301
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Zhdanov R, Schirmer E, Venkatasubramani AV, Kerr A, Mandrou E, Rodriguez Blanco G, Kagansky A. Lipids contribute to epigenetic control via chromatin structure and functions. SCIENCEOPEN RESEARCH 2015. [DOI: 10.14293/s2199-1006.1.sor-life.auxytr.v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Abstract
Isolated cases of experimental evidence over the last few decades have shown that, where specifically tested, both prokaryotes and eukaryotes have specific lipid molecules bound to nucleoproteins of the genome. In vitro, some of these lipids exhibit stoichiometric association with DNA polynucleotides with differential affinities toward certain secondary and tertiary structures. Hydrophobic interactions with inner nuclear membrane could provide attractive anchor points for lipid-modified nucleoproteins in organizing the dynamic genome and accordingly there are precedents for covalent bonds between lipids and core histones and, under certain conditions, even DNA. Advances in biophysics, functional genomics, and proteomics in recent years brought about the first sparks of light that promises to uncover some coherent new level of the epigenetic code governed by certain types of lipid–lipid, DNA–lipid, and protein–lipid interactions among other biochemical lipid transactions in the nucleus. Here, we review some of the older and more recent findings and speculate on how critical nuclear lipid transactions are for individual cells, tissues, and organisms.
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302
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Abstract
Recent studies show that nuclear lamins, the type V intermediate filament proteins, are required for proper building of at least some organs. As the major structural components of the nuclear lamina found underneath the inner nuclear membranes, lamins are ubiquitously expressed in all animal cells. How the broadly expressed lamins support the building of specific tissues is not understood. By studying Drosophila testis, we have uncovered a mechanism by which lamin-B functions in the cyst stem cell (CySC) and its differentiated cyst cell, the cell types known to form the niche/microenvironment for the germline stem cells (GSC) and the developing germ line, to ensure testis organogenesis (1). In this extra view, we discuss some remaining questions and the implications of our findings in the understanding of how the ubiquitous nuclear lamina regulates tissue building in a context-dependent manner.
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Affiliation(s)
- Haiyang Chen
- a Department of Embryology; Carnegie Institution for Science; Baltimore, MD USA
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303
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Cortés A, Sotillo J, Muñoz-Antoli C, Fried B, Esteban JG, Toledo R. Altered Protein Expression in the Ileum of Mice Associated with the Development of Chronic Infections with Echinostoma caproni (Trematoda). PLoS Negl Trop Dis 2015; 9:e0004082. [PMID: 26390031 PMCID: PMC4577103 DOI: 10.1371/journal.pntd.0004082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/22/2015] [Indexed: 12/12/2022] Open
Abstract
Background Echinostoma caproni (Trematoda: Echinostomatidae) is an intestinal trematode that has been extensively used as experimental model to investigate the factors determining the expulsion of intestinal helminths or, in contrast, the development of chronic infections. Herein, we analyze the changes in protein expression induced by E. caproni infection in ICR mice, a host of high compatibility in which the parasites develop chronic infections. Methodology/Principal Findings To determine the changes in protein expression, a two-dimensional DIGE approach using protein extracts from the intestine of naïve and infected mice was employed; and spots showing significant differential expression were analyzed by mass spectrometry. A total of 37 spots were identified differentially expressed in infected mice (10 were found to be over-expressed and 27 down-regulated). These proteins were related to the restoration of the intestinal epithelium and the control of homeostatic dysregulation, concomitantly with mitochondrial and cytoskeletal proteins among others. Conclusion/Significance Our results suggests that changes in these processes in the ileal epithelium of ICR mice may facilitate the establishment of the parasite and the development of chronic infections. These results may serve to explain the factors determining the development of chronicity in intestinal helminth infection. Intestinal helminth infections are among the most prevalent parasitic diseases and about 1 billion people are currently infected with intestinal helminths. Incidence of intestinal helminth infections is high due to both socio-economic factors that facilitates continuous re-infections and the lack of effective vaccines. In this context, further knowledge on the host-parasite relationships is required to elucidate the factors that determine the expulsion of the intestinal helminths or, in contrast, the chronic establishment of the infections. Echinostoma caproni (Trematoda) is an intestinal trematode that has been extensively used as experimental model to investigate these factors. Depending on the host species. E. caproni is rapidly rejected or develops chronic infections. Herein, we analyze the changes in protein expression induced by E. caproni infection in a host in which the parasites develop chronic infections. These data may serve to get a better understanding of the factors determining the development of chronic intestinal infections. A total of 37 spots were identified differentially expressed. These proteins were related to the restoration of the intestinal epithelium and the control of homeostatic dysregulation, mitochondrial and cytoskeletal proteins among others. This suggests that the changes in these processes in the intestinal mucosa may facilitate the development of chronic infections.
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Affiliation(s)
- Alba Cortés
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Burjassot, Valencia, Spain
| | - Javier Sotillo
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Burjassot, Valencia, Spain
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Carla Muñoz-Antoli
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Burjassot, Valencia, Spain
| | - Bernard Fried
- Department of Biology, Lafayette College, Easton, Pennsylvania, United States of America
| | - J. Guillermo Esteban
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Burjassot, Valencia, Spain
| | - Rafael Toledo
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Burjassot, Valencia, Spain
- * E-mail:
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304
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Glucotoxic and diabetic conditions induce caspase 6-mediated degradation of nuclear lamin A in human islets, rodent islets and INS-1 832/13 cells. Apoptosis 2015; 19:1691-701. [PMID: 25292013 DOI: 10.1007/s10495-014-1038-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nuclear lamins form the lamina on the interior surface of the nuclear envelope, and regulate nuclear metabolic events, including DNA replication and organization of chromatin. The current study is aimed at understanding the role of executioner caspase 6 on lamin A integrity in islet β-cells under duress of glucotoxic (20 mM glucose; 24 h) and diabetic conditions. Under glucotoxic conditions, glucose-stimulated insulin secretion and metabolic cell viability were significantly attenuated in INS-1 832/13 cells. Further, exposure of normal human islets, rat islets and INS-1 832/13 cells to glucotoxic conditions leads to caspase 6 activation and lamin A degradation, which is also observed in islets from the Zucker diabetic fatty rat, a model for type 2 diabetes (T2D), and in islets from a human donor with T2D. Z-Val-Glu-Ile-Asp-fluoromethylketone, a specific inhibitor of caspase 6, markedly attenuated high glucose-induced caspase 6 activation and lamin A degradation, confirming that caspase 6 mediates lamin A degradation under high glucose exposure conditions. Moreover, Z-Asp-Glu-Val-Asp-fluoromethylketone, a known caspase 3 inhibitor, significantly inhibited high glucose-induced caspase 6 activation and lamin A degradation, suggesting that activation of caspase 3 might be upstream to caspase 6 activation in the islet β-cell under glucotoxic conditions. Lastly, we report expression of ZMPSTE24, a zinc metallopeptidase involved in the processing of prelamin A to mature lamin A, in INS-1 832/13 cells and human islets; was unaffected by high glucose. We conclude that caspases 3 and 6 could contribute to alterations in the integrity of nuclear lamins leading to metabolic dysregulation and failure of the islet β-cell.
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305
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Rønningen T, Shah A, Oldenburg AR, Vekterud K, Delbarre E, Moskaug JØ, Collas P. Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B. Genome Res 2015; 25:1825-35. [PMID: 26359231 PMCID: PMC4665004 DOI: 10.1101/gr.193748.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/10/2015] [Indexed: 12/15/2022]
Abstract
Dynamic interactions of nuclear lamins with chromatin through lamin-associated domains (LADs) contribute to spatial arrangement of the genome. Here, we provide evidence for prepatterning of differentiation-driven formation of lamin A/C LADs by domains of histone H2B modified on serine 112 by the nutrient sensor O-linked N-acetylglucosamine (H2BS112GlcNAc), which we term GADs. We demonstrate a two-step process of lamin A/C LAD formation during in vitro adipogenesis, involving spreading of lamin A/C–chromatin interactions in the transition from progenitor cell proliferation to cell-cycle arrest, and genome-scale redistribution of these interactions through a process of LAD exchange within hours of adipogenic induction. Lamin A/C LADs are found both in active and repressive chromatin contexts that can be influenced by cell differentiation status. De novo formation of adipogenic lamin A/C LADs occurs nonrandomly on GADs, which consist of megabase-size intergenic and repressive chromatin domains. Accordingly, whereas predifferentiation lamin A/C LADs are gene-rich, post-differentiation LADs harbor repressive features reminiscent of lamin B1 LADs. Release of lamin A/C from genes directly involved in glycolysis concurs with their transcriptional up-regulation after adipogenic induction, and with downstream elevations in H2BS112GlcNAc levels and O-GlcNAc cycling. Our results unveil an epigenetic prepatterning of adipogenic LADs by GADs, suggesting a coupling of developmentally regulated lamin A/C-genome interactions to a metabolically sensitive chromatin modification.
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Affiliation(s)
- Torunn Rønningen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Akshay Shah
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Anja R Oldenburg
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway; Norwegian Center for Stem Cell Research, Oslo University Hospital, 0317 Oslo, Norway
| | - Kristin Vekterud
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Jan Øivind Moskaug
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway; Norwegian Center for Stem Cell Research, Oslo University Hospital, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway; Norwegian Center for Stem Cell Research, Oslo University Hospital, 0317 Oslo, Norway
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306
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Infante A, Rodríguez CI. Pathologically Relevant Prelamin A Interactions with Transcription Factors. Methods Enzymol 2015; 569:485-501. [PMID: 26778572 DOI: 10.1016/bs.mie.2015.08.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
LMNA-linked laminopathies are a group of rare human diseases caused by mutations in LMNA or by disrupted posttranslational processing of its largest encoded isoform, prelamin A. The accumulation of mutated or immature forms of farnesylated prelamin A, named progerin or prelamin A, respectively, dominantly disrupts nuclear lamina structure with toxic effects in cells. One hypothesis is that aberrant lamin filament networks disrupt or "trap" proteins such as transcription factors, thereby interfering with their normal activity. Since laminopathies mainly affect tissues of mesenchymal origin, we tested this hypothesis by generating an experimental model of laminopathy by inducing prelamin A accumulation in human mesenchymal stem cells (hMSCs). We provide detailed protocols for inducing and detecting prelamin A accumulation in hMSCs, and describe the bioinformatic analysis and in vitro assays of transcription factors potentially affected by prelamin A accumulation.
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Affiliation(s)
- Arantza Infante
- Stem Cells and Cell Therapy Laboratory, BioCruces Health Research Institute, Cruces University Hospital, Barakaldo, Spain
| | - Clara I Rodríguez
- Stem Cells and Cell Therapy Laboratory, BioCruces Health Research Institute, Cruces University Hospital, Barakaldo, Spain.
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307
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Lenain C, Gusyatiner O, Douma S, van den Broek B, Peeper DS. Autophagy-mediated degradation of nuclear envelope proteins during oncogene-induced senescence. Carcinogenesis 2015; 36:1263-74. [DOI: 10.1093/carcin/bgv124] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 07/16/2015] [Indexed: 01/12/2023] Open
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308
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The Cardiomyopathy Lamin A/C D192G Mutation Disrupts Whole-Cell Biomechanics in Cardiomyocytes as Measured by Atomic Force Microscopy Loading-Unloading Curve Analysis. Sci Rep 2015; 5:13388. [PMID: 26323789 PMCID: PMC4555041 DOI: 10.1038/srep13388] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 07/23/2015] [Indexed: 12/30/2022] Open
Abstract
Atomic force microscopy (AFM) cell loading/unloading curves were used to provide comprehensive insights into biomechanical behavior of cardiomyocytes carrying the lamin A/C (LMNA) D192G mutation known to cause defective nuclear wall, myopathy and severe cardiomyopathy. Our results suggested that the LMNA D192G mutation increased maximum nuclear deformation load, nuclear stiffness and fragility as compared to controls. Furthermore, there seems to be a connection between this lamin nuclear mutation and cell adhesion behavior since LMNA D192G cardiomyocytes displayed loss of AFM probe-to-cell membrane adhesion. We believe that this loss of adhesion involves the cytoskeletal architecture since our microscopic analyses highlighted that mutant LMNA may also lead to a morphological alteration in the cytoskeleton. Furthermore, chemical disruption of the actin cytoskeleton by cytochalasin D in control cardiomyocytes mirrored the alterations in the mechanical properties seen in mutant cells, suggesting a defect in the connection between the nucleoskeleton, cytoskeleton and cell adhesion molecules in cells expressing the mutant protein. These data add to our understanding of potential mechanisms responsible for this fatal cardiomyopathy, and show that the biomechanical effects of mutant lamin extend beyond nuclear mechanics to include interference of whole-cell biomechanical properties.
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309
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Liang Z, Brown RC, Fletcher JC, Opsahl-Sorteberg HG. Calpain-Mediated Positional Information Directs Cell Wall Orientation to Sustain Plant Stem Cell Activity, Growth and Development. PLANT & CELL PHYSIOLOGY 2015. [PMID: 26220906 DOI: 10.1093/pcp/pcv110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Eukaryotic development and stem cell control depend on the integration of cell positional sensing with cell cycle control and cell wall positioning, yet few factors that directly link these events are known. The DEFECTIVE KERNEL1 (DEK1) gene encoding the unique plant calpain protein is fundamental for development and growth, being essential to confer and maintain epidermal cell identity that allows development beyond the globular embryo stage. We show that DEK1 expression is highest in the actively dividing cells of seeds, meristems and vasculature. We further show that eliminating Arabidopsis DEK1 function leads to changes in developmental cues from the first zygotic division onward, altered microtubule patterns and misshapen cells, resulting in early embryo abortion. Expression of the embryonic marker genes WOX2, ATML1, PIN4, WUS and STM, related to axis organization, cell identity and meristem functions, is also altered in dek1 embryos. By monitoring cell layer-specific DEK1 down-regulation, we show that L1- and 35S-induced down-regulation mainly affects stem cell functions, causing severe shoot apical meristem phenotypes. These results are consistent with a requirement for DEK1 to direct layer-specific cellular activities and set downstream developmental cues. Our data suggest that DEK1 may anchor cell wall positions and control cell division and differentiation, thereby balancing the plant's requirement to maintain totipotent stem cell reservoirs while simultaneously directing growth and organ formation. A role for DEK1 in regulating microtubule-orchestrated cell wall orientation during cell division can explain its effects on embryonic development, and suggests a more general function for calpains in microtubule organization in eukaryotic cells.
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Affiliation(s)
- Zhe Liang
- Department of Plant Sciences, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, Norway
| | - Roy C Brown
- Department of Biology, University of Louisiana, Lafayette, LA 70504, USA
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310
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Zwerger M, Roschitzki-Voser H, Zbinden R, Denais C, Herrmann H, Lammerding J, Grütter MG, Medalia O. Altering lamina assembly reveals lamina-dependent and -independent functions for A-type lamins. J Cell Sci 2015; 128:3607-20. [PMID: 26275827 DOI: 10.1242/jcs.171843] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/13/2015] [Indexed: 01/26/2023] Open
Abstract
Lamins are intermediate filament proteins that form a fibrous meshwork, called the nuclear lamina, between the inner nuclear membrane and peripheral heterochromatin of metazoan cells. The assembly and incorporation of lamin A/C into the lamina, as well as their various functions, are still not well understood. Here, we employed designed ankyrin repeat proteins (DARPins) as new experimental tools for lamin research. We screened for DARPins that specifically bound to lamin A/C, and interfered with lamin assembly in vitro and with incorporation of lamin A/C into the native lamina in living cells. The selected DARPins inhibited lamin assembly and delocalized A-type lamins to the nucleoplasm without modifying lamin expression levels or the amino acid sequence. Using these lamin binders, we demonstrate the importance of proper integration of lamin A/C into the lamina for nuclear mechanical properties and nuclear envelope integrity. Finally, our study provides evidence for cell-type-specific differences in lamin functions.
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Affiliation(s)
- Monika Zwerger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Heidi Roschitzki-Voser
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Reto Zbinden
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Celine Denais
- Cornell University, Weill Institute for Cell and Molecular Biology, Department of Biomedical Engineering, Weill Hall, Ithaca, NY 14853, USA
| | - Harald Herrmann
- Functional Architecture of the Cell, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Jan Lammerding
- Cornell University, Weill Institute for Cell and Molecular Biology, Department of Biomedical Engineering, Weill Hall, Ithaca, NY 14853, USA
| | - Markus G Grütter
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - 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
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311
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Guo Y, Zheng Y. Lamins position the nuclear pores and centrosomes by modulating dynein. Mol Biol Cell 2015; 26:3379-89. [PMID: 26246603 PMCID: PMC4591684 DOI: 10.1091/mbc.e15-07-0482] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/29/2015] [Indexed: 12/30/2022] Open
Abstract
Nuclear lamins counterbalance dynein forces on nuclear pore complexes through BICD2 and ensure even nuclear pore complex distribution and proper centrosome separation at prophase. Lamins, the type V nuclear intermediate filament proteins, are reported to function in both interphase and mitosis. For example, lamin deletion in various cell types can lead to an uneven distribution of the nuclear pore complexes (NPCs) in the interphase nuclear envelope, whereas deletion of B-type lamins results in spindle orientation defects in mitotic neural progenitor cells. How lamins regulate these functions is unknown. Using mouse cells deleted of different combinations or all lamins, we show that lamins are required to prevent the aggregation of NPCs in the nuclear envelope near centrosomes in late G2 and prophase. This asymmetric NPC distribution in the absence of lamins is caused by dynein forces acting on NPCs via the dynein adaptor BICD2. We further show that asymmetric NPC distribution upon lamin depletion disrupts the distribution of BICD2 and p150 dynactin on the nuclear envelope at prophase, which results in inefficient dynein-driven centrosome separation during prophase. Therefore lamins regulate microtubule-based motor forces in vivo to ensure proper NPC distribution in interphase and centrosome separation in the mitotic prophase.
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Affiliation(s)
- Yuxuan Guo
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218; Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Yixian Zheng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218; Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
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312
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Dileep V, Ay F, Sima J, Vera DL, Noble WS, Gilbert DM. Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. Genome Res 2015; 25:1104-13. [PMID: 25995270 PMCID: PMC4509995 DOI: 10.1101/gr.183699.114] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 05/18/2015] [Indexed: 01/28/2023]
Abstract
Mammalian genomes are partitioned into domains that replicate in a defined temporal order. These domains can replicate at similar times in all cell types (constitutive) or at cell type-specific times (developmental). Genome-wide chromatin conformation capture (Hi-C) has revealed sub-megabase topologically associating domains (TADs), which are the structural counterparts of replication domains. Hi-C also segregates inter-TAD contacts into defined 3D spatial compartments that align precisely to genome-wide replication timing profiles. Determinants of the replication-timing program are re-established during early G1 phase of each cell cycle and lost in G2 phase, but it is not known when TAD structure and inter-TAD contacts are re-established after their elimination during mitosis. Here, we use multiplexed 4C-seq to study dynamic changes in chromatin organization during early G1. We find that both establishment of TADs and their compartmentalization occur during early G1, within the same time frame as establishment of the replication-timing program. Once established, this 3D organization is preserved either after withdrawal into quiescence or for the remainder of interphase including G2 phase, implying 3D structure is not sufficient to maintain replication timing. Finally, we find that developmental domains are less well compartmentalized than constitutive domains and display chromatin properties that distinguish them from early and late constitutive domains. Overall, this study uncovers a strong connection between chromatin re-organization during G1, establishment of replication timing, and its developmental control.
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Affiliation(s)
- Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Daniel L Vera
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
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313
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Wang S, Reuveny A, Volk T. Nesprin provides elastic properties to muscle nuclei by cooperating with spectraplakin and EB1. ACTA ACUST UNITED AC 2015; 209:529-38. [PMID: 26008743 PMCID: PMC4442817 DOI: 10.1083/jcb.201408098] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The myonuclear scaffold in Drosophila larval muscles exhibits both elastic features, contributed by the stretching capacity of MSP300/nesprin, and rigidity, provided by a perinuclear network of microtubules stabilized by Shot/spectraplakin and EB1. Muscle nuclei are exposed to variable cytoplasmic strain produced by muscle contraction and relaxation, but their morphology remains stable. Still, the mechanism responsible for maintaining myonuclear architecture, and its importance, is currently elusive. Herein, we uncovered a unique myonuclear scaffold in Drosophila melanogaster larval muscles, exhibiting both elastic features contributed by the stretching capacity of MSP300 (nesprin) and rigidity provided by a perinuclear network of microtubules stabilized by Shot (spectraplakin) and EB1. Together, they form a flexible perinuclear shield that protects myonuclei from intrinsic or extrinsic forces. The loss of this scaffold resulted in significantly aberrant nuclear morphology and subsequently reduced levels of essential nuclear factors such as lamin A/C, lamin B, and HP1. Overall, we propose a novel mechanism for maintaining myonuclear morphology and reveal its critical link to correct levels of nuclear factors in differentiated muscle fibers. These findings may shed light on the underlying mechanism of various muscular dystrophies.
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Affiliation(s)
- Shuoshuo Wang
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adriana Reuveny
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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314
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Qi R, Xu N, Wang G, Ren H, Li S, Lei J, Lin Q, Wang L, Gu X, Zhang H, Jiang Q, Zhang C. The lamin-A/C-LAP2α-BAF1 protein complex regulates mitotic spindle assembly and positioning. J Cell Sci 2015; 128:2830-41. [PMID: 26092935 DOI: 10.1242/jcs.164566] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 06/15/2015] [Indexed: 01/31/2023] Open
Abstract
Some nuclear proteins that are crucial in interphase relocate during the G2/M-phase transition in order to perform their mitotic functions. However, how they perform these functions and the underlying mechanisms remain largely unknown. Here, we report that a fraction of the nuclear periphery proteins lamin-A/C, LAP2α and BAF1 (also known as BANF1) relocate to the spindle and the cell cortex in mitosis. Knockdown of these proteins by using RNA interference (RNAi) induces short and fluffy spindle formation, and disconnection of the spindle from the cell cortex. Disrupting the microtubule assembly leads to accumulation of these proteins in the cell cortex, whereas depolymerizing the actin microfilaments results in the formation of short spindles. We further demonstrate that these proteins are part of a stable complex that links the mitotic spindle to the cell cortex and the spindle matrix by binding to spindle-associated dynein, the actin filaments in the cell cortex and the spindle matrix. Taken together, our findings unveil a unique mechanism where the nuclear periphery proteins lamin-A/C, LAP2α and BAF1 are assembled into a protein complex during mitosis in order to regulate assembly and positioning of the mitotic spindle.
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Affiliation(s)
- Ran Qi
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Nan Xu
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Gang Wang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - He Ren
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Si Li
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Jun Lei
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Qiaoyu Lin
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Lihao Wang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Xin Gu
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Hongyin Zhang
- Cancer Research Center, Peking University Hospital, Peking University, Beijing 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Beijing 100871, China
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315
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Panneer Selvam S, De Palma RM, Oaks JJ, Oleinik N, Peterson YK, Stahelin RV, Skordalakes E, Ponnusamy S, Garrett-Mayer E, Smith CD, Ogretmen B. Binding of the sphingolipid S1P to hTERT stabilizes telomerase at the nuclear periphery by allosterically mimicking protein phosphorylation. Sci Signal 2015; 8:ra58. [PMID: 26082434 DOI: 10.1126/scisignal.aaa4998] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During DNA replication, the enzyme telomerase maintains the ends of chromosomes, called telomeres. Shortened telomeres trigger cell senescence, and cancer cells often have increased telomerase activity to promote their ability to proliferate indefinitely. The catalytic subunit, human telomerase reverse transcriptase (hTERT), is stabilized by phosphorylation. We found that the lysophospholipid sphingosine 1-phosphate (S1P), generated by sphingosine kinase 2 (SK2), bound hTERT at the nuclear periphery in human and mouse fibroblasts. Docking predictions and mutational analyses revealed that binding occurred between a hydroxyl group (C'3-OH) in S1P and Asp(684) in hTERT. Inhibiting or depleting SK2 or mutating the S1P binding site decreased the stability of hTERT in cultured cells and promoted senescence and loss of telomere integrity. S1P binding inhibited the interaction of hTERT with makorin ring finger protein 1 (MKRN1), an E3 ubiquitin ligase that tags hTERT for degradation. Murine Lewis lung carcinoma (LLC) cells formed smaller tumors in mice lacking SK2 than in wild-type mice, and knocking down SK2 in LLC cells before implantation into mice suppressed their growth. Pharmacologically inhibiting SK2 decreased the growth of subcutaneous A549 lung cancer cell-derived xenografts in mice, and expression of wild-type hTERT, but not an S1P-binding mutant, restored tumor growth. Thus, our data suggest that S1P binding to hTERT allosterically mimicks phosphorylation, promoting telomerase stability and hence telomere maintenance, cell proliferation, and tumor growth.
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Affiliation(s)
- Shanmugam Panneer Selvam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ryan M De Palma
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joshua J Oaks
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Natalia Oleinik
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yuri K Peterson
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA. Department of Pharmaceutical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Robert V Stahelin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine-South Bend, South Bend, IN 46617, USA. Department of Chemistry and Biochemistry and the Mike and Josie Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46556, USA
| | - Emmanuel Skordalakes
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Suriyan Ponnusamy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | | | - Charles D Smith
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA. Department of Pharmaceutical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA.
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316
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Abstract
Signaling classically involves the secretion of diverse molecules that bind specific cell-surface receptors and engage intracellular transduction cascades. Some exceptions-namely, lipophilic agents-can cross plasma membranes to bind intracellular receptors and be carried to the nucleus to regulate transcription. Homeoprotein transcription factors are among the few proteins with such a capacity. Here, we review the signaling activities of homeoproteins in the developing and adult nervous system, with particular emphasis on axon/cell migration and postnatal critical periods of cerebral cortex plasticity. We also describe homeoprotein non-cell-autonomous mechanisms and explore how this "novel" signaling pathway impacts emerging research in brain development and physiology. In this context, we explore hypotheses on the evolution of signaling, the role of homeoproteins as early morphogens, and their therapeutic potential for neurological and psychiatric diseases.
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317
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Razafsky D, Hodzic D. Nuclear envelope: positioning nuclei and organizing synapses. Curr Opin Cell Biol 2015; 34:84-93. [PMID: 26079712 DOI: 10.1016/j.ceb.2015.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 05/28/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022]
Abstract
The nuclear envelope plays an essential role in nuclear positioning within cells and tissues. This review highlights advances in understanding the mechanisms of nuclear positioning during skeletal muscle and central nervous system development. New findings, particularly about A-type lamins and Nesprin1, may link nuclear envelope integrity to synaptic integrity. Thus synaptic defects, rather than nuclear mispositioning, may underlie human pathologies associated with mutations of nuclear envelope proteins.
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Affiliation(s)
- David Razafsky
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, 660 S. Euclid Avenue, St Louis, MO 63110, USA
| | - Didier Hodzic
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, 660 S. Euclid Avenue, St Louis, MO 63110, USA.
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318
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Ungricht R, Klann M, Horvath P, Kutay U. Diffusion and retention are major determinants of protein targeting to the inner nuclear membrane. J Cell Biol 2015; 209:687-703. [PMID: 26056139 PMCID: PMC4460150 DOI: 10.1083/jcb.201409127] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 03/04/2015] [Indexed: 01/07/2023] Open
Abstract
Newly synthesized membrane proteins are constantly sorted from the endoplasmic reticulum (ER) to various membranous compartments. How proteins specifically enrich at the inner nuclear membrane (INM) is not well understood. We have established a visual in vitro assay to measure kinetics and investigate requirements of protein targeting to the INM. Using human LBR, SUN2, and LAP2β as model substrates, we show that INM targeting is energy-dependent but distinct from import of soluble cargo. Accumulation of proteins at the INM relies on both a highly interconnected ER network, which is affected by energy depletion, and an efficient immobilization step at the INM. Nucleoporin depletions suggest that translocation through nuclear pore complexes (NPCs) is rate-limiting and restricted by the central NPC scaffold. Our experimental data combined with mathematical modeling support a diffusion-retention-based mechanism of INM targeting. We experimentally confirmed the sufficiency of diffusion and retention using an artificial reporter lacking natural sorting signals that recapitulates the energy dependence of the process in vivo.
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Affiliation(s)
- Rosemarie Ungricht
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland Molecular Life Sciences PhD Program, CH-8057 Zurich, Switzerland
| | - Michael Klann
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Peter Horvath
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
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319
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Malashicheva A, Bogdanova M, Zabirnyk A, Smolina N, Ignatieva E, Freilikhman O, Fedorov A, Dmitrieva R, Sjöberg G, Sejersen T, Kostareva A. Various lamin A/C mutations alter expression profile of mesenchymal stem cells in mutation specific manner. Mol Genet Metab 2015; 115:118-27. [PMID: 25982065 DOI: 10.1016/j.ymgme.2015.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 12/31/2022]
Abstract
Various mutations in LMNA gene, encoding for nuclear lamin A/C protein, lead to laminopathies and contribute to over ten human disorders, mostly affecting tissues of mesenchymal origin such as fat tissue, muscle tissue, and bones. Recently it was demonstrated that lamins not only play a structural role providing communication between extra-nuclear structures and components of cell nucleus but also control cell fate and differentiation. In our study we assessed the effect of various LMNA mutations on the expression profile of mesenchymal multipotent stem cells (MMSC) during adipogenic and osteogenic differentiation. We used lentiviral approach to modify human MMSC with LMNA-constructs bearing mutations associated with different laminopathies--G465D, R482L, G232E, R527C, and R471C. The impact of various mutations on MMSC differentiation properties and expression profile was assessed by colony-forming unit analysis, histological staining, expression of the key differentiation markers promoting adipogenesis and osteogenesis followed by the analysis of the whole set of genes involved in lineage-specific differentiation using PCR expression arrays. We demonstrate that various LMNA mutations influence the differentiation efficacy of MMSC in mutation-specific manner. Each LMNA mutation promotes a unique expression pattern of genes involved in a lineage-specific differentiation and this pattern is shared by the phenotype-specific mutations.
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Affiliation(s)
- Anna Malashicheva
- Almazov Federal Medical Research Centre, St. Petersburg, Russia; St. Petersburg State University, St. Petersburg, Russia; ITMO University, Institute of translational Medicine, St. Petersburg, Russia
| | - Maria Bogdanova
- Almazov Federal Medical Research Centre, St. Petersburg, Russia; St. Petersburg State University, St. Petersburg, Russia
| | | | - Natalia Smolina
- Almazov Federal Medical Research Centre, St. Petersburg, Russia; Department of Woman and Child Health, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Elena Ignatieva
- Almazov Federal Medical Research Centre, St. Petersburg, Russia
| | | | - Anton Fedorov
- Almazov Federal Medical Research Centre, St. Petersburg, Russia
| | | | - Gunnar Sjöberg
- Department of Woman and Child Health, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Thomas Sejersen
- Department of Woman and Child Health, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anna Kostareva
- Almazov Federal Medical Research Centre, St. Petersburg, Russia; Department of Woman and Child Health, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden; ITMO University, Institute of translational Medicine, St. Petersburg, Russia.
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320
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Worman HJ, Schirmer EC. Nuclear membrane diversity: underlying tissue-specific pathologies in disease? Curr Opin Cell Biol 2015; 34:101-12. [PMID: 26115475 PMCID: PMC4522394 DOI: 10.1016/j.ceb.2015.06.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 11/16/2022]
Abstract
Human 'laminopathy' diseases result from mutations in genes encoding nuclear lamins or nuclear envelope (NE) transmembrane proteins (NETs). These diseases present a seeming paradox: the mutated proteins are widely expressed yet pathology is limited to specific tissues. New findings suggest tissue-specific pathologies arise because these widely expressed proteins act in various complexes that include tissue-specific components. Diverse mechanisms to achieve NE tissue-specificity include tissue-specific regulation of the expression, mRNA splicing, signaling, NE-localization and interactions of potentially hundreds of tissue-specific NETs. New findings suggest these NETs underlie tissue-specific NE roles in cytoskeletal mechanics, cell-cycle regulation, signaling, gene expression and genome organization. This view of the NE as 'specialized' in each cell type is important to understand the tissue-specific pathology of NE-linked diseases.
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Affiliation(s)
- Howard J Worman
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, USA
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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321
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Polyphyly of nuclear lamin genes indicates an early eukaryotic origin of the metazoan-type intermediate filament proteins. Sci Rep 2015; 5:10652. [PMID: 26024016 PMCID: PMC4448529 DOI: 10.1038/srep10652] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 04/20/2015] [Indexed: 12/24/2022] Open
Abstract
The nuclear lamina is a protein meshwork associated with the inner side of the nuclear envelope contributing structural, signalling and regulatory functions. Here, I report on the evolution of an important component of the lamina, the lamin intermediate filament proteins, across the eukaryotic tree of life. The lamins show a variety of protein domain and sequence motif architectures beyond the classical α-helical rod, nuclear localisation signal, immunoglobulin domain and CaaX motif organisation, suggesting extension and adaptation of functions in many species. I identified lamin genes not only in metazoa and Amoebozoa as previously described, but also in other opisthokonts including Ichthyosporea and choanoflagellates, in oomycetes, a sub-family of Stramenopiles, and in Rhizaria, implying that they must have been present very early in eukaryotic evolution if not even the last common ancestor of all extant eukaryotes. These data considerably extend the current perception of lamin evolution and have important implications with regard to the evolution of the nuclear envelope.
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322
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Zhu L, Brangwynne CP. Nuclear bodies: the emerging biophysics of nucleoplasmic phases. Curr Opin Cell Biol 2015; 34:23-30. [PMID: 25942753 DOI: 10.1016/j.ceb.2015.04.003] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/16/2015] [Accepted: 04/14/2015] [Indexed: 01/02/2023]
Abstract
The cell nucleus contains a large number of membrane-less bodies that play important roles in the spatiotemporal regulation of gene expression. Recent work suggests that low complexity/disordered protein motifs and repetitive binding domains drive assembly of droplets of nuclear RNA/protein by promoting nucleoplasmic phase separation. Nucleation and maturation of these structures is regulated by, and may in turn affect, factors including post-translational modifications, protein concentration, transcriptional activity, and chromatin state. Here we present a concise review of these exciting recent advances, and discuss current and future challenges in understanding the assembly, regulation, and function of nuclear RNA/protein bodies.
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Affiliation(s)
- Lian Zhu
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA
| | - Clifford P Brangwynne
- Princeton University, Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA.
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323
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Structural analysis of multicellular organisms with cryo-electron tomography. Nat Methods 2015; 12:634-6. [PMID: 25961413 DOI: 10.1038/nmeth.3401] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/16/2015] [Indexed: 01/22/2023]
Abstract
We developed a method for visualizing tissues from multicellular organisms using cryo-electron tomography. Our protocol involves vitrifying samples with high-pressure freezing, thinning them with cryo-FIB-SEM (focused-ion-beam scanning electron microscopy) and applying fiducial gold markers under cryogenic conditions to the lamellae post-milling. We applied this protocol to acquire tomograms of vitrified Caenorhabditis elegans embryos and worms, which showed the intracellular organization of selected tissues at particular developmental stages in otherwise intact specimens.
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324
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Li Q, Makhija E, Hameed F, Shivashankar G. Micropillar displacements by cell traction forces are mechanically correlated with nuclear dynamics. Biochem Biophys Res Commun 2015; 461:372-7. [DOI: 10.1016/j.bbrc.2015.04.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 12/31/2022]
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325
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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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326
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Mojica SA, Hovis KM, Frieman MB, Tran B, Hsia RC, Ravel J, Jenkins-Houk C, Wilson KL, Bavoil PM. SINC, a type III secreted protein of Chlamydia psittaci, targets the inner nuclear membrane of infected cells and uninfected neighbors. Mol Biol Cell 2015; 26:1918-34. [PMID: 25788290 PMCID: PMC4436835 DOI: 10.1091/mbc.e14-11-1530] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/06/2015] [Indexed: 12/31/2022] Open
Abstract
SINC, a new type III secreted protein of the avian and human pathogen Chlamydia psittaci, uniquely targets the nuclear envelope of C. psittaci-infected cells and uninfected neighboring cells. Digitonin-permeabilization studies of SINC-GFP-transfected HeLa cells indicate that SINC targets the inner nuclear membrane. SINC localization at the nuclear envelope was blocked by importazole, confirming SINC import into the nucleus. Candidate partners were identified by proximity to biotin ligase-fused SINC in HEK293 cells and mass spectrometry (BioID). This strategy identified 22 candidates with high confidence, including the nucleoporin ELYS, lamin B1, and four proteins (emerin, MAN1, LAP1, and LBR) of the inner nuclear membrane, suggesting that SINC interacts with host proteins that control nuclear structure, signaling, chromatin organization, and gene silencing. GFP-SINC association with the native LEM-domain protein emerin, a conserved component of nuclear "lamina" structure, or with a complex containing emerin was confirmed by GFP pull down. Our findings identify SINC as a novel bacterial protein that targets the nuclear envelope with the capability of globally altering nuclear envelope functions in the infected host cell and neighboring uninfected cells. These properties may contribute to the aggressive virulence of C. psittaci.
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Affiliation(s)
- Sergio A Mojica
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Kelley M Hovis
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Bao Tran
- Mass Spectrometry Center, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Ru-ching Hsia
- Core Imaging Facility and Department of Neural and Pain Sciences, University of Maryland School of Dentistry, Baltimore, MD 21201
| | - Jacques Ravel
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Clifton Jenkins-Houk
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Patrik M Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201
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327
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Abstract
The intermediate filament proteins, A- and B-type lamins, form the nuclear lamina scaffold adjacent to the inner nuclear membrane. Lamins also contribute to chromatin regulation and various signaling pathways affecting gene expression. In this review, Osmanagic-Myers et al. focus on the role of nuclear lamins in mechanosensing and also discuss how disease-linked lamin mutants may impair the response of cells to mechanical stimuli and influence the properties of the extracellular matrix. The intermediate filament proteins, A- and B-type lamins, form the nuclear lamina scaffold adjacent to the inner nuclear membrane. B-type lamins confer elasticity, while A-type lamins lend viscosity and stiffness to nuclei. Lamins also contribute to chromatin regulation and various signaling pathways affecting gene expression. The mechanical roles of lamins and their functions in gene regulation are often viewed as independent activities, but recent findings suggest a highly cross-linked and interdependent regulation of these different functions, particularly in mechanosignaling. In this newly emerging concept, lamins act as a “mechanostat” that senses forces from outside and responds to tension by reinforcing the cytoskeleton and the extracellular matrix. A-type lamins, emerin, and the linker of the nucleoskeleton and cytoskeleton (LINC) complex directly transmit forces from the extracellular matrix into the nucleus. These mechanical forces lead to changes in the molecular structure, modification, and assembly state of A-type lamins. This in turn activates a tension-induced “inside-out signaling” through which the nucleus feeds back to the cytoskeleton and the extracellular matrix to balance outside and inside forces. These functions regulate differentiation and may be impaired in lamin-linked diseases, leading to cellular phenotypes, particularly in mechanical load-bearing tissues.
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328
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Jeong K, Kwon H, Lee J, Jang D, Pak Y. Insulin-response epigenetic activation of Egr-1 and JunB genes at the nuclear periphery by A-type lamin-associated pY19-Caveolin-2 in the inner nuclear membrane. Nucleic Acids Res 2015; 43:3114-27. [PMID: 25753664 PMCID: PMC4381080 DOI: 10.1093/nar/gkv181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/20/2015] [Indexed: 11/15/2022] Open
Abstract
Insulin controls transcription to sustain its physiologic effects for the organism to adapt to environmental changes added to genetic predisposition. Nevertheless, insulin-induced transcriptional regulation by epigenetic factors and in defined nuclear territory remains elusive. Here we show that inner nuclear membrane (INM)-integrated caveolin-2 (Cav-2) regulates insulin-response epigenetic activation of Egr-1 and JunB genes at the nuclear periphery. INM-targeted pY19-Cav-2 in response to insulin associates specifically with the A-type lamin, disengages the repressed Egr-1 and JunB promoters from lamin A/C through disassembly of H3K9me3, and facilitates assembly of H3K9ac, H3K18ac and H3K27ac by recruitment of GCN5 and p300 and the subsequent enrichment of RNA polymerase II (Pol II) on the promoters at the nuclear periphery. Our findings show that Cav-2 is an epigenetic regulator of histone H3 modifications, and provide novel mechanisms of insulin-response epigenetic activation at the nuclear periphery.
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Affiliation(s)
- Kyuho Jeong
- Department of Biochemistry, Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Korea
| | - Hayeong Kwon
- Department of Biochemistry, Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Korea
| | - Jaewoong Lee
- Department of Biochemistry, Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Korea
| | - Donghwan Jang
- Department of Biochemistry, Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Korea
| | - Yunbae Pak
- Department of Biochemistry, Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 660-701, Korea
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329
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Warren DT, Tajsic T, Porter LJ, Minaisah RM, Cobb A, Jacob A, Rajgor D, Zhang QP, Shanahan CM. Nesprin-2-dependent ERK1/2 compartmentalisation regulates the DNA damage response in vascular smooth muscle cell ageing. Cell Death Differ 2015; 22:1540-50. [PMID: 25744025 PMCID: PMC4532777 DOI: 10.1038/cdd.2015.12] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/19/2014] [Accepted: 01/21/2015] [Indexed: 11/30/2022] Open
Abstract
Prelamin A accumulation and persistent DNA damage response (DDR) are hallmarks of vascular smooth muscle cell (VSMC) ageing and dysfunction. Although prelamin A is proposed to interfere with DNA repair, our understanding of the crosstalk between prelamin A and the repair process remains limited. The extracellular signal-regulated kinases 1 and 2 (ERK1/2) have emerged as key players in the DDR and are known to enhance ataxia telangiectasia-mutated protein (ATM) activity at DNA lesions, and in this study, we identified a novel relationship between prelamin A accumulation and ERK1/2 nuclear compartmentalisation during VSMC ageing. We show both prelamin A accumulation and increased DNA damage occur concomitantly, before VSMC replicative senescence, and induce the localisation of ERK1/2 to promyelocytic leukaemia protein nuclear bodies (PML NBs) at the sites of DNA damage via nesprin-2 and lamin A interactions. Importantly, VSMCs treated with DNA damaging agents also displayed prelamin A accumulation and ERK compartmentalisation at PML NBs, suggesting that prelamin A and nesprin-2 are novel components of the DDR. In support of this, disruption of ERK compartmentalisation at PML NBs, by either depletion of nesprin-2 or lamins A/C, resulted in the loss of ATM from DNA lesions. However, ATM signalling and DNA repair remained intact after lamins A/C depletion, whereas nesprin-2 disruption ablated downstream Chk2 activation and induced genomic instability. We conclude that lamins A/C and PML act as scaffolds to organise DNA-repair foci and compartmentalise nesprin-2/ERK signalling. However, nesprin-2/ERK signalling fidelity, but not their compartmentalisation at PML NBs, is essential for efficient DDR in VSMCs.
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Affiliation(s)
- D T Warren
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - T Tajsic
- Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - L J Porter
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - R M Minaisah
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - A Cobb
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - A Jacob
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - D Rajgor
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - Q P Zhang
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - C M Shanahan
- British Heart Foundation Centre of Research Excellence, Cardiovascular Division, King's College London, London SE5 9NU, UK
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330
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Tamura K, Goto C, Hara-Nishimura I. Recent advances in understanding plant nuclear envelope proteins involved in nuclear morphology. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1641-7. [PMID: 25711706 DOI: 10.1093/jxb/erv036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The nuclear envelope (NE) is a fundamental structure of the nucleus and plays an important role in nuclear morphology through the strict regulation of NE protein function. Beyond its physical barrier function between nucleoplasm and cytoplasm, recent studies of the plant NE have provided novel insights into basic aspects of nuclear morphology as well as cellular organization. In this review, we focus on plant NE proteins that have emerged from recent studies in nuclear morphology, and we discuss their physiological functions in cellular activities. A better understanding of the NE protein functions should provide key insights into the physiological significance of proper nuclear structure in plants.
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Affiliation(s)
- Kentaro Tamura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Chieko Goto
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Ikuko Hara-Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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331
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Elkhatib R, Longepied G, Paci M, Achard V, Grillo JM, Levy N, Mitchell MJ, Metzler-Guillemain C. Nuclear envelope remodelling during human spermiogenesis involves somatic B-type lamins and a spermatid-specific B3 lamin isoform. Mol Hum Reprod 2015; 21:225-36. [PMID: 25477337 DOI: 10.1093/molehr/gau111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The nuclear lamina (NL) is a filamentous protein meshwork, composed essentially of lamins, situated between the inner nuclear membrane and the chromatin. There is mounting evidence that the NL plays a role in spermatid differentiation during spermiogenesis. The mouse spermatid NL is composed of the ubiquitous lamin B1 and the spermatid-specific lamin B3, an N-terminally truncated isoform of lamin B2. However, nothing is known about the NL in human spermatids. We therefore investigated the expression pattern and localization of A-type lamins (A, C and C2) and B-type lamins (B1, B2 and B3) during human spermiogenesis. Here, we show that a lamin B3 transcript is present in human spermatids and that B-type lamins are the only lamins detectable in human spermatids. We determine that, as shown for their mouse counterparts, human lamin B3, but not lamin B2, induces strong nuclear deformation, when ectopically expressed in HeLa cells. Co-immunofluorescence revealed that, in human spermatids, B-type lamins are present at the nuclear periphery, except in the region covered by the acrosome, and that as the spermatid matures the B-type lamins recede towards the posterior pole. Only lamin B1 remains detectable on 33-47% of ejaculated spermatozoa. On spermatozoa selected for normal head density, however, this fell to <6%, suggesting that loss of the NL signal may be linked to complete sperm nucleus compaction. The similarities revealed between lamin expression during human and rodent spermiogenesis, strengthen evidence that the NL and lamin B3 have conserved functions during the intense remodelling of the mammalian spermatid nucleus.
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Affiliation(s)
- Razan Elkhatib
- Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385, Marseille, France
| | - Guy Longepied
- Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385, Marseille, France
| | - Marine Paci
- Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385, Marseille, France APHM Hôpital La Conception, Gynépôle, Laboratoire de Biologie de la Reproduction-CECOS, 13385 Marseille Cedex 5, France
| | - Vincent Achard
- APHM Hôpital La Conception, Gynépôle, Laboratoire de Biologie de la Reproduction-CECOS, 13385 Marseille Cedex 5, France
| | - Jean-Marie Grillo
- APHM Hôpital La Conception, Gynépôle, Laboratoire de Biologie de la Reproduction-CECOS, 13385 Marseille Cedex 5, France Aix Marseille Université, Laboratoire de Biogénotoxicologie et Mutagenèse Environnementale, EA 1784 - Fédération de Recherche CNRS no 3098 Ecosystèmes Continentaux et Risques Environnementaux, 13385 Marseille Cedex 5, France
| | - Nicolas Levy
- Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385, Marseille, France
| | - Michael J Mitchell
- Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385, Marseille, France
| | - Catherine Metzler-Guillemain
- Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385, Marseille, France APHM Hôpital La Conception, Gynépôle, Laboratoire de Biologie de la Reproduction-CECOS, 13385 Marseille Cedex 5, France
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332
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Zhou X, Graumann K, Meier I. The plant nuclear envelope as a multifunctional platform LINCed by SUN and KASH. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1649-59. [PMID: 25740919 DOI: 10.1093/jxb/erv082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The nuclear envelope (NE) is a double membrane system enclosing the genome of eukaryotes. Besides nuclear pore proteins, which form channels at the NE, nuclear membranes are populated by a collection of NE proteins that perform various cellular functions. However, in contrast to well-conserved nuclear pore proteins, known NE proteins share little homology between opisthokonts and plants. Recent studies on NE protein complexes formed by Sad1/UNC-84 (SUN) and Klarsicht/ANC-1/Syne-1 Homology (KASH) proteins have advanced our understanding of plant NE proteins and revealed their function in anchoring other proteins at the NE, nuclear shape determination, nuclear positioning, anti-pathogen defence, root development, and meiotic chromosome organization. In this review, we discuss the current understanding of plant SUN, KASH, and other related NE proteins, and compare their function with the opisthokont counterparts.
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Affiliation(s)
- Xiao Zhou
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington Campus, Oxford OX3 OBP, UK
| | - Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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333
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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334
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Link J, Jahn D, Alsheimer M. Structural and functional adaptations of the mammalian nuclear envelope to meet the meiotic requirements. Nucleus 2015; 6:93-101. [PMID: 25674669 PMCID: PMC4615672 DOI: 10.1080/19491034.2015.1004941] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Numerous studies in the past years provided definite evidence that the nuclear envelope is much more than just a simple barrier. It rather constitutes a multifunctional platform combining structural and dynamic features to fulfill many fundamental functions such as chromatin organization, regulation of transcription, signaling, but also structural duties like maintaining general nuclear architecture and shape. One additional and, without doubt, highly impressive aspect is the recently identified key function of selected nuclear envelope components in driving meiotic chromosome dynamics, which in turn is essential for accurate recombination and segregation of the homologous chromosomes. Here, we summarize the recent work identifying new key players in meiotic telomere attachment and movement and discuss the latest advances in our understanding of the actual function of the meiotic nuclear envelope.
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Affiliation(s)
- Jana Link
- a Department of Cell and Developmental Biology ; Biocenter University Würzburg ; Würzburg , Germany
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335
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Aguilar A, Wagstaff KM, Suárez-Sánchez R, Zinker S, Jans DA, Cisneros B. Nuclear localization of the dystrophin-associated protein α-dystrobrevin through importin α2/β1 is critical for interaction with the nuclear lamina/maintenance of nuclear integrity. FASEB J 2015; 29:1842-58. [PMID: 25636738 DOI: 10.1096/fj.14-257147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/31/2014] [Indexed: 01/06/2023]
Abstract
Although α-dystrobrevin (DB) is assembled into the dystrophin-associated protein complex, which is central to cytoskeletal organization, it has also been found in the nucleus. Here we delineate the nuclear import pathway responsible for nuclear targeting of α-DB for the first time, together with the importance of nuclear α-DB in determining nuclear morphology. We map key residues of the nuclear localization signal of α-DB within the zinc finger domain (ZZ) using various truncated versions of the protein, and site-directed mutagenesis. Pulldown, immunoprecipitation, and AlphaScreen assays showed that the importin (IMP) α2/β1 heterodimer interacts with high affinity with the ZZ domain of α-DB. In vitro nuclear import assays using antibodies to specific importins, as well as in vivo studies using siRNA or a dominant negative importin construct, confirmed the key role of IMPα2/β1 in α-DB nuclear translocation. Knockdown of α-DB expression perturbed cell cycle progression in C2C12 myoblasts, with decreased accumulation of cells in S phase and, significantly, altered localization of lamins A/C, B1, and B2 with accompanying gross nuclear morphology defects. Because α-DB interacts specifically with lamin B1 in vivo and in vitro, nuclear α-DB would appear to play a key role in nuclear shape maintenance through association with the nuclear lamina.
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Affiliation(s)
- Areli Aguilar
- *Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, Mexico; Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; and Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación, México City, Mexico
| | - Kylie M Wagstaff
- *Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, Mexico; Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; and Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación, México City, Mexico
| | - Rocío Suárez-Sánchez
- *Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, Mexico; Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; and Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación, México City, Mexico
| | - Samuel Zinker
- *Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, Mexico; Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; and Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación, México City, Mexico
| | - David A Jans
- *Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, Mexico; Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; and Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación, México City, Mexico
| | - Bulmaro Cisneros
- *Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México City, Mexico; Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; and Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación, México City, Mexico
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336
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Abstract
The proper folding of proteins is continuously challenged by intrinsic and extrinsic stresses, and the accumulation of toxic misfolded proteins is associated with many human diseases. Eukaryotic cells have evolved a complex network of protein quality control pathways to protect the proteome, and these pathways are specialized for each subcellular compartment. While many details have been elucidated for how the cytosol and endoplasmic reticulum counteract proteotoxic stress, relatively little is known about the pathways protecting the nucleus from protein misfolding. Proper maintenance of nuclear proteostasis has important implications in preserving genomic integrity, as well as for aging and disease. Here, we offer a conceptual framework for how proteostasis is maintained in this organelle. We define the particular requirements that must be considered for the nucleus to manage proteotoxic stress, summarize the known and implicated pathways of nuclear protein quality control, and identify the unresolved questions in the field.
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Affiliation(s)
- Yoko Shibata
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA.
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337
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Wang AS, Kozlov SV, Stewart CL, Horn HF. Tissue specific loss of A-type lamins in the gastrointestinal epithelium can enhance polyp size. Differentiation 2015; 89:11-21. [PMID: 25578479 DOI: 10.1016/j.diff.2014.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/08/2014] [Accepted: 12/17/2014] [Indexed: 12/19/2022]
Abstract
The nuclear lamina, comprised of the A and B-type lamins, is important in maintaining nuclear shape and in regulating key nuclear functions such as chromatin organization and transcription. Deletion of the A-type lamins results in genome instability and many cancers show altered levels of A-type lamin expression. Loss of function mutations in the mouse Lmna gene result in early postnatal lethality, usually within 3-5 weeks of birth making an analysis of the role of lamins in carcinogenesis difficult. To circumvent early lethality, and determine the role of the A-type lamins in specific tissues in older mice we derived a conditional allele of Lmna(FL/FL) (floxed). Lmna(FL/FL) was specifically deleted in the gastrointestinal (GI) epithelium by crossing the Lmna(FL/FL) mice with Villin-Cre mice. Mice lacking Lmna in the GI are overtly normal with no effects on overall growth, longevity or GI morphology. On a GI specific sensitized (Apc(Min/+)) background, polyp numbers are unchanged, but polyp size is slightly increased, and only in the duodenum. Our findings reveal that although A-type lamins are dispensable in the postnatal GI epithelium, loss of Lmna under malignant conditions may, to a limited extent, enhance polyp size indicating that A-type lamins may regulate cell proliferation in the transformed GI epithelium.
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Affiliation(s)
- Audrey S Wang
- Developmental and Regenerative Biology, Institute of Medical Biology, 8A Biomedical Grove, 138648, Singapore; Department of Biological Sciences, NUS, Singapore
| | - Serguei V Kozlov
- Center for Advanced Preclinical Research, Science Applications International Corporation-Frederick, Frederick, MD 21702, United States
| | - Colin L Stewart
- Developmental and Regenerative Biology, Institute of Medical Biology, 8A Biomedical Grove, 138648, Singapore; Department of Biological Sciences, NUS, Singapore.
| | - Henning F Horn
- Developmental and Regenerative Biology, Institute of Medical Biology, 8A Biomedical Grove, 138648, Singapore
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338
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Sorting nexin 6 enhances lamin a synthesis and incorporation into the nuclear envelope. PLoS One 2014; 9:e115571. [PMID: 25535984 PMCID: PMC4275242 DOI: 10.1371/journal.pone.0115571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 10/21/2014] [Indexed: 01/20/2023] Open
Abstract
Nuclear lamins are important structural and functional proteins in mammalian cells, but little is known about the mechanisms and cofactors that regulate their traffic into the nucleus. Here, we demonstrate that trafficking of lamin A, but not lamin B1, and its assembly into the nuclear envelope are regulated by sorting nexin 6 (SNX6), a major component of the retromer that targets proteins and other molecules to specific subcellular locations. SNX6 interacts with lamin A in vitro and in vivo and links it to the outer surface of the endoplasmic reticulum in human and mouse cells. SNX6 transports its lamin A cargo to the nuclear envelope in a process that takes several hours. Lamin A protein levels in the nucleus augment or decrease, respectively, upon gain or loss of SNX6 function. We further show that SNX6-dependent lamin A nuclear import occurs across the nuclear pore complex via a RAN-GTP-dependent mechanism. These results identify SNX6 as a key regulator of lamin A synthesis and incorporation into the nuclear envelope.
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339
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Mu W, Starmer J, Fedoriw AM, Yee D, Magnuson T. Repression of the soma-specific transcriptome by Polycomb-repressive complex 2 promotes male germ cell development. Genes Dev 2014; 28:2056-69. [PMID: 25228648 PMCID: PMC4173155 DOI: 10.1101/gad.246124.114] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Using conditional mutagenesis to remove the core PRC2 subunits EED and SUZ12 during male germ cell development, Mu et al. identified a requirement for PRC2 in both mitotic and meiotic germ cells. Mutant spermatocytes exhibited ectopic expression of somatic lamins and an abnormal distribution of SUN1 proteins on the nuclear envelope. These defects were coincident with abnormal chromosome dynamics, affecting homologous chromosome pairing and synapsis. Polycomb-repressive complex 2 (PRC2) catalyzes the methylation of histone H3 Lys27 (H3K27) and functions as a critical epigenetic regulator of both stem cell pluripotency and somatic differentiation, but its role in male germ cell development is unknown. Using conditional mutagenesis to remove the core PRC2 subunits EED and SUZ12 during male germ cell development, we identified a requirement for PRC2 in both mitotic and meiotic germ cells. We observed a paucity of mutant spermatogonial stem cells (SSCs), which appears independent of repression of the known cell cycle inhibitors Ink4a/Ink4b/Arf. Moreover, mutant spermatocytes exhibited ectopic expression of somatic lamins and an abnormal distribution of SUN1 proteins on the nuclear envelope. These defects were coincident with abnormal chromosome dynamics, affecting homologous chromosome pairing and synapsis. We observed acquisition of H3K27me3 on stage-specific genes during meiotic progression, indicating a requirement for PRC2 in regulating the meiotic transcriptional program. Together, these data demonstrate that transcriptional repression of soma-specific genes by PRC2 facilitates homeostasis and differentiation during mammalian spermatogenesis.
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Affiliation(s)
- Weipeng Mu
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Joshua Starmer
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Andrew M Fedoriw
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Della Yee
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Terry Magnuson
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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340
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Kodiha M, Hutter E, Boridy S, Juhas M, Maysinger D, Stochaj U. Gold nanoparticles induce nuclear damage in breast cancer cells, which is further amplified by hyperthermia. Cell Mol Life Sci 2014; 71:4259-73. [PMID: 24740795 PMCID: PMC11113384 DOI: 10.1007/s00018-014-1622-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 02/28/2014] [Accepted: 03/31/2014] [Indexed: 02/07/2023]
Abstract
Gold nanoparticles have emerged as promising tools for cancer research and therapy, where they can promote thermal killing. The molecular mechanisms underlying these events are not fully understood. The geometry and size of gold nanoparticles can determine the severity of cellular damage. Therefore, small and big gold nanospheres as well as gold nanoflowers were evaluated side-by-side. To obtain quantitative data at the subcellular and molecular level, we assessed how gold nanoparticles, either alone or in combination with mild hyperthermia, altered the physiology of cultured human breast cancer cells. Our analyses focused on the nucleus, because this organelle is essential for cell survival. We showed that all the examined gold nanoparticles associated with nuclei. However, their biological effects were quantitatively different. Thus, depending on the shape and size, gold nanoparticles changed multiple nuclear parameters. They redistributed stress-sensitive regulators of nuclear biology, altered the nuclear morphology, reorganized nuclear laminae and envelopes, and inhibited nucleolar functions. In particular, gold nanoparticles reduced the de novo biosynthesis of RNA in nucleoli, the subnuclear compartments that produce ribosomes. While small gold nanospheres and nanoflowers, but not big gold nanospheres, damaged the nucleus at normal growth temperature, several of these defects were further exacerbated by mild hyperthermia. Taken together, the toxicity of gold nanoparticles correlated with changes in nuclear organization and function. These results emphasize that the cell nucleus is a prominent target for gold nanoparticles of different morphologies. Moreover, we demonstrated that RNA synthesis in nucleoli provides quantitative information on nuclear damage and cancer cell survival.
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Affiliation(s)
- Mohamed Kodiha
- Department of Physiology, McGill University, Montreal, H3G 1Y6 Canada
| | - Eliza Hutter
- Department of Pharmacology and Therapeutics, McGill University, Montreal, H3G 1Y6 Canada
| | - Sebastien Boridy
- Department of Pharmacology and Therapeutics, McGill University, Montreal, H3G 1Y6 Canada
| | - Michal Juhas
- Department of Pharmacology and Therapeutics, McGill University, Montreal, H3G 1Y6 Canada
| | - Dusica Maysinger
- Department of Pharmacology and Therapeutics, McGill University, Montreal, H3G 1Y6 Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, H3G 1Y6 Canada
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341
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Motegi SI, Yokoyama Y, Uchiyama A, Ogino S, Takeuchi Y, Yamada K, Hattori T, Hashizume H, Ishikawa Y, Goto M, Ishikawa O. First Japanese case of atypical progeroid syndrome/atypical Werner syndrome with heterozygous LMNA mutation. J Dermatol 2014; 41:1047-52. [PMID: 25327215 DOI: 10.1111/1346-8138.12657] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/04/2014] [Indexed: 01/08/2023]
Abstract
Atypical progeroid syndrome (APS), including atypical Werner syndrome (AWS), is a progeroid syndrome involving heterozygous mutations in the LMNA gene encoding the nuclear protein lamin A/C. We report the first Japanese case of APS/AWS with a LMNA mutation (p.D300N). A 53-year-old Japanese man had a history of recurrent severe cardiovascular diseases as well as brain infarction and hemorrhages. Although our APS/AWS patient had overlapping features with Werner syndrome (WS), such as high-pitched voice, scleroderma, lipoatrophy and atherosclerosis, several cardinal features of WS, including short stature, premature graying/alopecia, cataract, bird-like face, flat feet, hyperkeratosis on the soles and diabetes mellitus, were absent. In immunofluorescence staining and electron microscopic analyses of the patient's cultured fibroblasts, abnormal nuclear morphology, an increase in small aggregation of heterochromatin and a decrease in interchromatin granules in nuclei of fibroblasts were observed, suggesting that abnormal nuclear morphology and chromatin disorganization may be associated with the pathogenesis of APS/AWS.
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Affiliation(s)
- Sei-ichiro Motegi
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
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342
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Ramdas NM, Shivashankar GV. Cytoskeletal control of nuclear morphology and chromatin organization. J Mol Biol 2014; 427:695-706. [PMID: 25281900 DOI: 10.1016/j.jmb.2014.09.008] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/03/2014] [Accepted: 09/06/2014] [Indexed: 02/06/2023]
Abstract
The nucleus is sculpted toward various morphologies during cellular differentiation and development. Alterations in nuclear shape often result in changes to chromatin organization and genome function. This is thought to be reflective of its role as a cellular mechanotransducer. Recent evidence has highlighted the importance of cytoskeletal organization in defining how nuclear morphology regulates chromatin dynamics. However, the mechanisms underlying cytoskeletal control of chromatin remodeling are not well understood. We demonstrate here the differential influence of perinuclear actin- and microtubule-driven assemblies on nuclear architecture using pharmacological inhibitors and targeted RNA interference knockdown of cytoskeleton components in Drosophila cells. We find evidence that the loss of perinuclear actin assembly results in basolateral enhancement of microtubule organization and this is reflected functionally by enhanced nuclear dynamics. Cytoskeleton reorganization leads to nuclear lamina deformation that influences heterochromatin localization and core histone protein mobility. We also show that modulations in actin-microtubule assembly result in differential gene expression patterns. Taken together, we suggest that perinuclear actin and basolateral microtubule organization exerts mechanical control on nuclear morphology and chromatin dynamics.
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Affiliation(s)
- Nisha M Ramdas
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560 065, India
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 21 Lower Kent Ridge Road 119077, Singapore.
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343
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Bogdanova MA, Gudkova AY, Zabirnik AS, Ignatieva EV, Dmitrieva RI, Smolina NA, Kostareva AA, Malashicheva AB. Nuclear lamins regulate osteogenic differentiation of mesenchymal stem cells. ACTA ACUST UNITED AC 2014. [DOI: 10.1134/s1990519x14040026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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344
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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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345
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Lee JM, Jung HJ, Fong LG, Young SG. Do lamin B1 and lamin B2 have redundant functions? Nucleus 2014; 5:287-92. [PMID: 25482116 PMCID: PMC4152341 DOI: 10.4161/nucl.29615] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 12/29/2022] Open
Abstract
Lamins B1 and B2 have a high degree of sequence similarity and are widely expressed from the earliest stages of development. Studies of Lmnb1 and Lmnb2 knockout mice revealed that both of the B-type lamins are crucial for neuronal migration in the developing brain. These observations naturally posed the question of whether the two B-type lamins might play redundant functions in the development of the brain. To explore that issue, Lee and coworkers generated "reciprocal knock-in mice" (knock-in mice that produce lamin B1 from the Lmnb2 locus and knock-in mice that produce lamin B2 from the Lmnb1 locus). Both lines of knock-in mice manifested neurodevelopmental abnormalities similar to those in conventional knockout mice, indicating that lamins B1 and B2 have unique functions and that increased production of one B-type lamin cannot compensate for the loss of the other.
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Affiliation(s)
- John M Lee
- Department of Medicine; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Hea-Jin Jung
- Molecular Biology Institute; University of California; Los Angeles, CA USA
| | - Loren G Fong
- Department of Medicine; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - Stephen G Young
- Department of Medicine; David Geffen School of Medicine; University of California; Los Angeles, CA USA
- Molecular Biology Institute; University of California; Los Angeles, CA USA
- Department of Human Genetics; David Geffen School of Medicine; University of California; Los Angeles, CA USA
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346
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Maric M, Haugo AC, Dauer W, Johnson D, Roller RJ. Nuclear envelope breakdown induced by herpes simplex virus type 1 involves the activity of viral fusion proteins. Virology 2014; 460-461:128-37. [PMID: 25010278 DOI: 10.1016/j.virol.2014.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/21/2014] [Accepted: 05/07/2014] [Indexed: 12/31/2022]
Abstract
Herpesvirus infection reorganizes components of the nuclear lamina usually without loss of integrity of the nuclear membranes. We report that wild-type HSV infection can cause dissolution of the nuclear envelope in transformed mouse embryonic fibroblasts that do not express torsinA. Nuclear envelope breakdown is accompanied by an eight-fold inhibition of virus replication. Breakdown of the membrane is much more limited during infection with viruses that lack the gB and gH genes, suggesting that breakdown involves factors that promote fusion at the nuclear membrane. Nuclear envelope breakdown is also inhibited during infection with virus that does not express UL34, but is enhanced when the US3 gene is deleted, suggesting that envelope breakdown may be enhanced by nuclear lamina disruption. Nuclear envelope breakdown cannot compensate for deletion of the UL34 gene suggesting that mixing of nuclear and cytoplasmic contents is insufficient to bypass loss of the normal nuclear egress pathway.
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Affiliation(s)
- Martina Maric
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
| | - Alison C Haugo
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
| | - William Dauer
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Johnson
- Department of Microbiology and Immunology, Oregon Health Sciences University, Portland, OR 97201, USA
| | - Richard J Roller
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA.
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347
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Lund E, Oldenburg AR, Collas P. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 2014; 42:e92. [PMID: 24782521 PMCID: PMC4066758 DOI: 10.1093/nar/gku324] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 12/31/2022] Open
Abstract
Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations.
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Affiliation(s)
- Eivind Lund
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Anja R Oldenburg
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
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348
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Chromatin maintenance and dynamics in senescence: a spotlight on SAHF formation and the epigenome of senescent cells. Chromosoma 2014; 123:423-36. [PMID: 24861957 DOI: 10.1007/s00412-014-0469-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 01/28/2023]
Abstract
Senescence is a stable proliferation arrest characterized by profound changes in cellular morphology and metabolism as well as by extensive chromatin reorganization in the nucleus. One particular hallmark of chromatin changes during senescence is the formation of punctate DNA foci in DAPI-stained senescent cells that have been called senescence-associated heterochromatin foci (SAHF). While many advances have been made concerning our understanding of the effectors of senescence, how chromatin is reorganized and maintained in senescent cells has remained largely elusive. Because chromatin structure is inherently dynamic, senescent cells face the challenge of developing chromatin maintenance mechanisms in the absence of DNA replication in order to maintain the senescent phenotype. Here, we summarize and review recent findings shedding light on SAHF composition and formation via spatial repositioning of chromatin, with a specific focus on the role of lamin B1 for this process. In addition, we discuss the physiological implication of SAHF formation, the role of histone variants, and histone chaperones during senescence and also elaborate on the more general changes observed in the epigenome of the senescent cells.
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349
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Abstract
Much of the work on nuclear lamins during the past 15 years has focused on mutations in LMNA (the gene for prelamin A and lamin C) that cause particular muscular dystrophy, cardiomyopathy, partial lipodystrophy, and progeroid syndromes. These disorders, often called "laminopathies," mainly affect mesenchymal tissues (e.g., striated muscle, bone, and fibrous tissue). Recently, however, a series of papers have identified important roles for nuclear lamins in the central nervous system. Studies of knockout mice uncovered a key role for B-type lamins (lamins B1 and B2) in neuronal migration in the developing brain. Also, duplications of LMNB1 (the gene for lamin B1) have been shown to cause autosome-dominant leukodystrophy. Finally, recent studies have uncovered a peculiar pattern of nuclear lamin expression in the brain. Lamin C transcripts are present at high levels in the brain, but prelamin A expression levels are very low-due to regulation of prelamin A transcripts by microRNA 9. This form of prelamin A regulation likely explains why "prelamin A diseases" such as Hutchinson-Gilford progeria syndrome spare the central nervous system. In this review, we summarize recent progress in elucidating links between nuclear lamins and neurobiology.
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350
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Nuclear envelope-related lipodystrophies. Semin Cell Dev Biol 2014; 29:148-57. [DOI: 10.1016/j.semcdb.2013.12.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/06/2013] [Accepted: 12/20/2013] [Indexed: 12/12/2022]
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