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Rose M, Burgess JT, Cheong CM, Adams MN, Shahrouzi P, O’Byrne KJ, Richard DJ, Bolderson E. The expression and role of the Lem-D proteins Ankle2, Emerin, Lemd2, and TMPO in triple-negative breast cancer cell growth. Front Oncol 2024; 14:1222698. [PMID: 38720803 PMCID: PMC11076778 DOI: 10.3389/fonc.2024.1222698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 02/28/2024] [Indexed: 05/12/2024] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a sub-classification of breast carcinomas, which leads to poor survival outcomes for patients. TNBCs do not possess the hormone receptors that are frequently targeted as a therapeutic in other cancer subtypes and, therefore, chemotherapy remains the standard treatment for TNBC. Nuclear envelope proteins are frequently dysregulated in cancer cells, supporting their potential as novel cancer therapy targets. The Lem-domain (Lem-D) (LAP2, Emerin, MAN1 domain, and Lem-D) proteins are a family of inner nuclear membrane proteins, which share a ~45-residue Lem-D. The Lem-D proteins, including Ankle2, Lemd2, TMPO, and Emerin, have been shown to be associated with many of the hallmarks of cancer. This study aimed to define the association between the Lem-D proteins and TNBC and determine whether these proteins could be promising therapeutic targets. Methods GENT2, TCGA, and KM plotter were utilized to investigate the expression and prognostic implications of several Lem-D proteins: Ankle2, TMPO, Emerin, and Lemd2 in publicly available breast cancer patient data. Immunoblotting and immunofluorescent analysis of immortalized non-cancerous breast cells and a panel of TNBC cells were utilized to establish whether protein expression of the Lem-D proteins was significantly altered in TNBC. SiRNA was used to decrease individual Lem-D protein expression, and functional assays, including proliferation assays and apoptosis assays, were conducted. Results The Lem-D proteins were generally overexpressed in TNBC patient samples at the mRNA level and showed variable expression at the protein level in TNBC cell lysates. Similarly, protein levels were generally negatively correlated with patient survival outcomes. siRNA-mediated depletion of the individual Lem-D proteins in TNBC cells induced aberrant nuclear morphology, decreased proliferation, and induced cell death. However, minimal effects on nuclear morphology or cell viability were observed following Lem-D depletion in non-cancerous MCF10A cells. Conclusion There is evidence to suggest that Ankle2, TMPO, Emerin, and Lemd2 expressions are correlated with breast cancer patient outcomes, but larger patient sample numbers are required to confirm this. siRNA-mediated depletion of these proteins was shown to specifically impair TNBC cell growth, suggesting that the Lem-D proteins may be a specific anti-cancer target.
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Affiliation(s)
- Maddison Rose
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Joshua T. Burgess
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Chee Man Cheong
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mark N. Adams
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Parastoo Shahrouzi
- Department of Medical Genetics, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Kenneth J. O’Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
- Cancer Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Emma Bolderson
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
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Barger SR, Penfield L, Bahmanyar S. Nuclear envelope assembly relies on CHMP-7 in the absence of BAF-LEM-mediated hole closure. J Cell Sci 2023; 136:jcs261385. [PMID: 37795681 PMCID: PMC10668030 DOI: 10.1242/jcs.261385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Barrier-to-autointegration factor (BAF) protein is a DNA-binding protein that crosslinks chromatin to allow mitotic nuclear envelope (NE) assembly. The LAP2-emerin-MAN1 (LEM)-domain protein LEMD2 and ESCRT-II/III hybrid protein CHMP7 close NE holes surrounding spindle microtubules (MTs). BAF binds LEM-domain family proteins to repair NE ruptures in interphase, but whether BAF-LEM binding participates in NE hole closure around spindle MTs is not known. Here, we took advantage of the stereotypical event of NE formation in fertilized Caenorhabditis elegans oocytes to show that BAF-LEM binding and LEM-2-CHMP-7 have distinct roles in NE closure around spindle MTs. LEM-2 and EMR-1 (homologs of LEMD2 and emerin) function redundantly with BAF-1 (the C. elegans BAF protein) in NE closure. Compromising BAF-LEM binding revealed an additional role for EMR-1 in the maintenance of the NE permeability barrier. In the absence of BAF-LEM binding, LEM-2-CHMP-7 was required for NE assembly and embryo survival. The winged helix domain of LEM-2 recruits CHMP-7 to the NE in C. elegans and a LEM-2-independent nucleoplasmic pool of CHMP-7 also contributes to NE stability. Thus, NE hole closure surrounding spindle MTs requires redundant mechanisms that safeguard against failure in NE assembly to support embryogenesis.
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Affiliation(s)
- Sarah R. Barger
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511, USA
| | - Lauren Penfield
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511, USA
| | - Shirin Bahmanyar
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511, USA
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3
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Ross JA, Arcos-Villacis N, Battey E, Boogerd C, Orellana CA, Marhuenda E, Swiatlowska P, Hodzic D, Prin F, Mohun T, Catibog N, Tapia O, Gerace L, Iskratsch T, Shah AM, Stroud MJ. Lem2 is essential for cardiac development by maintaining nuclear integrity. Cardiovasc Res 2023; 119:2074-2088. [PMID: 37067297 PMCID: PMC10478753 DOI: 10.1093/cvr/cvad061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 04/18/2023] Open
Abstract
AIMS Nuclear envelope integrity is essential for the compartmentalization of the nucleus and cytoplasm. Importantly, mutations in genes encoding nuclear envelope (NE) and associated proteins are the second highest cause of familial dilated cardiomyopathy. One such NE protein that causes cardiomyopathy in humans and affects mouse heart development is Lem2. However, its role in the heart remains poorly understood. METHODS AND RESULTS We generated mice in which Lem2 was specifically ablated either in embryonic cardiomyocytes (Lem2 cKO) or in adult cardiomyocytes (Lem2 iCKO) and carried out detailed physiological, tissue, and cellular analyses. High-resolution episcopic microscopy was used for three-dimensional reconstructions and detailed morphological analyses. RNA-sequencing and immunofluorescence identified altered pathways and cellular phenotypes, and cardiomyocytes were isolated to interrogate nuclear integrity in more detail. In addition, echocardiography provided a physiological assessment of Lem2 iCKO adult mice. We found that Lem2 was essential for cardiac development, and hearts from Lem2 cKO mice were morphologically and transcriptionally underdeveloped. Lem2 cKO hearts displayed high levels of DNA damage, nuclear rupture, and apoptosis. Crucially, we found that these defects were driven by muscle contraction as they were ameliorated by inhibiting myosin contraction and L-type calcium channels. Conversely, reducing Lem2 levels to ∼45% in adult cardiomyocytes did not lead to overt cardiac dysfunction up to 18 months of age. CONCLUSIONS Our data suggest that Lem2 is critical for integrity at the nascent NE in foetal hearts, and protects the nucleus from the mechanical forces of muscle contraction. In contrast, the adult heart is not detectably affected by partial Lem2 depletion, perhaps owing to a more established NE and increased adaptation to mechanical stress. Taken together, these data provide insights into mechanisms underlying cardiomyopathy in patients with mutations in Lem2 and cardio-laminopathies in general.
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Affiliation(s)
- Jacob A Ross
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular & Metabolic Medicine & Sciences, Faculty of Life Sciences & Medicine, King’s College London, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Nathaly Arcos-Villacis
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular & Metabolic Medicine & Sciences, Faculty of Life Sciences & Medicine, King’s College London, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Edmund Battey
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular & Metabolic Medicine & Sciences, Faculty of Life Sciences & Medicine, King’s College London, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
- Centre of Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 1UL, UK
| | - Cornelis Boogerd
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands
| | - Constanza Avalos Orellana
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular & Metabolic Medicine & Sciences, Faculty of Life Sciences & Medicine, King’s College London, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Emilie Marhuenda
- Division of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - Pamela Swiatlowska
- Division of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - Didier Hodzic
- Department of Developmental Biology, Washington University School of Medicine, 660S. Euclid Avenue, St Louis, MO 63110, USA
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London NW1 1AT, UK
| | - Tim Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London NW1 1AT, UK
| | - Norman Catibog
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular & Metabolic Medicine & Sciences, Faculty of Life Sciences & Medicine, King’s College London, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Olga Tapia
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Santander 39011, Spain
- Department of Basic Medical Sciences, Institute of Biomedical Technologies, University of La Laguna, Tenerife 38200, Spain
| | - Larry Gerace
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas Iskratsch
- Division of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - Ajay M Shah
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular & Metabolic Medicine & Sciences, Faculty of Life Sciences & Medicine, King’s College London, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
| | - Matthew J Stroud
- British Heart Foundation Centre of Research Excellence, School of Cardiovascular & Metabolic Medicine & Sciences, Faculty of Life Sciences & Medicine, King’s College London, James Black Centre, 125 Coldharbour Lane, London SE5 9NU, UK
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Barger SR, Penfield L, Bahmanyar S. Nuclear envelope assembly relies on CHMP-7 in the absence of BAF-LEM-mediated hole closure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547980. [PMID: 37461528 PMCID: PMC10350047 DOI: 10.1101/2023.07.06.547980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Barrier-to-autointegration factor (BAF) is a DNA binding protein that crosslinks chromatin to assemble the nuclear envelope (NE) after mitosis. BAF also binds the Lap2b-Emerin-Man1 (LEM) domain family of NE proteins to repair interphase ruptures. The NE adaptors to ESCRTs, LEMD2-CHMP7, seal NE holes surrounding mitotic spindle microtubules (MTs), but whether NE hole closure in mitosis involves BAF-LEM binding is not known. Here, we analyze NE sealing after meiosis II in C. elegans oocytes to show that BAF-LEM binding and LEM-2 LEMD2 -CHMP-7 have distinct roles in hole closure around spindle MTs. LEM-2/EMR-1 emerin function redundantly with BAF-1 to seal the NE. Compromising BAF-LEM binding revealed an additional role for EMR-1 in maintenance of the NE permeability barrier and an essential role for LEM-2-CHMP-7 in preventing NE assembly failure. The WH domain of LEM-2 recruits the majority of CHMP-7 to the NE in C. elegans and a LEM-2 -independent pool of CHMP-7, which is mostly enriched in the nucleoplasm, also contributes to NE stability. Thus, NE hole closure surrounding spindle MTs requires redundant mechanisms that safeguard against failure in NE assembly to support embryogenesis.
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Affiliation(s)
- Sarah R. Barger
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511
| | - Lauren Penfield
- Current address: Department of Molecular, Cellular, and Developmental Biology at University of California, Santa Barbara, CA
| | - Shirin Bahmanyar
- Yale University, Department of Molecular, Cellular, Developmental Biology, 266 Whitney Ave., New Haven, CT 06511
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Hou X, Xu M, Zhu C, Gao J, Li M, Chen X, Sun C, Nashan B, Zang J, Zhou Y, Guang S, Feng X. Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans. Nat Commun 2023; 14:1254. [PMID: 36878913 PMCID: PMC9988841 DOI: 10.1038/s41467-023-36898-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
The chromatin organization modifier domain (chromodomain) is an evolutionally conserved motif across eukaryotic species. The chromodomain mainly functions as a histone methyl-lysine reader to modulate gene expression, chromatin spatial conformation and genome stability. Mutations or aberrant expression of chromodomain proteins can result in cancer and other human diseases. Here, we systematically tag chromodomain proteins with green fluorescent protein (GFP) using CRISPR/Cas9 technology in C. elegans. By combining ChIP-seq analysis and imaging, we delineate a comprehensive expression and functional map of chromodomain proteins. We then conduct a candidate-based RNAi screening and identify factors that regulate the expression and subcellular localization of the chromodomain proteins. Specifically, we reveal an H3K9me1/2 reader, CEC-5, both by in vitro biochemistry and in vivo ChIP assays. MET-2, an H3K9me1/2 writer, is required for CEC-5 association with heterochromatin. Both MET-2 and CEC-5 are required for the normal lifespan of C. elegans. Furthermore, a forward genetic screening identifies a conserved Arginine124 of CEC-5's chromodomain, which is essential for CEC-5's association with chromatin and life span regulation. Thus, our work will serve as a reference to explore chromodomain functions and regulation in C. elegans and allow potential applications in aging-related human diseases.
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Affiliation(s)
- Xinhao Hou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Mingjing Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Jianing Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Meili Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Cheng Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Björn Nashan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Jianye Zang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 230027, Hefei, Anhui, P. R. China.
| | - Xuezhu Feng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
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Caravia XM, Ramirez-Martinez A, Gan P, Wang F, McAnally JR, Xu L, Bassel-Duby R, Liu N, Olson EN. Loss of function of the nuclear envelope protein LEMD2 causes DNA damage-dependent cardiomyopathy. J Clin Invest 2022; 132:e158897. [PMID: 36377660 PMCID: PMC9663152 DOI: 10.1172/jci158897] [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: 02/03/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Mutations in nuclear envelope proteins (NEPs) cause devastating genetic diseases, known as envelopathies, that primarily affect the heart and skeletal muscle. A mutation in the NEP LEM domain-containing protein 2 (LEMD2) causes severe cardiomyopathy in humans. However, the roles of LEMD2 in the heart and the pathological mechanisms responsible for its association with cardiac disease are unknown. We generated knockin (KI) mice carrying the human c.T38>G Lemd2 mutation, which causes a missense amino acid exchange (p.L13>R) in the LEM domain of the protein. These mice represent a preclinical model that phenocopies the human disease, as they developed severe dilated cardiomyopathy and cardiac fibrosis leading to premature death. At the cellular level, KI/KI cardiomyocytes exhibited disorganization of the transcriptionally silent heterochromatin associated with the nuclear envelope. Moreover, mice with cardiac-specific deletion of Lemd2 also died shortly after birth due to heart abnormalities. Cardiomyocytes lacking Lemd2 displayed nuclear envelope deformations and extensive DNA damage and apoptosis linked to p53 activation. Importantly, cardiomyocyte-specific Lemd2 gene therapy via adeno-associated virus rescued cardiac function in KI/KI mice. Together, our results reveal the essentiality of LEMD2 for genome stability and cardiac function and unveil its mechanistic association with human disease.
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Affiliation(s)
- Xurde M. Caravia
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, and
| | - Andres Ramirez-Martinez
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, and
| | - Peiheng Gan
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, and
| | - Feng Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John R. McAnally
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, and
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, and
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, and
| | - Eric N. Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, and
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Shankar R, Lettman MM, Whisler W, Frankel EB, Audhya A. The ESCRT machinery directs quality control over inner nuclear membrane architecture. Cell Rep 2022; 38:110263. [PMID: 35045304 PMCID: PMC8801257 DOI: 10.1016/j.celrep.2021.110263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 11/21/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022] Open
Abstract
The late-acting endosomal sorting complex required for transport (ESCRT) machinery has been implicated in facilitating the resealing of the nuclear envelope (NE) after mitosis, enabling compartmentalization of the genome away from the cytoplasm. Here, we leverage the stereotypic first division of the C. elegans embryo to identify additional functions of the ESCRT machinery in maintaining the structure of the inner nuclear membrane. Specifically, impaired ESCRT function results in a defect in the pruning of inner nuclear membrane invaginations, which arise normally during NE reformation and expansion. Additionally, in combination with a hypomorphic mutation that interferes with assembly of the underlying nuclear lamina, inhibition of ESCRT function significantly perturbs NE architecture and increases chromosome segregation defects, resulting in penetrant embryonic lethality. Our findings highlight links between ESCRT-mediated inner nuclear membrane remodeling, maintenance of nuclear envelope morphology, and the preservation of the genome during early development. In this study, Shankar et al. demonstrate that defects in ESCRT machinery functions impair pruning of inner nuclear membrane invaginations that form normally after mitotic exit as the nuclear envelope undergoes expansion. These findings highlight a critical role for the ESCRT machinery in the maintenance of inner nuclear membrane morphology.
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Affiliation(s)
- Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Molly M Lettman
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - William Whisler
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Elisa B Frankel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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8
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Drosophila female germline stem cells undergo mitosis without nuclear breakdown. Curr Biol 2021; 31:1450-1462.e3. [PMID: 33548191 DOI: 10.1016/j.cub.2021.01.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/18/2020] [Accepted: 01/11/2021] [Indexed: 02/02/2023]
Abstract
Stem cell homeostasis requires nuclear lamina (NL) integrity. In Drosophila germ cells, compromised NL integrity activates the ataxia telangiectasia and Rad3-related (ATR) and checkpoint kinase 2 (Chk2) checkpoint kinases, blocking germ cell differentiation and causing germline stem cell (GSC) loss. Checkpoint activation occurs upon loss of either the NL protein emerin or its partner barrier-to-autointegration factor, two proteins required for nuclear reassembly at the end of mitosis. Here, we examined how mitosis contributes to NL structural defects linked to checkpoint activation. These analyses led to the unexpected discovery that wild-type female GSCs utilize a non-canonical mode of mitosis, one that retains a permeable but intact nuclear envelope and NL. We show that the interphase NL is remodeled during mitosis for insertion of centrosomes that nucleate the mitotic spindle within the confines of the nucleus. We show that depletion or loss of NL components causes mitotic defects, including compromised chromosome segregation associated with altered centrosome positioning and structure. Further, in emerin mutant GSCs, centrosomes remain embedded in the interphase NL. Notably, these embedded centrosomes carry large amounts of pericentriolar material and nucleate astral microtubules, revealing a role for emerin in the regulation of centrosome structure. Epistasis studies demonstrate that defects in centrosome structure are upstream of checkpoint activation, suggesting that these centrosome defects might trigger checkpoint activation and GSC loss. Connections between NL proteins and centrosome function have implications for mechanisms associated with NL dysfunction in other stem cell populations, including NL-associated diseases, such as laminopathies.
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Charar C, Metsuyanim-Cohen S, Gruenbaum Y, Bar DZ. Exploring the nuclear lamina in health and pathology using C. elegans. Curr Top Dev Biol 2021; 144:91-110. [PMID: 33992162 DOI: 10.1016/bs.ctdb.2020.12.005] [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] [Indexed: 12/23/2022]
Abstract
The eukaryotic genome inside the nucleus is enveloped by two membranes, the Outer Nuclear Membrane (ONM) and the Inner Nuclear Membrane (INM). Tethered to the INM is the nuclear lamina, a fibrillar network composed of lamins-the nuclear intermediate filaments, and membrane associated proteins. The nuclear lamina interacts with several nuclear structures, including chromatin. As most nuclear functions, including regulation of gene expression, chromosome segregation and duplication as well as nuclear structure, are highly conserved in metazoans, the Caenorhabditis elegans nematode serves as a powerful model organism to study nuclear processes and architecture. This translucent organism can easily be observed under a microscope as a live embryo, larvae and even adult. Here we will review the data on nuclear lamina composition and functions gathered from studies using C. elegans model organisms: We will discuss genome spatial organization and its contribution to gene expression. We will review both the interaction between the cytoplasm and the nucleus and mechanotransduction mechanism. Finally, we will discuss disease causing mutation in nuclear lamins, including the use of this animal model in diseases research.
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Affiliation(s)
- Chayki Charar
- Department of Genetics, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel; Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sally Metsuyanim-Cohen
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yosef Gruenbaum
- Department of Genetics, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Z Bar
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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10
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AlKhaleefa A, Snider FL, Duff HJ, McGhee JD. -Using the C. elegans lem-2 Gene to Reconstruct the Human LEMD2 Mutation Associated with Hutterite-type Cataract/Cardiomyopathy. MICROPUBLICATION BIOLOGY 2020; 2020. [PMID: 32666044 PMCID: PMC7351585 DOI: 10.17912/micropub.biology.000273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ayaa AlKhaleefa
- 1. Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
| | - Frances L Snider
- 1. Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
| | - Henry J Duff
- Cardiac Sciences, Libin Cardiology Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
| | - James D McGhee
- 1. Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta CANADA
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11
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Loss of an H3K9me anchor rescues laminopathy-linked changes in nuclear organization and muscle function in an Emery-Dreifuss muscular dystrophy model. Genes Dev 2020; 34:560-579. [PMID: 32139421 PMCID: PMC7111258 DOI: 10.1101/gad.332213.119] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/14/2020] [Indexed: 12/30/2022]
Abstract
In this study, Harr et al. use C. elegans to investigate the consequences of a missense mutation (Y45C) in lamin A (encoded by LMNA) found in the human Emery-Dreifuss muscular dystrophy (EDMD) syndrome. Using muscle-specific emerin Dam-ID and other in vivo approaches, the authors report that they were able to counteract the dominant muscle-specific defects provoked by LMNA mutation by the ablation of a lamin-associated H3K9me anchor, suggesting a novel therapeutic pathway for treating EDMD. Mutations in the nuclear structural protein lamin A produce rare, tissue-specific diseases called laminopathies. The introduction of a human Emery-Dreifuss muscular dystrophy (EDMD)-inducing mutation into the C. elegans lamin (LMN-Y59C), recapitulates many muscular dystrophy phenotypes, and correlates with hyper-sequestration of a heterochromatic array at the nuclear periphery in muscle cells. Using muscle-specific emerin Dam-ID in worms, we monitored the effects of the mutation on endogenous chromatin. An increased contact with the nuclear periphery along chromosome arms, and an enhanced release of chromosomal centers, coincided with the disease phenotypes of reduced locomotion and compromised sarcomere integrity. The coupling of the LMN-Y59C mutation with the ablation of CEC-4, a chromodomain protein that anchors H3K9-methylated chromatin at the nuclear envelope (NE), suppressed the muscle-associated disease phenotypes. Deletion of cec-4 also rescued LMN-Y59C-linked alterations in chromatin organization and some changes in transcription. Sequences that changed position in the LMN-Y59C mutant, are enriched for E2F (EFL-2)-binding sites, consistent with previous studies suggesting that altered Rb-E2F interaction with lamin A may contribute to muscle dysfunction. In summary, we were able to counteract the dominant muscle-specific defects provoked by LMNA mutation by the ablation of a lamin-associated H3K9me anchor, suggesting a novel therapeutic pathway for EDMD.
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12
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Moser B, Basílio J, Gotzmann J, Brachner A, Foisner R. Comparative Interactome Analysis of Emerin, MAN1 and LEM2 Reveals a Unique Role for LEM2 in Nucleotide Excision Repair. Cells 2020; 9:cells9020463. [PMID: 32085595 PMCID: PMC7072835 DOI: 10.3390/cells9020463] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/19/2022] Open
Abstract
LAP2-Emerin-MAN1 (LEM) domain-containing proteins represent an abundant group of inner nuclear membrane proteins involved in diverse nuclear functions, but their functional redundancies remain unclear. Here, using the biotinylation-dependent proximity approach, we report proteome-wide comparative interactome analysis of the two structurally related LEM proteins MAN1 (LEMD3) and LEM2 (LEMD2), and the more distantly related emerin (EMD). While over 60% of the relatively small group of MAN1 and emerin interactors were also found in the LEM2 interactome, the latter included a large number of candidates (>85%) unique for LEM2. The interacting partners unique for emerin support and provide further insight into the previously reported role of emerin in centrosome positioning, and the MAN1-specific interactors suggest a role of MAN1 in ribonucleoprotein complex assembly. Interestingly, the LEM2-specific interactome contained several proteins of the nucleotide excision repair pathway. Accordingly, LEM2-depleted cells, but not MAN1- and emerin-depleted cells, showed impaired proliferation following ultraviolet-C (UV-C) irradiation and prolonged accumulation of γH2AX, similar to cells deficient in the nucleotide excision repair protein DNA damage-binding protein 1 (DDB1). These findings indicate impaired DNA damage repair in LEM2-depleted cells. Overall, this interactome study identifies new potential interaction partners of emerin, MAN1 and particularly LEM2, and describes a novel potential involvement of LEM2 in nucleotide excision repair at the nuclear periphery.
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Affiliation(s)
- Bernhard Moser
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - José Basílio
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Josef Gotzmann
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
| | - Andreas Brachner
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
- Correspondence: (A.B.); (R.F.)
| | - Roland Foisner
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
- Correspondence: (A.B.); (R.F.)
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13
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Dharmaraj T, Guan Y, Liu J, Badens C, Gaborit B, Wilson KL. Rare BANF1 Alleles and Relatively Frequent EMD Alleles Including 'Healthy Lipid' Emerin p.D149H in the ExAC Cohort. Front Cell Dev Biol 2019; 7:48. [PMID: 31024910 PMCID: PMC6459885 DOI: 10.3389/fcell.2019.00048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/19/2019] [Indexed: 01/05/2023] Open
Abstract
Emerin (EMD) and barrier to autointegration factor 1 (BANF1) each bind A-type lamins (LMNA) as fundamental components of nuclear lamina structure. Mutations in LMNA, EMD and BANF1 are genetically linked to many tissue-specific disorders including Emery-Dreifuss muscular dystrophy and cardiomyopathy (LMNA, EMD), lipodystrophy, insulin resistance and type 2 diabetes (LMNA) and progeria (LMNA, BANF1). To explore human genetic variation in these genes, we analyzed EMD and BANF1 alleles in the Exome Aggregation Consortium (ExAC) cohort of 60,706 unrelated individuals. We identified 13 rare heterozygous BANF1 missense variants (p.T2S, p.H7Y, p.D9N, p.S22R, p.G25E, p.D55N, p.D57Y, p.L63P, p.N70T, p.K72R, p.R75W, p.R75Q, p.G79R), and one homozygous variant (p.D9H). Several variants are known (p.G25E) or predicted (e.g., p.D9H, p.D9N, p.L63P) to perturb BANF1 and warrant further study. Analysis of EMD revealed two previously identified variants associated with adult-onset cardiomyopathy (p.K37del, p.E35K) and one deemed 'benign' in an Emery-Dreifuss patient (p.D149H). Interestingly p.D149H was the most frequent emerin variant in ExAC, identified in 58 individuals (overall allele frequency 0.06645%), of whom 55 were East Asian (allele frequency 0.8297%). Furthermore, p.D149H associated with four 'healthy' traits: reduced triglycerides (-0.336; p = 0.0368), reduced waist circumference (-0.321; p = 0.0486), reduced cholesterol (-0.572; p = 0.000346) and reduced LDL cholesterol (-0.599; p = 0.000272). These traits are distinct from LMNA-associated metabolic disorders and provide the first insight that emerin influences metabolism. We also identified one novel in-frame deletion (p.F39del) and 62 novel emerin missense variants, many of which were relatively frequent and potentially disruptive including p.N91S and p.S143F (∼0.041% and ∼0.034% of non-Finnish Europeans, respectively), p.G156S (∼0.39% of Africans), p.R204G (∼0.18% of Latinx), p.R207P (∼0.08% of South Asians) and p.R221L (∼0.15% of Latinx). Many novel BANF1 variants are predicted to disrupt dimerization or binding to DNA, histones, emerin or A-type lamins. Many novel emerin variants are predicted to disrupt emerin filament dynamics or binding to BANF1, HDAC3, A-type lamins or other partners. These new human variants provide a foundational resource for future studies to test the molecular mechanisms of BANF1 and emerin function, and to understand the link between emerin variant p.D149H and a 'healthy' lipid profile.
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Affiliation(s)
- Tejas Dharmaraj
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Youchen Guan
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Julie Liu
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | | | - Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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14
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Dubińska-Magiera M, Kozioł K, Machowska M, Piekarowicz K, Filipczak D, Rzepecki R. Emerin Is Required for Proper Nucleus Reassembly after Mitosis: Implications for New Pathogenetic Mechanisms for Laminopathies Detected in EDMD1 Patients. Cells 2019; 8:cells8030240. [PMID: 30871242 PMCID: PMC6468536 DOI: 10.3390/cells8030240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 12/29/2022] Open
Abstract
Emerin is an essential LEM (LAP2, Emerin, MAN1) domain protein in metazoans and an integral membrane protein associated with inner and outer nuclear membranes. Mutations in the human EMD gene coding for emerin result in the rare genetic disorder: Emery–Dreifuss muscular dystrophy type 1 (EDMD1). This disease belongs to a broader group called laminopathies—a heterogeneous group of rare genetic disorders affecting tissues of mesodermal origin. EDMD1 phenotype is characterized by progressive muscle wasting, contractures of the elbow and Achilles tendons, and cardiac conduction defects. Emerin is involved in many cellular and intranuclear processes through interactions with several partners: lamins; barrier-to-autointegration factor (BAF), β-catenin, actin, and tubulin. Our study demonstrates the presence of the emerin fraction which associates with mitotic spindle microtubules and centrosomes during mitosis and colocalizes during early mitosis with lamin A/C, BAF, and membranes at the mitotic spindle. Transfection studies with cells expressing EGFP-emerin protein demonstrate that the emerin fusion protein fraction also localizes to centrosomes and mitotic spindle microtubules during mitosis. Transient expression of emerin deletion mutants revealed that the resulting phenotypes vary and are mutant dependent. The most frequent phenotypes include aberrant nuclear shape, tubulin network mislocalization, aberrant mitosis, and mislocalization of centrosomes. Emerin deletion mutants demonstrated different chromatin binding capacities in an in vitro nuclear assembly assay and chromatin-binding properties correlated with the strength of phenotypic alteration in transfected cells. Aberrant tubulin staining and microtubule network phenotype appearance depended on the presence of the tubulin binding region in the expressed deletion mutants. We believe that the association with tubulin might help to “deliver” emerin and associated membranes to decondensing chromatin. Preliminary analyses of cells from Polish patients with EDMD1 revealed that for several mutations thought to be null for emerin protein, a truncated emerin protein was present. We infer that the EDMD1 phenotype may be strengthened by the toxicity of truncated emerin expressed in patients with certain nonsense mutations in EMD.
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Affiliation(s)
- Magda Dubińska-Magiera
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wroclaw, Poland.
| | - Katarzyna Kozioł
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Magdalena Machowska
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Katarzyna Piekarowicz
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Daria Filipczak
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
| | - Ryszard Rzepecki
- Laboratory of Nuclear Proteins, Faculty of Biotechnology, University of Wroclaw, Fryderyka Joliot-Curie 14a, 50-383 Wroclaw, Poland.
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15
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Iwamoto M, Fukuda Y, Osakada H, Mori C, Hiraoka Y, Haraguchi T. Identification of the evolutionarily conserved nuclear envelope proteins Lem2 and MicLem2 in Tetrahymena thermophila. Gene 2019; 721S:100006. [PMID: 32550543 PMCID: PMC7285967 DOI: 10.1016/j.gene.2019.100006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/18/2018] [Accepted: 01/11/2019] [Indexed: 11/26/2022]
Abstract
Lem2 family proteins, i.e. the LAP2-Emerin-MAN1 (LEM) domain-containing nuclear envelope proteins, are well-conserved from yeasts to humans, both of which belong to the Opisthokonta supergroup. However, whether their homologs are present in other eukaryotic phylogenies remains unclear. In this study, we identified two Lem2 homolog proteins, which we named as Lem2 and MicLem2, in a ciliate Tetrahymena thermophila belonging to the SAR supergroup. Lem2 was localized to the nuclear envelope of the macronucleus (MAC) and micronucleus (MIC), while MicLem2 was exclusively localized to the nuclear envelope of the MIC. Immunoelectron microscopy revealed that Lem2 in T. thermophila was localized to both the inner and outer nuclear envelopes of the MAC and MIC, while MicLem2 was mostly localized to the nuclear pores of the MIC. Molecular domain analysis using GFP-fused protein showed that the N-terminal and luminal domains, including the transmembrane segments, are responsible for nuclear envelope localization. During sexual reproduction, enrichment of Lem2 occurred in the nuclear envelopes of the MAC and MIC to be degraded, while MicLem2 was enriched in the nuclear envelope of the MIC that escaped degradation. These findings suggest the unique characteristics of Tetrahymena Lem2 proteins. Our findings provide insight into the evolutionary divergence of nuclear envelope proteins. Conserved nuclear envelope proteins Lem2 and MicLem2 are identified in Tetrahymena. Lem2 is localized to the nuclear envelope of the macronucleus and the micronucleus. MicLem2 is localized to the nuclear pore complex of the micronucleus. In sexual reproduction, Lem2 is enriched to the nuclei assigned to degradation. MicLem2 is enriched to the micronuclei that are escaped from degradation.
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Key Words
- BAF, barrier-to-autointegration factor
- DAPI, 4′,6‑diamidino‑2‑phenylindole
- DDW, double distilled water
- EDTA, ethylenediaminetetraacetic acid
- ER, endoplasmic reticulum
- GA, glutaraldehyde
- HeH domain
- HeH, helix-extension-helix
- LAP2, lamina associated polypeptide 2
- LEM domain
- LEM, LAP2-Emerin-MAN1
- MAC, macronucleus
- MIC, micronucleus
- MSC domain
- MSC, Man1-Src1p-C-terminal
- Man1
- Man1-Src1p-C-terminal domain
- NE, nuclear envelope
- NLS, nuclear localization signal
- NPC, nuclear pore complex
- Nuclear dimorphism
- Nuclear envelope
- ONM and INM, outer and inner nuclear membranes
- PB, phosphate buffer
- PBS, phosphate buffered saline
- Protist
- RRM, RNA recognition motif
- TM, transmembrane
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Affiliation(s)
- Masaaki Iwamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Osaki, 989-6711, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
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16
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Linker of nucleoskeleton and cytoskeleton complex proteins in cardiomyopathy. Biophys Rev 2018; 10:1033-1051. [PMID: 29869195 PMCID: PMC6082319 DOI: 10.1007/s12551-018-0431-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/24/2018] [Indexed: 12/21/2022] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex couples the nuclear lamina to the cytoskeleton. The LINC complex and its associated proteins play diverse roles in cells, ranging from genome organization, nuclear morphology, gene expression, to mechanical stability. The importance of a functional LINC complex is highlighted by the large number of mutations in genes encoding LINC complex proteins that lead to skeletal and cardiac myopathies. In this review, the structure, function, and interactions between components of the LINC complex will be described. Mutations that are known to cause cardiomyopathy in patients will be discussed alongside their respective mouse models. Furthermore, future challenges for the field and emerging technologies to investigate LINC complex function will be discussed.
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17
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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol 2017; 15:55. [PMID: 28662661 PMCID: PMC5492503 DOI: 10.1186/s12915-017-0391-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
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Affiliation(s)
- James J Russell
- Department of Biology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Departments of Biochemistry and of Microbiology & Immunology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA.
| | - Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA
| | | | - Jessica K Polka
- Visiting Scholar, Whitehead Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Therese Gerbich
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Amy Gladfelter
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - James Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | | | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH, Cambridge, UK
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, CA, 94305, USA
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18
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Thanisch K, Song C, Engelkamp D, Koch J, Wang A, Hallberg E, Foisner R, Leonhardt H, Stewart CL, Joffe B, Solovei I. Nuclear envelope localization of LEMD2 is developmentally dynamic and lamin A/C dependent yet insufficient for heterochromatin tethering. Differentiation 2017; 94:58-70. [PMID: 28056360 DOI: 10.1016/j.diff.2016.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 11/28/2022]
Abstract
Peripheral heterochromatin in mammalian nuclei is tethered to the nuclear envelope by at least two mechanisms here referred to as the A- and B-tethers. The A-tether includes lamins A/C and additional unknown components presumably INM protein(s) interacting with both lamins A/C and chromatin. The B-tether includes the inner nuclear membrane (INM) protein Lamin B-receptor, which binds B-type lamins and chromatin. Generally, at least one of the tethers is always present in the nuclear envelope of mammalian cells. Deletion of both causes the loss of peripheral heterochromatin and consequently inversion of the entire nuclear architecture, with this occurring naturally in rod photoreceptors of nocturnal mammals. The tethers are differentially utilized during development, regulate gene expression in opposite manners, and play an important role during cell differentiation. Here we aimed to identify the unknown chromatin binding component(s) of the A-tether. We analyzed 10 mouse tissues by immunostaining with antibodies against 7 INM proteins and found that every cell type has specific, although differentially and developmentally regulated, sets of these proteins. In particular, we found that INM protein LEMD2 is concomitantly expressed with A-type lamins in various cell types but is lacking in inverted nuclei of rod cells. Truncation or deletion of Lmna resulted in the downregulation and mislocalization of LEMD2, suggesting that the two proteins interact and pointing at LEMD2 as a potential chromatin binding mediator of the A-tether. Using nuclei of mouse rods as an experimental model lacking peripheral heterochromatin, we expressed a LEMD2 transgene alone or in combination with lamin C in these cells and observed no restoration of peripheral heterochromatin in either case. We conclude that in contrary to the B-tether, the A-tether has a more intricate composition and consists of multiple components that presumably vary, at differing degrees of redundancy, between cell types and differentiation stages.
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Affiliation(s)
- Katharina Thanisch
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Congdi Song
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Dieter Engelkamp
- Transgenic Service Facility, BTE, Franz-Penzoldt-Centre, Friedrich-Alexander-University of Erlangen-Nürnberg, Erwin-Rommel-Str.3, D-91058 Erlangen, Germany
| | - Jeannette Koch
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Audrey Wang
- Institute of Medical Biology, 8A Biomedical Grove and Dept of Biological Sciences, NUS, 138648, Singapore
| | - Einar Hallberg
- Department of Neurochemistry, Stockholm University, Se-106 91 Stockholm, Sweden
| | - Roland Foisner
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Colin L Stewart
- Institute of Medical Biology, 8A Biomedical Grove and Dept of Biological Sciences, NUS, 138648, Singapore.
| | - Boris Joffe
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Irina Solovei
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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19
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Cohen-Fix O, Askjaer P. Cell Biology of the Caenorhabditis elegans Nucleus. Genetics 2017; 205:25-59. [PMID: 28049702 PMCID: PMC5216270 DOI: 10.1534/genetics.116.197160] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/09/2016] [Indexed: 12/25/2022] Open
Abstract
Studies on the Caenorhabditis elegans nucleus have provided fascinating insight to the organization and activities of eukaryotic cells. Being the organelle that holds the genetic blueprint of the cell, the nucleus is critical for basically every aspect of cell biology. The stereotypical development of C. elegans from a one cell-stage embryo to a fertile hermaphrodite with 959 somatic nuclei has allowed the identification of mutants with specific alterations in gene expression programs, nuclear morphology, or nuclear positioning. Moreover, the early C. elegans embryo is an excellent model to dissect the mitotic processes of nuclear disassembly and reformation with high spatiotemporal resolution. We review here several features of the C. elegans nucleus, including its composition, structure, and dynamics. We also discuss the spatial organization of chromatin and regulation of gene expression and how this depends on tight control of nucleocytoplasmic transport. Finally, the extensive connections of the nucleus with the cytoskeleton and their implications during development are described. Most processes of the C. elegans nucleus are evolutionarily conserved, highlighting the relevance of this powerful and versatile model organism to human biology.
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Affiliation(s)
- Orna Cohen-Fix
- Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Peter Askjaer
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
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20
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Goldstein B, Agranat-Tamir L, Light D, Ben-Naim Zgayer O, Fishman A, Lamm AT. A-to-I RNA editing promotes developmental stage-specific gene and lncRNA expression. Genome Res 2016; 27:462-470. [PMID: 28031250 PMCID: PMC5340973 DOI: 10.1101/gr.211169.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/20/2016] [Indexed: 01/02/2023]
Abstract
A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. Previous studies in C. elegans indicated competition between RNA interference (RNAi) and RNA editing mechanisms, based on the observation that worms that lack both mechanisms do not exhibit defects, in contrast to the developmental defects observed when only RNA editing is absent. To study the effects of RNA editing on gene expression and function, we established a novel screen that enabled us to identify thousands of RNA editing sites in nonrepetitive regions in the genome. These include dozens of genes that are edited at their 3′ UTR region. We found that these genes are mainly germline and neuronal genes, and that they are down-regulated in the absence of ADAR enzymes. Moreover, we discovered that almost half of these genes are edited in a developmental-specific manner, indicating that RNA editing is a highly regulated process. We found that many pseudogenes and other lncRNAs are also extensively down-regulated in the absence of ADARs in the embryo but not in the fourth larval (L4) stage. This down-regulation is not observed upon additional knockout of RNAi. Furthermore, levels of siRNAs aligned to pseudogenes in ADAR mutants are enhanced. Taken together, our results suggest a role for RNA editing in normal growth and development by regulating silencing via RNAi.
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Affiliation(s)
- Boaz Goldstein
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Lily Agranat-Tamir
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Dean Light
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Orna Ben-Naim Zgayer
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Alla Fishman
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Ayelet T Lamm
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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Barton LJ, Lovander KE, Pinto BS, Geyer PK. Drosophila male and female germline stem cell niches require the nuclear lamina protein Otefin. Dev Biol 2016; 415:75-86. [PMID: 27174470 DOI: 10.1016/j.ydbio.2016.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 04/28/2016] [Accepted: 05/02/2016] [Indexed: 12/11/2022]
Abstract
The nuclear lamina is an extensive protein network that underlies the inner nuclear envelope. This network includes the LAP2-emerin-MAN1-domain (LEM-D) protein family, proteins that share an association with the chromatin binding protein Barrier-to-autointegration factor (BAF). Loss of individual LEM-D proteins causes progressive, tissue-restricted diseases, known as laminopathies. Mechanisms associated with laminopathies are not yet understood. Here we present our studies of one of the Drosophila nuclear lamina LEM-D proteins, Otefin (Ote), a homologue of emerin. Previous studies have shown that Ote is autonomously required for the survival of female germline stem cells (GSCs). We demonstrate that Ote is also required for survival of somatic cells in the ovarian niche, with loss of Ote causing a decrease in cap cell number and altered signal transduction. We show germ cell-restricted expression of Ote rescues these defects, revealing a non-autonomous function for Ote in niche maintenance and emphasizing that GSCs contribute to the maintenance of their own niches. Further, we investigate the requirement of Ote in the male fertility. We show that ote mutant males become prematurely sterile as they age. Parallel to observations in females, this sterility is associated with GSC loss and changes in somatic cells of the niche, phenotypes that are largely rescued by germ cell-restricted Ote expression. Taken together, our studies demonstrate that Ote is required autonomously for survival of two stem cell populations, as well as non-autonomously for maintenance of two somatic niches. Finally, our data add to growing evidence that LEM-D proteins have critical roles in stem cell survival and tissue homeostasis.
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Affiliation(s)
- Lacy J Barton
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Kaylee E Lovander
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Belinda S Pinto
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Pamela K Geyer
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
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22
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Zuela N, Zwerger M, Levin T, Medalia O, Gruenbaum Y. Impaired mechanical response of an EDMD mutation leads to motility phenotypes that are repaired by loss of prenylation. J Cell Sci 2016; 129:1781-91. [PMID: 27034135 DOI: 10.1242/jcs.184309] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/21/2016] [Indexed: 12/20/2022] Open
Abstract
There are roughly 14 distinct heritable autosomal dominant diseases associated with mutations in lamins A/C, including Emery-Dreifuss muscular dystrophy (EDMD). The mechanical model proposes that the lamin mutations change the mechanical properties of muscle nuclei, leading to cell death and tissue deterioration. Here, we developed an experimental protocol that analyzes the effect of disease-linked lamin mutations on the response of nuclei to mechanical strain in living Caenorhabditis elegans We found that the EDMD mutation L535P disrupts the nuclear mechanical response specifically in muscle nuclei. Inhibiting lamin prenylation rescued the mechanical response of the EDMD nuclei, reversed the muscle phenotypes and led to normal motility. The LINC complex and emerin were also required to regulate the mechanical response of C. elegans nuclei. This study provides evidence to support the mechanical model and offers a potential future therapeutic approach towards curing EDMD.
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Affiliation(s)
- Noam Zuela
- Department of Genetics, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Monika Zwerger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Tal Levin
- Department of Genetics, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel
| | - Yosef Gruenbaum
- Department of Genetics, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Abstract
More than 70 different genes in humans and 12 different genes in Caenorhabditis elegans encode the superfamily of intermediate filament (IF) proteins. In C. elegans, similar to humans, these proteins are expressed in a cell- and tissue-specific manner, can assemble into heteropolymers and into 5-10nm wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. At least 5 of the 11 cytoplasmic IFs, as well as the nuclear IF, lamin, are essential. In this chapter, we will include a short review of our current knowledge of both cytoplasmic and nuclear IFs in C. elegans and will describe techniques used for their analyses.
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Affiliation(s)
- Noam Zuela
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yosef Gruenbaum
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Abstract
The nuclear lamina, composed of lamins and numerous lamin-associated proteins, is required for mechanical stability, mechanosensing, chromatin organization, developmental gene regulation, mRNA transcription, DNA replication, nuclear assembly, and nuclear positioning. Mutations in lamins or lamin-binding proteins cause at least 18 distinct human diseases that affect specific tissues such as muscle, adipose, bone, nerve, or skin, and range from muscular dystrophies to lipodystrophy, peripheral neuropathy, or accelerated aging. Caenorhabditis elegans has unique advantages in studying lamin-binding proteins. These advantages include the low complexity of genes encoding lamin and lamin-binding proteins, advanced transgenic techniques, simple application of RNA interference, sophisticated genetic strategies, and a large collection of mutant lines. This chapter provides detailed and comprehensive protocols for the genetic and phenotypic analysis of lamin-binding proteins in C. elegans.
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Affiliation(s)
- Agnieszka Dobrzynska
- Andalusian Center for Developmental Biology, CSIC-Junta de Andalucia-Universidad Pablo de Olavide, Carretera de Utrera, Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology, CSIC-Junta de Andalucia-Universidad Pablo de Olavide, Carretera de Utrera, Seville, Spain.
| | - Yosef Gruenbaum
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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25
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Barton LJ, Soshnev AA, Geyer PK. Networking in the nucleus: a spotlight on LEM-domain proteins. Curr Opin Cell Biol 2015; 34:1-8. [PMID: 25863918 DOI: 10.1016/j.ceb.2015.03.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 11/29/2022]
Abstract
Proteins resident in the inner nuclear membrane and underlying nuclear lamina form a network that regulates nuclear functions. This review highlights a prominent family of nuclear lamina proteins that carries the LAP2-emerin-MAN1-domain (LEM-D). LEM-D proteins share an ability to bind lamins and tether repressive chromatin at the nuclear periphery. The importance of this family is underscored by findings that loss of individual LEM-D proteins causes progressive, tissue-restricted diseases, known as laminopathies. Diverse functions of LEM-D proteins are linked to interactions with unique and overlapping partners including signal transduction effectors, transcription factors and architectural proteins. Recent investigations suggest that LEM-D proteins form hubs within the nuclear lamina that integrate external signals important for tissue homeostasis and maintenance of progenitor cell populations.
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Affiliation(s)
- Lacy J Barton
- Department of Biochemistry, University of Iowa, College of Medicine, Iowa City, IA 52242, USA; Skirball Institute, Department of Cell Biology, NYU School of Medicine, NYU Langone Medical Center, New York, NY 10016, USA
| | - Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Pamela K Geyer
- Department of Biochemistry, University of Iowa, College of Medicine, Iowa City, IA 52242, USA.
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26
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Tapia O, Fong LG, Huber MD, Young SG, Gerace L. Nuclear envelope protein Lem2 is required for mouse development and regulates MAP and AKT kinases. PLoS One 2015; 10:e0116196. [PMID: 25790465 PMCID: PMC4366207 DOI: 10.1371/journal.pone.0116196] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/21/2014] [Indexed: 12/31/2022] Open
Abstract
The nuclear lamina, along with associated nuclear membrane proteins, is a nexus for regulating signaling in the nucleus. Numerous human diseases arise from mutations in lamina proteins, and experimental models for these disorders have revealed aberrant regulation of various signaling pathways. Previously, we reported that the inner nuclear membrane protein Lem2, which is expressed at high levels in muscle, promotes the differentiation of cultured myoblasts by attenuating ERK signaling. Here, we have analyzed mice harboring a disrupted allele for the Lem2 gene (Lemd2). No gross phenotypic defects were seen in heterozygotes, although muscle regeneration induced by cardiotoxin was delayed. By contrast, homozygous Lemd2 knockout mice died by E11.5. Although many normal morphogenetic hallmarks were observed in E10.5 knockout embryos, most tissues were substantially reduced in size. This was accompanied by activation of multiple MAP kinases (ERK1/2, JNK, p38) and AKT. Knockdown of Lem2 expression in C2C12 myoblasts also led to activation of MAP kinases and AKT. These findings indicate that Lemd2 plays an essential role in mouse embryonic development and that it is involved in regulating several signaling pathways. Since increased MAP kinase and AKT/mTORC signaling is found in other animal models for diseases linked to nuclear lamina proteins, LEMD2 should be considered to be another candidate gene for human disease.
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Affiliation(s)
- Olga Tapia
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States of America
| | - Loren G. Fong
- Department of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Michael D. Huber
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States of America
| | - Stephen G. Young
- Department of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States of America
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California 90095, United States of America
| | - Larry Gerace
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, California 92037, United States of America
- * E-mail:
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27
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Gruenbaum Y, Foisner R. Lamins: nuclear intermediate filament proteins with fundamental functions in nuclear mechanics and genome regulation. Annu Rev Biochem 2015; 84:131-64. [PMID: 25747401 DOI: 10.1146/annurev-biochem-060614-034115] [Citation(s) in RCA: 368] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lamins are intermediate filament proteins that form a scaffold, termed nuclear lamina, at the nuclear periphery. A small fraction of lamins also localize throughout the nucleoplasm. Lamins bind to a growing number of nuclear protein complexes and are implicated in both nuclear and cytoskeletal organization, mechanical stability, chromatin organization, gene regulation, genome stability, differentiation, and tissue-specific functions. The lamin-based complexes and their specific functions also provide insights into possible disease mechanisms for human laminopathies, ranging from muscular dystrophy to accelerated aging, as observed in Hutchinson-Gilford progeria and atypical Werner syndromes.
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Affiliation(s)
- Yosef Gruenbaum
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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28
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Morales-Martínez A, Dobrzynska A, Askjaer P. Inner nuclear membrane protein LEM-2 is required for proper nuclear separation and morphology. J Cell Sci 2015; 128:1090-6. [DOI: 10.1242/jcs.164202] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The inner nuclear membrane proteins emerin and LEMD2 have both overlapping and separate functions in regulation of nuclear organization, gene expression and cell differentiation. We report here that emerin/EMR-1 and LEMD2/LEM-2 are expressed in all tissues throughout Caenorhaditis elegans development but their relative distribution differs between cell types. The ratio between EMR-1 and LEM-2 is particularly high in contractile tissues, intermediate in neurons and hypodermis and lowest in intestine and germ line. We find that LEM-2 is recruited earlier than EMR-1 to reforming nuclear envelopes, suggesting the presence of separate mitotic membrane compartments and specific functions of each protein. Concordantly, we observe that nuclei of lem-2 mutant embryos, but not of emr-1 mutants, have reduced nuclear circularity. Finally, we uncover a novel role of LEM-2 in nuclear separation and anchoring of microtubule organizing centers.
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29
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Berk JM, Simon DN, Jenkins-Houk CR, Westerbeck JW, Grønning-Wang LM, Carlson CR, Wilson KL. The molecular basis of emerin-emerin and emerin-BAF interactions. J Cell Sci 2014; 127:3956-69. [PMID: 25052089 DOI: 10.1242/jcs.148247] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Emerin is a conserved membrane component of nuclear lamina structure. Here, we report an advance in understanding the molecular basis of emerin function: intermolecular emerin-emerin association. There were two modes: one mediated by association of residues 170-220 in one emerin molecule to residues 170-220 in another, and the second involving residues 170-220 and 1-132. Deletion analysis showed residues 187-220 contain a positive element essential for intermolecular association in cells. By contrast, deletion of residues 168-186 inactivated a proposed negative element, required to limit or control association. Association of GFP-emerin with nuclear BAF in cells required the LEM domain (residues 1-47) and the positive element. Emerin peptide arrays revealed direct binding of residues 170-220 to residues 206-225 (the proposed positive element), residues 147-174 (particularly P(153)MYGRDSAYQSITHYRP(169)) and the LEM domain. Emerin residues 1-132 and 159-220 were each sufficient to bind lamin A or B1 tails in vitro, identifying two independent regions of molecular contact with lamins. These results, and predicted emerin intrinsic disorder, support the hypothesis that there are multiple 'backbone' and LEM-domain configurations in a proposed intermolecular emerin network at the nuclear envelope.
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Affiliation(s)
- Jason M Berk
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205 USA
| | - Dan N Simon
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205 USA
| | - Clifton R Jenkins-Houk
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205 USA
| | - Jason W Westerbeck
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205 USA
| | - Line M Grønning-Wang
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Cathrine R Carlson
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, 0450 Oslo, Norway
| | - Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205 USA
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30
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Abstract
The nuclear lamina is an extensive protein network that contributes to nuclear structure and function. LEM domain (LAP2, emerin, MAN1 domain, LEM-D) proteins are components of the nuclear lamina, identified by a shared ∼45-amino-acid motif that binds Barrier-to-autointegration factor (BAF), a chromatin-interacting protein. Drosophila melanogaster has three nuclear lamina LEM-D proteins, named Otefin (Ote), Bocksbeutel (Bocks), and dMAN1. Although these LEM-D proteins are globally expressed, loss of either Ote or dMAN1 causes tissue-specific defects in adult flies that differ from each other. The reason for such distinct tissue-restricted defects is unknown. Here, we generated null alleles of bocks, finding that loss of Bocks causes no overt adult phenotypes. Next, we defined phenotypes associated with lem-d double mutants. Although the absence of individual LEM-D proteins does not affect viability, loss of any two proteins causes lethality. Mutant phenotypes displayed by lem-d double mutants differ from baf mutants, suggesting that BAF function is retained in animals with a single nuclear lamina LEM-D protein. Interestingly, lem-d double mutants displayed distinct developmental and cellular mutant phenotypes, suggesting that Drosophila LEM-D proteins have developmental functions that are differentially shared with other LEM-D family members. This conclusion is supported by studies showing that ectopically produced LEM-D proteins have distinct capacities to rescue the tissue-specific phenotypes found in single lem-d mutants. Our findings predict that cell-specific mutant phenotypes caused by loss of LEM-D proteins reflect both the constellation of LEM-D proteins within the nuclear lamina and the capacity of functional compensation of the remaining LEM-D proteins.
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31
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Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans. Genome Biol 2014; 15:R21. [PMID: 24490688 PMCID: PMC4053756 DOI: 10.1186/gb-2014-15-2-r21] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/03/2014] [Indexed: 01/01/2023] Open
Abstract
Background Laminopathies are diseases characterized by defects in nuclear envelope structure. A well-known example is Emery-Dreifuss muscular dystrophy, which is caused by mutations in the human lamin A/C and emerin genes. While most nuclear envelope proteins are ubiquitously expressed, laminopathies often affect only a subset of tissues. The molecular mechanisms underlying these tissue-specific manifestations remain elusive. We hypothesize that different functional subclasses of genes might be differentially affected by defects in specific nuclear envelope components. Results Here we determine genome-wide DNA association profiles of two nuclear envelope components, lamin/LMN-1 and emerin/EMR-1 in adult Caenorhabditis elegans. Although both proteins bind to transcriptionally inactive regions of the genome, EMR-1 is enriched at genes involved in muscle and neuronal function. Deletion of either EMR-1 or LEM-2, another integral envelope protein, causes local changes in nuclear architecture as evidenced by altered association between DNA and LMN-1. Transcriptome analyses reveal that EMR-1 and LEM-2 are associated with gene repression, particularly of genes implicated in muscle and nervous system function. We demonstrate that emr-1, but not lem-2, mutants are sensitive to the cholinesterase inhibitor aldicarb, indicating altered activity at neuromuscular junctions. Conclusions We identify a class of elements that bind EMR-1 but do not associate with LMN-1, and these are enriched for muscle and neuronal genes. Our data support a redundant function of EMR-1 and LEM-2 in chromatin anchoring to the nuclear envelope and gene repression. We demonstrate a specific role of EMR-1 in neuromuscular junction activity that may contribute to Emery-Dreifuss muscular dystrophy in humans.
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32
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Koch AJ, Holaska JM. Emerin in health and disease. Semin Cell Dev Biol 2013; 29:95-106. [PMID: 24365856 DOI: 10.1016/j.semcdb.2013.12.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/02/2013] [Accepted: 12/15/2013] [Indexed: 12/27/2022]
Abstract
Emery-Dreifuss muscular dystrophy (EDMD) is caused by mutations in the genes encoding emerin, lamins A and C and FHL1. Additional EDMD-like syndromes are caused by mutations in nesprins and LUMA. This review will specifically focus on emerin function and the current thinking for how loss or mutations in emerin cause EDMD. Emerin is a well-conserved, ubiquitously expressed protein of the inner nuclear membrane. Emerin has been shown to have diverse functions, including the regulation of gene expression, cell signaling, nuclear structure and chromatin architecture. This review will focus on the relationships between these functions and the EDMD disease phenotype. Additionally it will highlight open questions concerning emerin's roles in cell and nuclear biology and disease.
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Affiliation(s)
- Adam J Koch
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - James M Holaska
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA; Committee on Developmental, Regeneration and Stem Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
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33
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Berk JM, Maitra S, Dawdy AW, Shabanowitz J, Hunt DF, Wilson KL. O-Linked β-N-acetylglucosamine (O-GlcNAc) regulates emerin binding to barrier to autointegration factor (BAF) in a chromatin- and lamin B-enriched "niche". J Biol Chem 2013; 288:30192-30209. [PMID: 24014020 DOI: 10.1074/jbc.m113.503060] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Emerin, a membrane component of nuclear "lamina" networks with lamins and barrier to autointegration factor (BAF), is highly O-GlcNAc-modified ("O-GlcNAcylated") in mammalian cells. Mass spectrometry analysis revealed eight sites of O-GlcNAcylation, including Ser-53, Ser-54, Ser-87, Ser-171, and Ser-173. Emerin O-GlcNAcylation was reduced ~50% by S53A or S54A mutation in vitro and in vivo. O-GlcNAcylation was reduced ~66% by the triple S52A/S53A/S54A mutant, and S173A reduced O-GlcNAcylation of the S52A/S53A/S54A mutant by ~30%, in vivo. We separated two populations of emerin, A-type lamins and BAF; one population solubilized easily, and the other required sonication and included histones and B-type lamins. Emerin and BAF associated only in histone- and lamin-B-containing fractions. The S173D mutation specifically and selectively reduced GFP-emerin association with BAF by 58% and also increased GFP-emerin hyper-phosphorylation. We conclude that β-N-acetylglucosaminyltransferase, an essential enzyme, controls two regions in emerin. The first region, defined by residues Ser-53 and Ser-54, flanks the LEM domain. O-GlcNAc modification at Ser-173, in the second region, is proposed to promote emerin association with BAF in the chromatin/lamin B "niche." These results reveal direct control of a conserved LEM domain nuclear lamina component by β-N-acetylglucosaminyltransferase, a nutrient sensor that regulates cell stress responses, mitosis, and epigenetics.
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Affiliation(s)
- Jason M Berk
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Sushmit Maitra
- the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Andrew W Dawdy
- the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Jeffrey Shabanowitz
- the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Donald F Hunt
- the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904
| | - Katherine L Wilson
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and.
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34
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Abstract
Emerin, a conserved LEM-domain protein, is among the few nuclear membrane proteins for which extensive basic knowledge—biochemistry, partners, functions, localizations, posttranslational regulation, roles in development and links to human disease—is available. This review summarizes emerin and its emerging roles in nuclear “lamina” structure, chromatin tethering, gene regulation, mitosis, nuclear assembly, development, signaling and mechano-transduction. We also highlight many open questions, exploration of which will be critical to understand how this intriguing nuclear membrane protein and its “family” influence the genome.
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Affiliation(s)
- Jason M Berk
- Department of Cell Biology; Johns Hopkins University School of Medicine; Baltimore, MD USA
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Solovei I, Wang AS, Thanisch K, Schmidt CS, Krebs S, Zwerger M, Cohen TV, Devys D, Foisner R, Peichl L, Herrmann H, Blum H, Engelkamp D, Stewart CL, Leonhardt H, Joffe B. LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation. Cell 2013; 152:584-98. [PMID: 23374351 DOI: 10.1016/j.cell.2013.01.009] [Citation(s) in RCA: 556] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 09/14/2012] [Accepted: 01/07/2013] [Indexed: 01/26/2023]
Abstract
Eukaryotic cells have a layer of heterochromatin at the nuclear periphery. To investigate mechanisms regulating chromatin distribution, we analyzed heterochromatin organization in different tissues and species, including mice with mutations in the lamin B receptor (Lbr) and lamin A (Lmna) genes that encode nuclear envelope (NE) proteins. We identified LBR- and lamin-A/C-dependent mechanisms tethering heterochromatin to the NE. The two tethers are sequentially used during cellular differentiation and development: first the LBR- and then the lamin-A/C-dependent tether. The absence of both LBR and lamin A/C leads to loss of peripheral heterochromatin and an inverted architecture with heterochromatin localizing to the nuclear interior. Myoblast transcriptome analyses indicated that selective disruption of the LBR- or lamin-A-dependent heterochromatin tethers have opposite effects on muscle gene expression, either increasing or decreasing, respectively. These results show how changes in NE composition contribute to regulating heterochromatin positioning, gene expression, and cellular differentiation during development.
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Affiliation(s)
- Irina Solovei
- Department of Biology II, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
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