Medicine, Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Functional and Structural Genomics, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Heidelberg University, Medical Faculty, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
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7
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Park SS, Ponce-Balbuena D, Kuick R, Guerrero-Serna G, Yoon J, Mellacheruvu D, Conlon KP, Basrur V, Nesvizhskii AI, Jalife J, Rual JF. Kir2.1 Interactome Mapping Uncovers PKP4 as a Modulator of the Kir2.1-Regulated Inward Rectifier Potassium Currents. Mol Cell Proteomics 2020; 19:1436-1449. [PMID: 32541000 PMCID: PMC8143648 DOI: 10.1074/mcp.ra120.002071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Indexed: 12/27/2022] Open
Abstract
Kir2.1, a strong inward rectifier potassium channel encoded by the KCNJ2 gene, is a key regulator of the resting membrane potential of the cardiomyocyte and plays an important role in controlling ventricular excitation and action potential duration in the human heart. Mutations in KCNJ2 result in inheritable cardiac diseases in humans, e.g. the type-1 Andersen-Tawil syndrome (ATS1). Understanding the molecular mechanisms that govern the regulation of inward rectifier potassium currents by Kir2.1 in both normal and disease contexts should help uncover novel targets for therapeutic intervention in ATS1 and other Kir2.1-associated channelopathies. The information available to date on protein-protein interactions involving Kir2.1 channels remains limited. Additional efforts are necessary to provide a comprehensive map of the Kir2.1 interactome. Here we describe the generation of a comprehensive map of the Kir2.1 interactome using the proximity-labeling approach BioID. Most of the 218 high-confidence Kir2.1 channel interactions we identified are novel and encompass various molecular mechanisms of Kir2.1 function, ranging from intracellular trafficking to cross-talk with the insulin-like growth factor receptor signaling pathway, as well as lysosomal degradation. Our map also explores the variations in the interactome profiles of Kir2.1WTversus Kir2.1Δ314-315, a trafficking deficient ATS1 mutant, thus uncovering molecular mechanisms whose malfunctions may underlie ATS1 disease. Finally, using patch-clamp analysis, we validate the functional relevance of PKP4, one of our top BioID interactors, to the modulation of Kir2.1-controlled inward rectifier potassium currents. Our results validate the power of our BioID approach in identifying functionally relevant Kir2.1 interactors and underline the value of our Kir2.1 interactome as a repository for numerous novel biological hypotheses on Kir2.1 and Kir2.1-associated diseases.
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Affiliation(s)
- Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Daniela Ponce-Balbuena
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Rork Kuick
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Guadalupe Guerrero-Serna
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin Yoon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Kevin P Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - José Jalife
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Vanderplanck C, Tassin A, Ansseau E, Charron S, Wauters A, Lancelot C, Vancutsem K, Laoudj-Chenivesse D, Belayew A, Coppée F. Overexpression of the double homeodomain protein DUX4c interferes with myofibrillogenesis and induces clustering of myonuclei. Skelet Muscle 2018; 8:2. [PMID: 29329560 PMCID: PMC5767009 DOI: 10.1186/s13395-017-0148-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/27/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is associated with DNA hypomethylation at the 4q35 D4Z4 repeat array. Both the causal gene DUX4 and its homolog DUX4c are induced. DUX4c is immunodetected in every myonucleus of proliferative cells, while DUX4 is present in only 1/1000 of myonuclei where it initiates a gene deregulation cascade. FSHD primary myoblasts differentiate into either atrophic or disorganized myotubes. DUX4 expression induces atrophic myotubes and associated FSHD markers. Although DUX4 silencing normalizes the FSHD atrophic myotube phenotype, this is not the case for the disorganized phenotype. DUX4c overexpression increases the proliferation rate of human TE671 rhabdomyosarcoma cells and inhibits their differentiation, suggesting a normal role during muscle differentiation. METHODS By gain- and loss-of-function experiments in primary human muscle cells, we studied the DUX4c impact on proliferation, differentiation, myotube morphology, and FSHD markers. RESULTS In primary myoblasts, DUX4c overexpression increased the staining intensity of KI67 (a proliferation marker) in adjacent cells and delayed differentiation. In differentiating cells, DUX4c overexpression led to the expression of some FSHD markers including β-catenin and to the formation of disorganized myotubes presenting large clusters of nuclei and cytoskeletal defects. These were more severe when DUX4c was expressed before the cytoskeleton reorganized and myofibrils assembled. In addition, endogenous DUX4c was detected at a higher level in FSHD myotubes presenting abnormal clusters of nuclei and cytoskeletal disorganization. We found that the disorganized FSHD myotube phenotype could be rescued by silencing of DUX4c, not DUX4. CONCLUSION Excess DUX4c could disturb cytoskeletal organization and nuclear distribution in FSHD myotubes. We suggest that DUX4c up-regulation could contribute to DUX4 toxicity in the muscle fibers by favoring the clustering of myonuclei and therefore facilitating DUX4 diffusion among them. Defining DUX4c functions in the healthy skeletal muscle should help to design new targeted FSHD therapy by DUX4 or DUX4c inhibition without suppressing DUX4c normal function.
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Affiliation(s)
- Céline Vanderplanck
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Eugénie Ansseau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Sébastien Charron
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Armelle Wauters
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Céline Lancelot
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Kelly Vancutsem
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | | | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
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9
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Ansseau E, Eidahl JO, Lancelot C, Tassin A, Matteotti C, Yip C, Liu J, Leroy B, Hubeau C, Gerbaux C, Cloet S, Wauters A, Zorbo S, Meyer P, Pirson I, Laoudj-Chenivesse D, Wattiez R, Harper SQ, Belayew A, Coppée F. Homologous Transcription Factors DUX4 and DUX4c Associate with Cytoplasmic Proteins during Muscle Differentiation. PLoS One 2016; 11:e0146893. [PMID: 26816005 PMCID: PMC4729438 DOI: 10.1371/journal.pone.0146893] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022] Open
Abstract
Hundreds of double homeobox (DUX) genes map within 3.3-kb repeated elements dispersed in the human genome and encode DNA-binding proteins. Among these, we identified DUX4, a potent transcription factor that causes facioscapulohumeral muscular dystrophy (FSHD). In the present study, we performed yeast two-hybrid screens and protein co-purifications with HaloTag-DUX fusions or GST-DUX4 pull-down to identify protein partners of DUX4, DUX4c (which is identical to DUX4 except for the end of the carboxyl terminal domain) and DUX1 (which is limited to the double homeodomain). Unexpectedly, we identified and validated (by co-immunoprecipitation, GST pull-down, co-immunofluorescence and in situ Proximal Ligation Assay) the interaction of DUX4, DUX4c and DUX1 with type III intermediate filament protein desmin in the cytoplasm and at the nuclear periphery. Desmin filaments link adjacent sarcomere at the Z-discs, connect them to sarcolemma proteins and interact with mitochondria. These intermediate filament also contact the nuclear lamina and contribute to positioning of the nuclei. Another Z-disc protein, LMCD1 that contains a LIM domain was also validated as a DUX4 partner. The functionality of DUX4 or DUX4c interactions with cytoplasmic proteins is underscored by the cytoplasmic detection of DUX4/DUX4c upon myoblast fusion. In addition, we identified and validated (by co-immunoprecipitation, co-immunofluorescence and in situ Proximal Ligation Assay) as DUX4/4c partners several RNA-binding proteins such as C1QBP, SRSF9, RBM3, FUS/TLS and SFPQ that are involved in mRNA splicing and translation. FUS and SFPQ are nuclear proteins, however their cytoplasmic translocation was reported in neuronal cells where they associated with ribonucleoparticles (RNPs). Several other validated or identified DUX4/DUX4c partners are also contained in mRNP granules, and the co-localizations with cytoplasmic DAPI-positive spots is in keeping with such an association. Large muscle RNPs were recently shown to exit the nucleus via a novel mechanism of nuclear envelope budding. Following DUX4 or DUX4c overexpression in muscle cell cultures, we observed their association with similar nuclear buds. In conclusion, our study demonstrated unexpected interactions of DUX4/4c with cytoplasmic proteins playing major roles during muscle differentiation. Further investigations are on-going to evaluate whether these interactions play roles during muscle regeneration as previously suggested for DUX4c.
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Affiliation(s)
- Eugénie Ansseau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Jocelyn O. Eidahl
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Céline Lancelot
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Christel Matteotti
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Cassandre Yip
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Jian Liu
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Baptiste Leroy
- Laboratory of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Céline Hubeau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Cécile Gerbaux
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Samuel Cloet
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Armelle Wauters
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Sabrina Zorbo
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Pierre Meyer
- Pediatric Department, CHRU Montpellier, Montpellier, France
| | - Isabelle Pirson
- I.R.I.B.H.M., Free University of Brussels, Brussels, Belgium
| | | | - Ruddy Wattiez
- Laboratory of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Scott Q. Harper
- Center for Gene Therapy, Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
- Department of Pediatrics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
- * E-mail:
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10
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NACA deficiency reveals the crucial role of somite-derived stromal cells in haematopoietic niche formation. Nat Commun 2015; 6:8375. [DOI: 10.1038/ncomms9375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 08/16/2015] [Indexed: 01/10/2023] Open
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11
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Gardner S, Gross SM, David LL, Klimek JE, Rotwein P. Separating myoblast differentiation from muscle cell fusion using IGF-I and the p38 MAP kinase inhibitor SB202190. Am J Physiol Cell Physiol 2015; 309:C491-500. [PMID: 26246429 DOI: 10.1152/ajpcell.00184.2015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/30/2015] [Indexed: 11/22/2022]
Abstract
The p38 MAP kinases play critical roles in skeletal muscle biology, but the specific processes regulated by these kinases remain poorly defined. Here we find that activity of p38α/β is important not only in early phases of myoblast differentiation, but also in later stages of myocyte fusion and myofibrillogenesis. By treatment of C2 myoblasts with the promyogenic growth factor insulin-like growth factor (IGF)-I, the early block in differentiation imposed by the p38 chemical inhibitor SB202190 could be overcome. Yet, under these conditions, IGF-I could not prevent the later impairment of muscle cell fusion, as marked by the nearly complete absence of multinucleated myofibers. Removal of SB202190 from the medium of differentiating myoblasts reversed the fusion block, as multinucleated myofibers were detected several hours later and reached ∼90% of the culture within 30 h. Analysis by quantitative mass spectroscopy of proteins that changed in abundance following removal of the inhibitor revealed a cohort of upregulated muscle-enriched molecules that may be important for both myofibrillogenesis and fusion. We have thus developed a model system that allows separation of myoblast differentiation from muscle cell fusion and should be useful in identifying specific steps regulated by p38 MAP kinase-mediated signaling in myogenesis.
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Affiliation(s)
- Samantha Gardner
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon; and
| | - Sean M Gross
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon; and
| | - Larry L David
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon; and
| | - John E Klimek
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon; and
| | - Peter Rotwein
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon; and Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, Texas
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12
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Du SJ, Tan X, Zhang J. SMYD proteins: key regulators in skeletal and cardiac muscle development and function. Anat Rec (Hoboken) 2015; 297:1650-62. [PMID: 25125178 DOI: 10.1002/ar.22972] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 11/07/2022]
Abstract
Muscle fibers are composed of myofibrils, one of the most highly ordered macromolecular assemblies in cells. Recent studies demonstrate that members of the Smyd family play critical roles in myofibril assembly of skeletal and cardiac muscle during development. The Smyd family consists of five members including Smyd1, Smyd2, Smyd3, Smyd4, and Smyd5. They share two highly conserved structural and functional domains, namely the SET and MYND domains involved in lysine methylation and protein-protein interaction, respectively. Smyd1 is specifically expressed in muscle cells under the regulation of myogenic transcriptional factors of the MyoD and Mef2 families and the serum responsive factor. Loss of function studies reveal that Smyd1 is required for cardiomyogenesis and sarcomere assembly in skeletal and cardiac muscles. Smyd2, on another hand, is dispensable for heart development in mice. However, Smyd2 appears to play a role in myofilament organization in both skeletal and cardiac muscles via Hsp90 methylation. A Drosophila Smyd4 homologue is a muscle-specific transcriptional modulator involved in the development or function of adult muscle. The molecular mechanisms by which Smyd family proteins function in muscle cells are not well understood. It has been suggested that members of the Smyd family may use multiple mechanisms to control muscle development and cell differentiation, including transcriptional regulation, epigenetic regulation via histone methylation, and methylation of proteins other than histones, such as molecular chaperone Hsp90.
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Affiliation(s)
- Shao Jun Du
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
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13
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Yang J, Hung LH, Licht T, Kostin S, Looso M, Khrameeva E, Bindereif A, Schneider A, Braun T. RBM24 is a major regulator of muscle-specific alternative splicing. Dev Cell 2015; 31:87-99. [PMID: 25313962 DOI: 10.1016/j.devcel.2014.08.025] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 06/23/2014] [Accepted: 08/27/2014] [Indexed: 11/29/2022]
Abstract
Cell-type-specific splicing generates numerous alternatively spliced transcripts playing important roles for organ development and homeostasis, but only a few tissue-specific splicing factors have been identified. We found that RBM24 governs a large number of muscle-specific splicing events that are critically involved in cardiac and skeletal muscle development and disease. Targeted inactivation of RBM24 in mice disrupted cardiac development and impaired sarcomerogenesis in striated muscles. In vitro splicing assays revealed that recombinant RBM24 is sufficient to promote muscle-specific exon inclusion in nuclear extracts of nonmuscle cells. Furthermore, we demonstrate that binding of RBM24 to an intronic splicing enhancer (ISE) is essential and sufficient to overcome repression of exon inclusion by an exonic splicing silencer (ESS) containing PTB and hnRNP A1/A2 binding sites. Introduction of ESS and ISE converted a constitutive exon into an RMB24-dependent alternative exon. We reason that RBM24 is a major regulator of alternative splicing in striated muscles.
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Affiliation(s)
- Jiwen Yang
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Thomas Licht
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Sawa Kostin
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Mario Looso
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany
| | - Ekaterina Khrameeva
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, Moscow 127994, Russia
| | - Albrecht Bindereif
- Institute of Biochemistry, University of Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Andre Schneider
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany.
| | - Thomas Braun
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstraße 43, 61231 Bad Nauheim, Germany.
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14
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Berkholz J, Michalick L, Munz B. The E3 SUMO ligase Nse2 regulates sumoylation and nuclear-to-cytoplasmic translocation of skNAC-Smyd1 in myogenesis. J Cell Sci 2014; 127:3794-804. [PMID: 25002400 DOI: 10.1242/jcs.150334] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Skeletal and heart muscle-specific variant of the α subunit of nascent polypeptide associated complex (skNAC; encoded by NACA) is exclusively found in striated muscle cells. Its function, however, is largely unknown. Previous reports have demonstrated that skNAC binds to m-Bop/Smyd1, a multi-functional protein that regulates myogenesis both through the control of transcription and the modulation of sarcomerogenesis, and that both proteins undergo nuclear-to-cytoplasmic translocation at the later stages of myogenic differentiation. Here, we show that skNAC binds to the E3 SUMO ligase mammalian Mms21/Nse2 and that knockdown of Nse2 expression inhibits specific aspects of myogenic differentiation, accompanied by a partial blockade of the nuclear-to-cytoplasmic translocation of the skNAC-Smyd1 complex, retention of the complex in promyelocytic leukemia (PML)-like nuclear bodies and disturbed sarcomerogenesis. In addition, we show that the skNAC interaction partner Smyd1 contains a putative sumoylation motif and is sumoylated in muscle cells, with depletion of Mms21/Nse2 leading to reduced concentrations of sumoylated Smyd1. Taken together, our data suggest that the function, specifically the balance between the nuclear and cytosolic roles, of the skNAC-Smyd1 complex might be regulated by sumoylation.
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Affiliation(s)
- Janine Berkholz
- Charité - University Medicine Berlin, Institute of Physiology, Charitéplatz 1, D-10117 Berlin, Germany
| | - Laura Michalick
- Charité - University Medicine Berlin, Institute of Physiology, Charitéplatz 1, D-10117 Berlin, Germany
| | - Barbara Munz
- University Hospital Tubingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Strasse 6, D-72076 Tubingen, Germany
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15
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16
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Fero K, Bergeron SA, Horstick EJ, Codore H, Li GH, Ono F, Dowling JJ, Burgess HA. Impaired embryonic motility in dusp27 mutants reveals a developmental defect in myofibril structure. Dis Model Mech 2013; 7:289-98. [PMID: 24203884 PMCID: PMC3917250 DOI: 10.1242/dmm.013235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
An essential step in muscle fiber maturation is the assembly of highly ordered myofibrils that are required for contraction. Much remains unknown about the molecular mechanisms governing the formation of the contractile apparatus. We identified an early embryonic motility mutant in zebrafish caused by integration of a transgene into the pseudophosphatase dual specificity phosphatase 27 (dusp27) gene. dusp27 mutants exhibit near complete paralysis at embryonic and larval stages, producing extremely low levels of spontaneous coiling movements and a greatly diminished touch response. Loss of dusp27 does not prevent somitogenesis but results in severe disorganization of the contractile apparatus in muscle fibers. Sarcomeric structures in mutants are almost entirely absent and only rare triads are observed. These findings are the first to implicate a functional role of dusp27 as a gene required for myofiber maturation and provide an animal model for analyzing the mechanisms governing myofibril assembly.
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Affiliation(s)
- Kandice Fero
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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17
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skNAC depletion stimulates myoblast migration and perturbs sarcomerogenesis by enhancing calpain 1 and 3 activity. Biochem J 2013; 453:303-10. [PMID: 23662692 DOI: 10.1042/bj20130195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
skNAC (skeletal and heart muscle specific variant of nascent polypeptide-associated complex α) is a skeletal and heart muscle-specific protein known to be involved in the regulation of sarcomerogenesis. The respective mechanism, however, is largely unknown. In the present paper, we demonstrate that skNAC regulates calpain activity. Specifically, we show that inhibition of skNAC gene expression leads to enhanced, and overexpression of the skNAC gene to repressed, activity of calpain 1 and, to a lesser extent, calpain 3 in myoblasts. In skNAC siRNA-treated cells, enhanced calpain activity is associated with increased migration rates, as well as with perturbed sarcomere architecture. Treatment of skNAC-knockdown cells with the calpain inhibitor ALLN (N-acetyl-leucyl-leucyl-norleucinal) reverts both the positive effect on myoblast migration and the negative effect on sarcomere architecture. Taken together, our data suggest that skNAC controls myoblast migration and sarcomere architecture in a calpain-dependent manner.
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18
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Jafarov T, Alexander JWM, St-Arnaud R. αNAC interacts with histone deacetylase corepressors to control Myogenin and Osteocalcin gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:1208-16. [PMID: 23092676 DOI: 10.1016/j.bbagrm.2012.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 10/15/2012] [Accepted: 10/16/2012] [Indexed: 01/27/2023]
Abstract
In the nucleus of differentiated osteoblasts, the DNA-binding αNAC protein acts as a transcriptional coactivator of the Osteocalcin gene. Chromatin immunoprecipitation-microarray assays (ChIP-chip) showed that αNAC binds the Osteocalcin promoter but also identified the Myogenin promoter as an αNAC target. Here, we confirm these array data using quantitative ChIP and further detected that αNAC binds to these promoters in myoblasts. Since these genes are differentially regulated during osteoblastogenesis or myogenesis, these results suggest cell- and promoter-context specific functions for αNAC. We hypothesized that αNAC dynamically recruits corepressors to inhibit Myogenin expression in cells committing to the osteoblastic lineage or to inhibit Osteocalcin transcription in differentiating myoblasts. Using co-immunoprecipitation assays, we detected complexes between αNAC and the corepressors HDAC1 and HDAC3, in myoblasts and osteoblasts. Sequential ChIP confirmed HDAC1 recruitment by αNAC at the Osteocalcin and Myogenin promoters. Interaction with the corepressors was detectable in pre-osteoblasts and in myoblasts but disappeared as the cells differentiate. Treatment with an HDAC inhibitor caused de-repression of Osteocalcin expression in myoblasts. Overexpression of αNAC in myoblasts inhibits expression of Myogenin and differentiation. However, overexpression of an N-terminus truncated αNAC mutant allowed myoblasts to express Myogenin and differentiate, and this mutant did not interact with HDAC1 or HDAC3. This study identified an additional DNA-binding target and novel protein-protein interactions for αNAC. We propose that αNAC plays a role in regulating gene transcription during mesenchymal cell differentiation by differentially recruiting corepressors at target promoters.
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Skeletal muscle-specific variant of nascent polypeptide associated complex alpha (skNAC): Implications for a specific role in mammalian myoblast differentiation. Eur J Cell Biol 2012; 91:150-5. [DOI: 10.1016/j.ejcb.2011.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 10/30/2011] [Accepted: 10/31/2011] [Indexed: 11/20/2022] Open
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20
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Rbfox-regulated alternative splicing is critical for zebrafish cardiac and skeletal muscle functions. Dev Biol 2011; 359:251-61. [PMID: 21925157 DOI: 10.1016/j.ydbio.2011.08.025] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/30/2011] [Accepted: 08/30/2011] [Indexed: 11/22/2022]
Abstract
Rbfox RNA binding proteins are implicated as regulators of phylogenetically-conserved alternative splicing events important for muscle function. To investigate the function of rbfox genes, we used morpholino-mediated knockdown of muscle-expressed rbfox1l and rbfox2 in zebrafish embryos. Single and double morphant embryos exhibited changes in splicing of overlapping sets of bioinformatically-predicted rbfox target exons, many of which exhibit a muscle-enriched splicing pattern that is conserved in vertebrates. Thus, conservation of intronic Rbfox binding motifs is a good predictor of Rbfox-regulated alternative splicing. Morphology and development of single morphant embryos were strikingly normal; however, muscle development in double morphants was severely disrupted. Defects in cardiac muscle were marked by reduced heart rate and in skeletal muscle by complete paralysis. The predominance of wavy myofibers and abnormal thick and thin filaments in skeletal muscle revealed that myofibril assembly is defective and disorganized in double morphants. Ultra-structural analysis revealed that although sarcomeres with electron dense M- and Z-bands are present in muscle fibers of rbfox1l/rbox2 morphants, they are substantially reduced in number and alignment. Importantly, splicing changes and morphological defects were rescued by expression of morpholino-resistant rbfox cDNA. Additionally, a target-blocking MO complementary to a single UGCAUG motif adjacent to an rbfox target exon of fxr1 inhibited inclusion in a similar manner to rbfox knockdown, providing evidence that Rbfox regulates the splicing of target exons via direct binding to intronic regulatory motifs. We conclude that Rbfox proteins regulate an alternative splicing program essential for vertebrate heart and skeletal muscle functions.
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21
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Codina M, Li J, Gutiérrez J, Kao JPY, Du SJ. Loss of Smyhc1 or Hsp90alpha1 function results in different effects on myofibril organization in skeletal muscles of zebrafish embryos. PLoS One 2010; 5:e8416. [PMID: 20049323 PMCID: PMC2797074 DOI: 10.1371/journal.pone.0008416] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 11/22/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Myofibrillogenesis requires the correct folding and assembly of sarcomeric proteins into highly organized sarcomeres. Heat shock protein 90alpha1 (Hsp90alpha1) has been implicated as a myosin chaperone that plays a key role in myofibrillogenesis. Knockdown or mutation of hsp90alpha1 resulted in complete disorganization of thick and thin filaments and M- and Z-line structures. It is not clear whether the disorganization of these sarcomeric structures is due to a direct effect from loss of Hsp90alpha1 function or indirectly through the disorganization of myosin thick filaments. METHODOLOGY/PRINCIPAL FINDINGS In this study, we carried out a loss-of-function analysis of myosin thick filaments via gene-specific knockdown or using a myosin ATPase inhibitor BTS (N-benzyl-p-toluene sulphonamide) in zebrafish embryos. We demonstrated that knockdown of myosin heavy chain 1 (myhc1) resulted in sarcomeric defects in the thick and thin filaments and defective alignment of Z-lines. Similarly, treating zebrafish embryos with BTS disrupted thick and thin filament organization, with little effect on the M- and Z-lines. In contrast, loss of Hsp90alpha1 function completely disrupted all sarcomeric structures including both thick and thin filaments as well as the M- and Z-lines. CONCLUSION/SIGNIFICANCE Together, these studies indicate that the hsp90alpha1 mutant phenotype is not simply due to disruption of myosin folding and assembly, suggesting that Hsp90alpha1 may play a role in the assembly and organization of other sarcomeric structures.
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Affiliation(s)
- Marta Codina
- Center of Marine Biotechnology, Biotechnology Institute, University of Maryland, Baltimore, Maryland, United States of America
- Department of Physiology, University of Barcelona, Barcelona, Spain
| | - Junling Li
- Center of Marine Biotechnology, Biotechnology Institute, University of Maryland, Baltimore, Maryland, United States of America
| | | | - Joseph P. Y. Kao
- Medical Biotechnology Center, Biotechnology Institute, University of Maryland, Baltimore, Maryland, United States of America
- Center for Biomedical Engineering and Technology, and Department of Physiology, University of Maryland, Baltimore, Maryland, United States of America
| | - Shao Jun Du
- Center of Marine Biotechnology, Biotechnology Institute, University of Maryland, Baltimore, Maryland, United States of America
- Interdisciplinary Training Program in Muscle Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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