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Cisterna B, Malatesta M. Molecular and Structural Alterations of Skeletal Muscle Tissue Nuclei during Aging. Int J Mol Sci 2024; 25:1833. [PMID: 38339110 PMCID: PMC10855217 DOI: 10.3390/ijms25031833] [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: 12/27/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Aging is accompanied by a progressive loss of skeletal muscle mass and strength. The mechanisms underlying this phenomenon are certainly multifactorial and still remain to be fully elucidated. Changes in the cell nucleus structure and function have been considered among the possible contributing causes. This review offers an overview of the current knowledge on skeletal muscle nuclei in aging, focusing on the impairment of nuclear pathways potentially involved in age-related muscle decline. In skeletal muscle two types of cells are present: fiber cells, constituting the contractile muscle mass and containing hundreds of myonuclei, and the satellite cells, i.e., the myogenic mononuclear stem cells occurring at the periphery of the fibers and responsible for muscle growth and repair. Research conducted on different experimental models and with different methodological approaches demonstrated that both the myonuclei and satellite cell nuclei of aged skeletal muscles undergo several structural and molecular alterations, affecting chromatin organization, gene expression, and transcriptional and post-transcriptional activities. These alterations play a key role in the impairment of muscle fiber homeostasis and regeneration, thus contributing to the age-related decrease in skeletal muscle mass and function.
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Affiliation(s)
| | - Manuela Malatesta
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy;
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2
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Martins-Marques T, Witschas K, Ribeiro I, Zuzarte M, Catarino S, Ribeiro-Rodrigues T, Caramelo F, Aasen T, Carreira IM, Goncalves L, Leybaert L, Girao H. Cx43 can form functional channels at the nuclear envelope and modulate gene expression in cardiac cells. Open Biol 2023; 13:230258. [PMID: 37907090 PMCID: PMC10645070 DOI: 10.1098/rsob.230258] [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: 08/02/2023] [Accepted: 09/12/2023] [Indexed: 11/02/2023] Open
Abstract
Classically associated with gap junction-mediated intercellular communication, connexin43 (Cx43) is increasingly recognized to possess non-canonical biological functions, including gene expression regulation. However, the mechanisms governing the localization and role played by Cx43 in the nucleus, namely in transcription modulation, remain unknown. Using comprehensive and complementary approaches encompassing biochemical assays, super-resolution and immunogold transmission electron microscopy, we demonstrate that Cx43 localizes to the nuclear envelope of different cell types and in cardiac tissue. We show that translocation of Cx43 to the nucleus relies on Importin-β, and that Cx43 significantly impacts the cellular transcriptome, likely by interacting with transcriptional regulators. In vitro patch-clamp recordings from HEK293 and adult primary cardiomyocytes demonstrate that Cx43 forms active channels at the nuclear envelope, providing evidence that Cx43 can participate in nucleocytoplasmic shuttling of small molecules. The accumulation of nuclear Cx43 during myogenic differentiation of cardiomyoblasts is suggested to modulate expression of genes implicated in this process. Altogether, our study provides new evidence for further defining the biological roles of nuclear Cx43, namely in cardiac pathophysiology.
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Affiliation(s)
- Tania Martins-Marques
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Katja Witschas
- Department of Basic Medical Sciences – Physiology group, Ghent University, 9000 Ghent, Belgium
| | - Ilda Ribeiro
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Univ Coimbra, Cytogenetics and Genomics Laboratory (CIMAGO), Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Mónica Zuzarte
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Steve Catarino
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Teresa Ribeiro-Rodrigues
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Francisco Caramelo
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Univ Coimbra, Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Trond Aasen
- Patologia Molecular Translacional, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
- CIBER de Cáncer (CIBERONC), Instituto de Salud Carlos III, Avenida de Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Isabel Marques Carreira
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Univ Coimbra, Cytogenetics and Genomics Laboratory (CIMAGO), Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Lino Goncalves
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Luc Leybaert
- Department of Basic Medical Sciences – Physiology group, Ghent University, 9000 Ghent, Belgium
| | - Henrique Girao
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, 3000-548 Coimbra, Portugal
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3004-504 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
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Welter AA, Wu WJ, Maurer R, O’Quinn TG, Chao MD, Boyle DL, Geisbrecht ER, Hartson SD, Bowker BC, Zhuang H. An Investigation of the Altered Textural Property in Woody Breast Myopathy Using an Integrative Omics Approach. Front Physiol 2022; 13:860868. [PMID: 35370787 PMCID: PMC8970568 DOI: 10.3389/fphys.2022.860868] [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: 01/23/2022] [Accepted: 02/04/2022] [Indexed: 12/02/2022] Open
Abstract
Woody breast (WB) is a myopathy observed in broiler Pectoralis major (PM) characterized by its tough and rubbery texture with greater level of calcium content. The objective of this study was to investigate the functionality/integrity of WB sarcoplasmic reticulum (SR), which may contribute to the elevated calcium content observed in WB and other factors that may influence WB texture. Fourteen Ross line broiler PM [7 severe WB and 7 normal (N)] were selected, packaged, and frozen at −20°C at 8 h postmortem from a commercial processing plant. Samples were used to measure pH, sarcomere length, proteolysis, calpain activity, collagenase activity, collagen content, collagen crosslinks density, and connective tissue peak transitional temperature. Exudate was also collected from each sample to evaluate free calcium concentration. The SR fraction of the samples was separated and utilized for proteomic and lipidomic analysis. The WB PM had a higher pH, shorter sarcomeres, lower % of intact troponin-T, more autolyzed μ/m calpain, more activated collagenase, greater collagen content, greater mature collagen crosslinks density, and higher connective tissue peak transitional temperature than the N PM (p ≤ 0.05). Exudate from WB PM had higher levels of free calcium than those from N PM (p < 0.05). Proteomics data revealed an upregulation of calcium transport proteins and a downregulation of proteins responsible for calcium release (p < 0.05) in WB SR. Interestingly, there was an upregulation of phospholipase A2 (PLA2), and cholinesterase exhibited a 7.6-fold increase in WB SR (p < 0.01). Lipidomics data revealed WB SR had less relative % of phosphatidylcholine (PC) and more lysophosphatidylcholine (LPC; p < 0.05). The results indicated that upregulation of calcium transport proteins and downregulation of calcium-release proteins in WB SR may be the muscle’s attempt to regulate this proposed excessive signaling of calcium release due to multiple factors, such as upregulation of PLA2 resulting in PC hydrolysis and presence of cholinesterase inhibitors in the system prolonging action potential. In addition, the textural abnormality of WB may be the combined effects of shorter sarcomere length and more collagen with greater crosslink density being deposited in the broiler PM.
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Affiliation(s)
- Amelia A. Welter
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, United States
| | - Wan Jun Wu
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, United States
| | - Ryan Maurer
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, United States
| | - Travis G. O’Quinn
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, United States
| | - Michael D. Chao
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, United States
- *Correspondence: Michael D. Chao,
| | - Daniel L. Boyle
- Division of Biology, Kansas State University Microscopy Facility, Manhattan, KS, United States
| | - Erika R. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Steve D. Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
| | - Brian C. Bowker
- United States National Poultry Research Center USDA, Agricultural Research Service, Athens, GA, United States
| | - Hong Zhuang
- United States National Poultry Research Center USDA, Agricultural Research Service, Athens, GA, United States
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Li R, Zou Z, Wang W, Zou P. Metabolic incorporation of electron-rich ribonucleosides enhances APEX-seq for profiling spatially restricted nascent transcriptome. Cell Chem Biol 2022; 29:1218-1231.e8. [PMID: 35245437 DOI: 10.1016/j.chembiol.2022.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 07/30/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
The spatial arrangement of newly synthesized transcriptome in eukaryotic cells underlies various biological processes including cell proliferation and differentiation. In this study, we combine metabolic incorporation of electron-rich ribonucleosides (e.g., 6-thioguanosine and 4-thiouridine) with a peroxidase-mediated proximity-dependent RNA labeling technique (APEX-seq) to develop a sensitive method, termed MERR APEX-seq, for selectively profiling newly transcribed RNAs at specific subcellular locations in live cells. We demonstrate that MERR APEX-seq is 20-fold more efficient than APEX-seq and offers both high spatial specificity and high coverage in mitochondrial matrix. At the ER membrane, 91% of the transcripts captured by MERR APEX-seq encode for secretory pathway proteins, thus demonstrating the high spatial specificity of MERR APEX-seq in open subcellular compartments. Application of MERR APEX-seq to the nuclear lamina of human cells reveals a local transcriptome of 1,012 RNAs, many of which encode for nuclear proteins involved in histone modification, chromosomal structure maintenance, and RNA processing.
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Affiliation(s)
- Ran Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhongyu Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Wentao Wang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China
| | - Peng Zou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China; Chinese Institute for Brain Research (CIBR), Beijing 102206, China.
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5
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Wette SG, Lamb GD, Murphy RM. Nuclei isolation methods fail to accurately assess the subcellular localization and behaviour of proteins in skeletal muscle. Acta Physiol (Oxf) 2021; 233:e13730. [PMID: 34492163 DOI: 10.1111/apha.13730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 12/17/2022]
Abstract
AIM Subcellular fractionation is often used to determine the subcellular localization of proteins, including whether a protein translocates to the nucleus in response to a given stimulus. Examining nuclear proteins in skeletal muscle is difficult because myonuclear proteins are challenging to isolate unless harsh treatments are used. This study aimed to determine the most effective method for isolating and preserving proteins in their native state in skeletal muscle. METHODS We compared the ability of detergents, commercially available kit-based and K+ -based physiological methodologies for isolating myonuclear proteins from resting samples of human muscle by determining the presence of marker proteins for each fraction by western blot analyses. RESULTS We found that following the initial pelleting of nuclei, treatment with 1% Triton-X 100, 1% CHAPS or 0.5% Na-deoxycholate under various ionic conditions resulted in the nuclear proteins being either resistant to isolation or the proteins present behaving aberrantly. The nuclear proteins in brain tissue were also resistant to 1% Triton-X 100 isolation. Here, we demonstrate aberrant behaviour and erroneous localization of proteins using the kit-based method. The aberrant behaviour was the activation of Ca2+ -dependent protease calpain-3, and the erroneous localization was the presence of calpain-3 and troponin I in the nuclear fraction. CONCLUSION Our findings indicate that it may not be possible to reliably determine the translocation of proteins between subcellular locations and the nucleus using subcellular fractionation techniques. This study highlights the importance of validating subcellular fractionation methodologies using several subcellular-specific markers and solutions that are physiologically relevant to the intracellular milieu.
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Affiliation(s)
- Stefan G. Wette
- Department of Biochemistry and Genetics La Trobe Institute for Molecular ScienceLa Trobe University Melbourne Victoria Australia
| | - Graham D. Lamb
- Department of Physiology, Anatomy and Microbiology School of Life Sciences La Trobe University Melbourne Victoria Australia
| | - Robyn M. Murphy
- Department of Biochemistry and Genetics La Trobe Institute for Molecular ScienceLa Trobe University Melbourne Victoria Australia
- Department of Physiology, Anatomy and Microbiology School of Life Sciences La Trobe University Melbourne Victoria Australia
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Mañas-García L, Guitart M, Duran X, Barreiro E. Satellite Cells and Markers of Muscle Regeneration during Unloading and Reloading: Effects of Treatment with Resveratrol and Curcumin. Nutrients 2020; 12:nu12061870. [PMID: 32585875 PMCID: PMC7353305 DOI: 10.3390/nu12061870] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022] Open
Abstract
We hypothesized that treatment with pharmacological agents known to increase sirtuin-1 activity (resveratrol and curcumin) may enhance muscle regeneration. In limb muscles of mice (C57BL/6J, 10 weeks) exposed to reloading for seven days following a seven-day period of hindlimb immobilization with/without curcumin or resveratrol treatment, progenitor muscle cell numbers (FACS), satellite cell subtypes (histology), early and late muscle regeneration markers, phenotype and morphometry, sirtuin-1 activity and content, and muscle function were assessed. Treatment with either resveratrol or curcumin in immobilized muscles elicited a significant improvement in numbers of progenitor, activated, quiescent, and total counts of muscle satellite cells, compared to non-treated animals. Treatment with either resveratrol or curcumin in reloaded muscles compared to non-treated mice induced a significant improvement in the CSA of both hybrid (curcumin) and fast-twitch fibers (resveratrol), sirtuin-1 activity (curcumin), sirtuin-1 content (resveratrol), and counts of progenitor muscle cells (resveratrol). Treatment with the pharmacological agents resveratrol and curcumin enhanced the numbers of satellite cells (muscle progenitor, quiescent, activated, and total satellite cells) in the unloaded limb muscles but not in the reloaded muscles. These findings have potential clinical implications as treatment with these phenolic compounds would predominantly be indicated during disuse muscle atrophy to enhance the muscle regeneration process.
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Affiliation(s)
- Laura Mañas-García
- Pulmonology Department-Muscle Wasting and Cachexia in Chronic Respiratory Diseases and Lung Cancer Research Group, IMIM-Hospital del Mar, Parc de Salut Mar, Health and Experimental Sciences Department (CEXS), Universitat Pompeu Fabra (UPF), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain; (L.M.-G.); (M.G.)
| | - Maria Guitart
- Pulmonology Department-Muscle Wasting and Cachexia in Chronic Respiratory Diseases and Lung Cancer Research Group, IMIM-Hospital del Mar, Parc de Salut Mar, Health and Experimental Sciences Department (CEXS), Universitat Pompeu Fabra (UPF), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain; (L.M.-G.); (M.G.)
- Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 08003 Barcelona, Spain
| | - Xavier Duran
- Scientific and Technical Department, Hospital del Mar-IMIM, 08003 Barcelona, Spain;
| | - Esther Barreiro
- Pulmonology Department-Muscle Wasting and Cachexia in Chronic Respiratory Diseases and Lung Cancer Research Group, IMIM-Hospital del Mar, Parc de Salut Mar, Health and Experimental Sciences Department (CEXS), Universitat Pompeu Fabra (UPF), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain; (L.M.-G.); (M.G.)
- Centro de Investigación en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 08003 Barcelona, Spain
- Correspondence: ; Tel.: +34-93-316-0385; Fax: +34-93-316-0410
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Dazzoni R, Buré C, Morvan E, Grélard A, Gounou C, Schmitter JM, Loquet A, Larijani B, Dufourc EJ. Tandem NMR and Mass Spectrometry Analysis of Human Nuclear Membrane Lipids. Anal Chem 2020; 92:6858-6868. [DOI: 10.1021/acs.analchem.9b05052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Régine Dazzoni
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, Université Bordeaux, Institut National Polytechnique Bordeaux, Pessac F-33600, France
- Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Plentzia, Spain
| | - Corinne Buré
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, Université Bordeaux, Institut National Polytechnique Bordeaux, Pessac F-33600, France
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie, University of Bordeaux, INSERM, CNRS (UMS 3033-US 001), 2 rue Escarpit, Pessac 33600, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, Université Bordeaux, Institut National Polytechnique Bordeaux, Pessac F-33600, France
| | - Céline Gounou
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, Université Bordeaux, Institut National Polytechnique Bordeaux, Pessac F-33600, France
| | - Jean-Marie Schmitter
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, Université Bordeaux, Institut National Polytechnique Bordeaux, Pessac F-33600, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, Université Bordeaux, Institut National Polytechnique Bordeaux, Pessac F-33600, France
| | - Banafshé Larijani
- Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Instituto Biofísika (CSIC, UPV/EHU) and Research Centre for Experimental Marine Biology and Biotechnology (PiE), University of the Basque Country (UPV/EHU), Plentzia, Spain
- Cell Biophysics Laboratory, Centre for Therapeutic Innovation, Department of Pharmacy and Pharmacology, Department of Physics, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Erick J. Dufourc
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR 5248, CNRS, Université Bordeaux, Institut National Polytechnique Bordeaux, Pessac F-33600, France
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Spracklin G, Pradhan S. Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin. Nucleic Acids Res 2020; 48:e16. [PMID: 31819993 PMCID: PMC7026637 DOI: 10.1093/nar/gkz1150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/11/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022] Open
Abstract
In metazoan cell nuclei, heterochromatin constitutes large chromatin domains that are in close contact with the nuclear lamina. These heterochromatin/lamina-associated domains (LADs) domains are difficult to profile and warrants a simpler and direct method. Here we report a new method, Protect-seq, aimed at identifying regions of heterochromatin via resistance to nuclease degradation followed by next-generation sequencing (NGS). We performed Protect-seq on the human colon cancer cell line HCT-116 and observed overlap with previously curated LADs. We provide evidence that these protected regions are enriched for and can distinguish between the repressive histone modification H3K9me3, H3K9me2 and H3K27me3. Moreover, in human cells the loss of H3K9me3 leads to an increase in chromatin accessibility and loss of Protect-seq signal. For further validation, we performed Protect-seq in the fibrosarcoma cell line HT1080 and found a similar correlation with previously curated LADs and repressive histone modifications. In sum, Protect-seq is an efficient technique that allows rapid identification of nuclease resistant chromatin, which correlate with heterochromatin and radial positioning.
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Affiliation(s)
- George Spracklin
- Genome Biology Division, New England Biolabs, Inc, Ipswich, MA 01938, USA
| | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Inc, Ipswich, MA 01938, USA
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9
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Muscle Phenotype, Proteolysis, and Atrophy Signaling During Reloading in Mice: Effects of Curcumin on the Gastrocnemius. Nutrients 2020; 12:nu12020388. [PMID: 32024036 PMCID: PMC7071295 DOI: 10.3390/nu12020388] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 12/31/2022] Open
Abstract
We hypothesized that curcumin may mitigate muscle protein degradation and loss through attenuation of proteolytic activity in limb muscles of mice exposed to reloading (7dR) following immobilization (7dI). In gastrocnemius of mice (female C57BL/6J, 10 weeks) exposed to recovery following a seven-day period of hindlimb immobilization with/without curcumin treatment, markers of muscle proteolysis (systemic troponin-I), atrophy signaling pathways and histone deacetylases, protein synthesis, and muscle phenotypic characteristics and function were analyzed. In gastrocnemius of reloading mice compared to unloaded, muscle function, structure, sirtuin-1, and protein synthesis improved, while proteolytic and signaling markers (FoxO1/3) declined. In gastrocnemius of unloaded and reloaded mice treated with curcumin, proteolytic and signaling markers (NF-kB p50) decreased and sirtuin-1 activity and hybrid fibers size increased (reloaded muscle), while no significant improvement was seen in muscle function. Treatment with curcumin elicited a rise in sirtuin-1 activity, while attenuating proteolysis in gastrocnemius of mice during reloading following a period of unloading. Curcumin attenuated muscle proteolysis probably via activation of histone deacetylase sirtuin-1, which also led to decreased levels of atrophy signaling pathways. These findings offer an avenue of research in the design of therapeutic strategies in clinical settings of patients exposed to periods of disuse muscle atrophy.
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10
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Indirect Measurement of CRAC Channel Activity Using NFAT Nuclear Translocation by Flow Cytometry in Jurkat Cells. Methods Mol Biol 2019; 1843:83-94. [PMID: 30203279 DOI: 10.1007/978-1-4939-8704-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Flow cytometry is a powerful technology to assess the presence of NFAT in the nuclei after CRAC channel activation. Here we described a simplified procedure for the analysis of CRAC channel activity using NFAT nuclear translocation by flow cytometry, based on the isolation of Jurkat E6-1 cell nuclei.
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Yeo KS, Tan MC, Lim YY, Ea CK. JMJD8 is a novel endoplasmic reticulum protein with a JmjC domain. Sci Rep 2017; 7:15407. [PMID: 29133832 PMCID: PMC5684140 DOI: 10.1038/s41598-017-15676-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/31/2017] [Indexed: 12/22/2022] Open
Abstract
Jumonji C (JmjC) domain-containing proteins have been shown to regulate cellular processes by hydroxylating or demethylating histone and non-histone targets. JMJD8 belongs to the JmjC domain-only family that was recently shown to be involved in angiogenesis and TNF-induced NF-κB signaling. Here, we employed bioinformatic analysis and immunofluorescence microscopy to examine the physiological properties of JMJD8. We demonstrated that JMJD8 localizes to the lumen of endoplasmic reticulum and that JMJD8 forms dimers or oligomers in vivo. Furthermore, we identified potential JMJD8-interacting proteins that are known to regulate protein complex assembly and protein folding. Taken together, this work demonstrates that JMJD8 is the first JmjC domain-containing protein found in the lumen of the endoplasmic reticulum that may function in protein complex assembly and protein folding.
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Affiliation(s)
- Kok Siong Yeo
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ming Cheang Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yat-Yuen Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chee-Kwee Ea
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9148, United States.
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miRNA-122 Protects Mice and Human Hepatocytes from Acetaminophen Toxicity by Regulating Cytochrome P450 Family 1 Subfamily A Member 2 and Family 2 Subfamily E Member 1 Expression. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2758-2774. [PMID: 28963035 DOI: 10.1016/j.ajpath.2017.08.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/26/2017] [Accepted: 08/17/2017] [Indexed: 12/18/2022]
Abstract
Acetaminophen toxicity is a leading cause of acute liver failure (ALF). We found that miRNA-122 (miR-122) is down-regulated in liver biopsy specimens of patients with ALF and in acetaminophen-treated mice. A marked decrease in the primary miR-122 expression occurs in mice on acetaminophen overdose because of suppression of its key transactivators, hepatocyte nuclear factor (HNF)-4α and HNF6. More importantly, the mortality rates of male and female liver-specific miR-122 knockout (LKO) mice were significantly higher than control mice when injected i.p. with an acetaminophen dose not lethal to the control. LKO livers exhibited higher basal expression of cytochrome P450 family 2 subfamily E member 1 (CYP2E1) and cytochrome P450 family 1 subfamily A member 2 (CYP1A2) that convert acetaminophen to highly reactive N-acetyl-p-benzoquinone imine. Upregulation of Cyp1a2 primary transcript and mRNA in LKO mice correlated with the elevation of aryl hydrocarbon receptor (AHR) and mediator 1 (MED1), two transactivators of Cyp1a2. Analysis of ChIP-seq data in the ENCODE (Encyclopedia of DNA Element) database identified association of CCCTC-binding factor (CTCF) with Ahr promoter in mouse livers. Both MED1 and CTCF are validated conserved miR-122 targets. Furthermore, depletion of Ahr, Med1, or Ctcf in Mir122-/- hepatocytes reduced Cyp1a2 expression. Pulse-chase studies found that CYP2E1 protein level is upregulated in LKO hepatocytes. Notably, miR-122 depletion sensitized differentiated human HepaRG cells to acetaminophen toxicity that correlated with upregulation of AHR, MED1, and CYP1A2 expression. Collectively, these results reveal a critical role of miR-122 in acetaminophen detoxification and implicate its therapeutic potential in patients with ALF.
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Cutler AA, Dammer EB, Doung DM, Seyfried NT, Corbett AH, Pavlath GK. Biochemical isolation of myonuclei employed to define changes to the myonuclear proteome that occur with aging. Aging Cell 2017; 16:738-749. [PMID: 28544616 PMCID: PMC5506426 DOI: 10.1111/acel.12604] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Skeletal muscle aging is accompanied by loss of muscle mass and strength. Examining changes in myonuclear proteins with age would provide insight into molecular processes which regulate these profound changes in muscle physiology. However, muscle tissue is highly adapted for contraction and thus comprised largely of contractile proteins making the nuclear proteins difficult to identify from whole muscle samples. By developing a method to purify myonuclei from whole skeletal muscle, we were able to collect myonuclei for analysis by flow cytometry, biochemistry, and mass spectrometry. Nuclear purification dramatically increased the number and intensity of nuclear proteins detected by mass spectrometry compared to whole tissue. We exploited this increased proteomic depth to investigate age-related changes to the myonuclear proteome. Nuclear levels of 54 of 779 identified proteins (7%) changed significantly with age; these proteins were primarily involved in chromatin maintenance and RNA processing. To determine whether the changes we detected were specific to myonuclei or were common to nuclei of excitatory tissues, we compared aging in myonuclei to aging in brain nuclei. Although several of the same processes were affected by aging in both brain and muscle nuclei, the specific proteins involved in these alterations differed between the two tissues. Isolating myonuclei allowed a deeper view into the myonuclear proteome than previously possible facilitating identification of novel age-related changes in skeletal muscle. Our technique will enable future studies into a heretofore underrepresented compartment of skeletal muscle.
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Affiliation(s)
- Alicia A. Cutler
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
- Graduate Program in Biochemistry, Cell and Developmental Biology; Emory University; Atlanta GA 30322 USA
| | - Eric B. Dammer
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | - Duc M. Doung
- Department of Biochemistry; Emory University; Atlanta GA 30322 USA
| | | | | | - Grace K. Pavlath
- Department of Pharmacology; Emory University; Atlanta GA 30322 USA
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14
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Nohara K, Chen Z, Yoo SH. A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation. J Vis Exp 2017. [PMID: 28715394 DOI: 10.3791/56013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a challenge for ChIP due to technical difficulty in isolation of high-quality nuclei with minimal contamination of myofibrils. Previous protocols have attempted to purify nuclei before cross-linking, which incurs the risk of altered DNA-protein interaction during the prolonged nuclei preparation process. In the current protocol, we first cross-linked the skeletal muscle tissue collected from mice, and the tissues were minced and sonicated. Since we found that ultracentrifugation was not able to separate nuclei from myofibrils using cross-linked muscle tissue, we devised a sequential filtration procedure to obtain high-quality nuclei devoid of significant myofibril contamination. We subsequently prepared chromatin by using an ultrasonicator, and ChIP assays with anti-BMAL1 antibody revealed robust circadian binding pattern of BMAL1 to target gene promoters. This filtration protocol constitutes an easily applicable method to isolate high-quality nuclei from cross-linked skeletal muscle tissue, allowing consistent sample processing for circadian and other time-sensitive studies. In combination with next-generation sequencing (NGS), our method can be deployed for various mechanistic and genomic studies focusing on skeletal muscle function.
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Affiliation(s)
- Kazunari Nohara
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston;
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15
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Cutler AA, Corbett AH, Pavlath GK. Biochemical Isolation of Myonuclei from Mouse Skeletal Muscle Tissue. Bio Protoc 2017; 7:e2654. [PMID: 29594187 DOI: 10.21769/bioprotoc.2654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Skeletal muscle provides the contractile force necessary for movement, swallowing, and breathing and, consequently, is necessary for survival. Skeletal muscle cells are unique in that they are extremely large cells containing thousands of nuclei. These nuclei must all work in concert to maintain skeletal muscle function and thereby maintain life. The nucleus is a major site of signaling integration and gene expression regulation. However, examining nuclear processes in skeletal muscle can be difficult because myonuclei are challenging to isolate. We optimized a protocol to purify myonuclei from whole muscle tissue using ultracentrifugation over a discontinuous sucrose gradient to separate the nuclear fraction. We used these purified nuclei for downstream applications including flow cytometry and mass spectrometry. We used this method to compare the myonuclear proteome of young and old mouse hindlimb muscles (Cutler et al., 2017). This protocol may be applied to isolating myonuclei for a variety of downstream analyses such as flow cytometry, microscopy, Western blot, and proteomics.
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16
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Korfali N, Florens L, Schirmer EC. Isolation, Proteomic Analysis, and Microscopy Confirmation of the Liver Nuclear Envelope Proteome. Methods Mol Biol 2016; 1411:3-44. [PMID: 27147032 DOI: 10.1007/978-1-4939-3530-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nuclei can be relatively easily extracted from homogenized liver due to the softness of the tissue and crudely separated from other cellular organelles by low-speed centrifugation due to the comparatively large size of nuclei. However, further purification is complicated by nuclear envelope continuity with the endoplasmic reticulum, invaginations containing mitochondria, and connections to the cytoskeleton. Subsequent purification to nuclear envelopes is additionally confounded by connections of inner nuclear membrane proteins to chromatin. For these reasons, it is necessary to confirm proteomic identification of nuclear envelope proteins by testing targeting of individual proteins. The proteomic identification of nuclear envelope fractions is affected by the tendencies of transmembrane proteins to have extreme isoelectric points, strongly hydrophobic peptides, posttranslational modifications, and a propensity to aggregate, thus making proteolysis inefficient. To circumvent these problems, we have developed a MudPIT approach that uses multiple extractions and sequential proteolysis to increase identifications. Here we describe methods for isolating nuclear envelopes, determining their proteome by MudPIT, and confirming their targeting to the nuclear periphery by microscopy.
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Affiliation(s)
- Nadia Korfali
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Laurence Florens
- The Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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17
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Makarov AA, Rizzotto A, Meinke P, Schirmer EC. Purification of Lamins and Soluble Fragments of NETs. Methods Enzymol 2015; 569:79-100. [PMID: 26778554 DOI: 10.1016/bs.mie.2015.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lamins and associated nuclear envelope transmembrane proteins (NETs) present unique problems for biochemical studies. Lamins form insoluble intermediate filament networks, associate with chromatin, and are also connected via specific NETs to the cytoskeleton, thus further complicating their isolation and purification from mammalian cells. Adding to this complexity, NETs at the inner nuclear membrane function in three distinct environments: (a) their nucleoplasmic domain(s) can bind lamins, chromatin, and transcriptional regulators; (b) they possess one or more integral transmembrane domains; and (c) their lumenal domain(s) function in the unique reducing environment of the nuclear envelope/ER lumen. This chapter describes strategic considerations and protocols to facilitate biochemical studies of lamins and NET proteins in vitro. Studying these proteins in vitro typically involves first expressing specific polypeptide fragments in bacteria and optimizing conditions to purify each fragment. We describe parameters for choosing specific fragments and designing purification strategies and provide detailed purification protocols. Biochemical studies can provide fundamental knowledge including binding strengths and the molecular consequences of disease-causing mutations that will be essential to understand nuclear envelope-genome interactions and nuclear envelope linked disease mechanisms.
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Affiliation(s)
- Alexandr A Makarov
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrea Rizzotto
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Meinke
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.
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Ori A, Andrés-Pons A, Beck M. The use of targeted proteomics to determine the stoichiometry of large macromolecular assemblies. Methods Cell Biol 2014; 122:117-46. [PMID: 24857728 DOI: 10.1016/b978-0-12-417160-2.00006-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate knowledge of the stoichiometry of protein complexes is a crucial prerequisite for understanding their structure and function. To purify or enrich large and intricate protein complexes such that their structure is preserved and to absolutely quantify all of their protein components is an enormous technical challenge. In this chapter, we describe how to purify nuclear envelopes from human tissue culture cells that are highly enriched for nuclear pore complexes. We use the nuclear pore as an example to discuss how the structural preservation of such preparations can be controlled. Furthermore, we give a practical guide how to develop and employ targeted proteomic assays for both, the absolute quantification of stoichiometries and the relative quantification of protein complex composition across multiple biological conditions. The concept discussed here is universally applicable to any protein complex.
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Affiliation(s)
- Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Amparo Andrés-Pons
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69117, Heidelberg, Germany
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Ramadan W, Marsili A, Huang S, Larsen PR, Silva JE. Type-2 iodothyronine 5'deiodinase in skeletal muscle of C57BL/6 mice. I. Identity, subcellular localization, and characterization. Endocrinology 2011; 152:3082-92. [PMID: 21628384 PMCID: PMC3138240 DOI: 10.1210/en.2011-0137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/06/2011] [Indexed: 01/21/2023]
Abstract
RT-PCR shows that mouse skeletal muscle contains type-2 iodothyronine deiodinase (D2) mRNA. However, the D2 activity has been hard to measure. Except for newborn mice, muscle homogenates have no detectable activity. However, we have reported D2 activity in mouse muscle microsomes. As the mRNA, activity is higher in slow- than in fast-twitch muscle. We addressed here the major problems in measuring D2 activity in muscle by: homogenizing muscle in high salt to improve yield of membranous structures; separating postmitochondrial supernatant between 38 and 50% sucrose, to eliminate lighter membranes lacking D2; washing these with 0.1 M Na(2)CO(3) to eliminate additional contaminating proteins; pretreating all buffers with Chelex, to eliminate catalytic metals; and eliminating the EDTA from the assay, as this can bind iron that enhances dithiothreitol oxidation and promotes peroxidation reactions. Maximum velocity of T(3) generation by postgradient microsomes from red muscles was approximately 1100 fmol/(h · mg) protein with a Michaelis-Menten constant for T(4) of 1.5 nM. D2-specific activity of Na(2)CO(3)-washed microsomes was 6-10 times higher. The enrichment in D2 activity increased in parallel with the capacity of microsomes to load (sarco/endoplasmic reticulum Ca(2+)-ATPase) and bind Ca(2+) (calsequestrin), indicating that D2 resides in the inner sarcoplasmic reticulum, close to the nuclei. The presence of D3 in the sarcolemma suggests that the most of D2-generated T(3) acts locally. Estimates from maximum velocity, Michaelis-Menten constant, and muscle T(4) content suggest that mouse red, type-1, aerobic mouse muscle fibers can generate physiologically relevant amounts of T(3) and, further, that muscle D2 plays an important role in thyroid hormone-dependent muscle thermogenesis.
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Affiliation(s)
- W Ramadan
- Baystate Medical Center, Tufts University School of Medicine, Springfield, Massachusetts 01199, USA
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20
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Wilkie GS, Korfali N, Swanson SK, Malik P, Srsen V, Batrakou DG, de las Heras J, Zuleger N, Kerr ARW, Florens L, Schirmer EC. Several novel nuclear envelope transmembrane proteins identified in skeletal muscle have cytoskeletal associations. Mol Cell Proteomics 2010; 10:M110.003129. [PMID: 20876400 PMCID: PMC3016689 DOI: 10.1074/mcp.m110.003129] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Nuclear envelopes from liver and a neuroblastoma cell line have previously been analyzed by proteomics; however, most diseases associated with the nuclear envelope affect muscle. To determine whether muscle has unique nuclear envelope proteins, rat skeletal muscle nuclear envelopes were prepared and analyzed by multidimensional protein identification technology. Many novel muscle-specific proteins were identified that did not appear in previous nuclear envelope data sets. Nuclear envelope residence was confirmed for 11 of these by expression of fusion proteins and by antibody staining of muscle tissue cryosections. Moreover, transcript levels for several of the newly identified nuclear envelope transmembrane proteins increased during muscle differentiation using mouse and human in vitro model systems. Some of these proteins tracked with microtubules at the nuclear surface in interphase cells and accumulated at the base of the microtubule spindle in mitotic cells, suggesting they may associate with complexes that connect the nucleus to the cytoskeleton. The finding of tissue-specific proteins in the skeletal muscle nuclear envelope proteome argues the importance of analyzing nuclear envelopes from all tissues linked to disease and suggests that general investigation of tissue differences in organellar proteomes might yield critical insights.
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Affiliation(s)
- Gavin S Wilkie
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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