1
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Zocher S, McCloskey A, Karasinsky A, Schulte R, Friedrich U, Lesche M, Rund N, Gage FH, Hetzer MW, Toda T. Lifelong persistence of nuclear RNAs in the mouse brain. Science 2024; 384:53-59. [PMID: 38574132 PMCID: PMC7615865 DOI: 10.1126/science.adf3481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/02/2024] [Indexed: 04/06/2024]
Abstract
Genomic DNA that resides in the nuclei of mammalian neurons can be as old as the organism itself. The life span of nuclear RNAs, which are critical for proper chromatin architecture and transcription regulation, has not been determined in adult tissues. In this work, we identified and characterized nuclear RNAs that do not turn over for at least 2 years in a subset of postnatally born cells in the mouse brain. These long-lived RNAs were stably retained in nuclei in a neural cell type-specific manner and were required for the maintenance of heterochromatin. Thus, the life span of neural cells may depend on both the molecular longevity of DNA for the storage of genetic information and also the extreme stability of RNA for the functional organization of chromatin.
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Affiliation(s)
- Sara Zocher
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
| | - Asako McCloskey
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
- Kura Oncology, Inc., 5510 Morehouse Dr., San Diego, CA 92121, USA
| | - Anne Karasinsky
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
| | - Roberta Schulte
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ulrike Friedrich
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
- German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mathias Lesche
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
| | - Nicole Rund
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martin W. Hetzer
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Tomohisa Toda
- Nuclear Architecture in Neural Plasticity and Aging, German Center for Neurodegenerative Diseases (DZNE), Dresden 01307, Germany
- Laboratory of Neural Epigenomics, Institute of Medical Physics and Micro-tissue Engineering, Faculty of Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
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2
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Kaneshiro JM, Capitanio JS, Hetzer MW. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus 2023; 14:2202548. [PMID: 37071033 PMCID: PMC10114975 DOI: 10.1080/19491034.2023.2202548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.
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Affiliation(s)
- Jeanae M Kaneshiro
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Juliana S Capitanio
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Paul F. Glenn Center for Biology of Aging Research, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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3
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Cho UH, Hetzer MW. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife 2023; 12:RP89066. [PMID: 37665327 PMCID: PMC10476967 DOI: 10.7554/elife.89066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. 'Trimmed' NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.
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Affiliation(s)
- Ukrae H Cho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Institute of Science and Technology Austria (IST Austria)KlosterneuburgAustria
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4
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Sharma R, Hetzer MW. Disulfide bond in SUN2 regulates dynamic remodeling of LINC complexes at the nuclear envelope. Life Sci Alliance 2023; 6:e202302031. [PMID: 37188462 PMCID: PMC10193101 DOI: 10.26508/lsa.202302031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023] Open
Abstract
The LINC complex tethers the cell nucleus to the cytoskeleton to regulate mechanical forces during cell migration, differentiation, and various diseases. The function of LINC complexes relies on the interaction between highly conserved SUN and KASH proteins that form higher-order assemblies capable of load bearing. These structural details have emerged from in vitro assembled LINC complexes; however, the principles of in vivo assembly remain obscure. Here, we report a conformation-specific SUN2 antibody as a tool to visualize LINC complex dynamics in situ. Using imaging, biochemical, and cellular methods, we find that conserved cysteines in SUN2 undergo KASH-dependent inter- and intra-molecular disulfide bond rearrangements. Disruption of the SUN2 terminal disulfide bond compromises SUN2 localization, turnover, LINC complex assembly in addition to cytoskeletal organization and cell migration. Moreover, using pharmacological and genetic perturbations, we identify components of the ER lumen as SUN2 cysteines redox state regulators. Overall, we provide evidence for SUN2 disulfide bond rearrangement as a physiologically relevant structural modification that regulates LINC complex functions.
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Affiliation(s)
- Rahul Sharma
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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5
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Shrestha S, Erikson G, Lyon J, Spigelman AF, Bautista A, Manning Fox JE, dos Santos C, Shokhirev M, Cartailler JP, Hetzer MW, MacDonald PE, Arrojo e Drigo R. Aging compromises human islet beta cell function and identity by decreasing transcription factor activity and inducing ER stress. Sci Adv 2022; 8:eabo3932. [PMID: 36197983 PMCID: PMC9534504 DOI: 10.1126/sciadv.abo3932] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/17/2022] [Indexed: 05/02/2023]
Abstract
Pancreatic islet beta cells are essential for maintaining glucose homeostasis. To understand the impact of aging on beta cells, we performed meta-analysis of single-cell RNA sequencing datasets, transcription factor (TF) regulon analysis, high-resolution confocal microscopy, and measured insulin secretion from nondiabetic donors spanning most of the human life span. This revealed the range of molecular and functional changes that occur during beta cell aging, including the transcriptional deregulation that associates with cellular immaturity and reorganization of beta cell TF networks, increased gene transcription rates, and reduced glucose-stimulated insulin release. These alterations associate with activation of endoplasmic reticulum (ER) stress and autophagy pathways. We propose that a chronic state of ER stress undermines old beta cell structure function to increase the risk of beta cell failure and type 2 diabetes onset as humans age.
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Affiliation(s)
- Shristi Shrestha
- Creative Data Solutions, Vanderbilt Center for Stem Cell Biology, Nashville, TN 37232, USA
| | - Galina Erikson
- Integrative Genomics and Bioinformatics Core, Salk Institute of Biological Studies, La Jolla, CA 92037, USA
| | - James Lyon
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Aliya F. Spigelman
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Austin Bautista
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Jocelyn E. Manning Fox
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Cristiane dos Santos
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Maxim Shokhirev
- Integrative Genomics and Bioinformatics Core, Salk Institute of Biological Studies, La Jolla, CA 92037, USA
| | | | - Martin W. Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute of Biological Studies, La Jolla, CA 92037, USA
| | - Patrick E. MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G2E1, Canada
| | - Rafael Arrojo e Drigo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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6
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Hetzer MW, Bersini S. Beyond Static Pipes: Mechanisms and In Vitro Models of Vascular Aging. Cold Spring Harb Perspect Med 2022; 12:cshperspect.a041180. [PMID: 35101902 DOI: 10.1101/cshperspect.a041180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The vascular system is a key player for the maintenance of healthy tissues, suggesting how the physiological decline of blood vessel functionality during aging could be a major contributor of organ degeneration. While basic research studies have begun to pinpoint potential mechanisms of vascular aging, it is now critical to translate them into therapeutically relevant options. Microphysiological systems represent a powerful tool to precisely control which combinations of stimuli are provided to in vitro reconstructed blood vessels and to analyze their functional consequences. After highlighting key aspects of vascular aging, this review discusses in vitro models that are able to recapitulate relevant features of blood vessel damage during aging. Strategies to improve current in vitro systems so that they will more faithfully recapitulate vascular aging are proposed, emphasizing the importance of combining in vivo models with microphysiological systems for an effective translation of vascular aging biomarkers and therapies to the clinical level.
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Affiliation(s)
- Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Simone Bersini
- Regenerative Medicine Technologies Laboratory, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland.,Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
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7
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Krishna S, Arrojo E Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer MW. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. Dev Cell 2021; 56:2952-2965.e9. [PMID: 34715012 DOI: 10.1016/j.devcel.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 07/28/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022]
Abstract
In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.
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Affiliation(s)
- Shefali Krishna
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rafael Arrojo E Drigo
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA; National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA
| | - Juliana S Capitanio
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ranjan Ramachandra
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA
| | - Mark Ellisman
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego School of Medicine (UCSD), La Jolla, CA 92093, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory (MCBL), Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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8
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Shadel GS, Adams PD, Berggren WT, Diedrich JK, Diffenderfer KE, Gage FH, Hah N, Hansen M, Hetzer MW, Molina AJA, Manor U, Marek K, O'Keefe DD, Pinto AFM, Sacco A, Sharpee TO, Shokriev MN, Zambetti S. The San Diego Nathan Shock Center: tackling the heterogeneity of aging. GeroScience 2021; 43:2139-2148. [PMID: 34370163 PMCID: PMC8599742 DOI: 10.1007/s11357-021-00426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/26/2022] Open
Abstract
Understanding basic mechanisms of aging holds great promise for developing interventions that prevent or delay many age-related declines and diseases simultaneously to increase human healthspan. However, a major confounding factor in aging research is the heterogeneity of the aging process itself. At the organismal level, it is clear that chronological age does not always predict biological age or susceptibility to frailty or pathology. While genetics and environment are major factors driving variable rates of aging, additional complexity arises because different organs, tissues, and cell types are intrinsically heterogeneous and exhibit different aging trajectories normally or in response to the stresses of the aging process (e.g., damage accumulation). Tackling the heterogeneity of aging requires new and specialized tools (e.g., single-cell analyses, mass spectrometry-based approaches, and advanced imaging) to identify novel signatures of aging across scales. Cutting-edge computational approaches are then needed to integrate these disparate datasets and elucidate network interactions between known aging hallmarks. There is also a need for improved, human cell-based models of aging to ensure that basic research findings are relevant to human aging and healthspan interventions. The San Diego Nathan Shock Center (SD-NSC) provides access to cutting-edge scientific resources to facilitate the study of the heterogeneity of aging in general and to promote the use of novel human cell models of aging. The center also has a robust Research Development Core that funds pilot projects on the heterogeneity of aging and organizes innovative training activities, including workshops and a personalized mentoring program, to help investigators new to the aging field succeed. Finally, the SD-NSC participates in outreach activities to educate the general community about the importance of aging research and promote the need for basic biology of aging research in particular.
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Affiliation(s)
- Gerald S Shadel
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - W Travis Berggren
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Jolene K Diedrich
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kenneth E Diffenderfer
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Fred H Gage
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Nasun Hah
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Martin W Hetzer
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anthony J A Molina
- Divison of Geriatrics, Gerontology and Palliative Care, Department of Medicine, University of California, San Diego, 9500 Gilman Dr, San Diego, CA, 92093, USA
| | - Uri Manor
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kurt Marek
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - David D O'Keefe
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | | | - Alessandra Sacco
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Tatyana O Sharpee
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Maxim N Shokriev
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Stefania Zambetti
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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9
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Cho UH, Hetzer MW. Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging. Neuron 2020; 106:899-911. [PMID: 32553207 DOI: 10.1016/j.neuron.2020.05.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 12/27/2022]
Abstract
In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging.
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Affiliation(s)
- Ukrae H Cho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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10
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Bersini S, Schulte R, Huang L, Tsai H, Hetzer MW. Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. eLife 2020; 9:54383. [PMID: 32896271 PMCID: PMC7478891 DOI: 10.7554/elife.54383] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro.
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Affiliation(s)
- Simone Bersini
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.,Paul F. Glenn Center for Biology of Aging Research at The Salk Institute, La Jolla, United States
| | - Roberta Schulte
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Ling Huang
- The Razavi Newman Integrative Genomics and Bioinformatics Core (IGC), The Salk Institute for Biological Studies, La Jolla, United States
| | - Hannah Tsai
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
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11
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Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer MW. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes Dev 2020; 34:913-930. [PMID: 32499403 PMCID: PMC7328517 DOI: 10.1101/gad.335794.119] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/28/2020] [Indexed: 12/18/2022]
Abstract
During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division.
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Affiliation(s)
- Hyeseon Kang
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Maxim N Shokhirev
- The Razavi Newman Integrative Genomics and Bioinformatics Core (IGC), Salk Institute for Biological Studies, 92037 La Jolla, California, USA
| | - Zhichao Xu
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Sahaana Chandran
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jesse R Dixon
- Peptide Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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12
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Bersini S, Arrojo E Drigo R, Huang L, Shokhirev MN, Hetzer MW. Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease. ACTA ACUST UNITED AC 2020; 4:e2000044. [PMID: 32402127 DOI: 10.1002/adbi.202000044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/21/2020] [Accepted: 03/02/2020] [Indexed: 12/31/2022]
Abstract
Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood-brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established.
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Affiliation(s)
- Simone Bersini
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Paul F. Glenn Center for Biology of Aging Research at The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Rafael Arrojo E Drigo
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ling Huang
- The Razavi Newman Integrative Genomics and Bioinformatics Core (IGC), The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Maxim N Shokhirev
- The Razavi Newman Integrative Genomics and Bioinformatics Core (IGC), The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
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13
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Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer MW. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Sci Alliance 2020; 3:3/1/e201900623. [PMID: 31959624 PMCID: PMC6971368 DOI: 10.26508/lsa.201900623] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/01/2023] Open
Abstract
This study highlights the role of Nup93-chromatin interactions in driving triple-negative breast cancer propagation through modulation of the actin cytoskeleton, cell migration and proliferation. Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis.
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Affiliation(s)
- Simone Bersini
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Paul F. Glenn Center for Biology of Aging Research at The Salk Institute, La Jolla, CA, USA
| | - Nikki K Lytle
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roberta Schulte
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ling Huang
- The Razavi Newman Integrative Genomics and Bioinformatics Core (IGC), The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Geoffrey M Wahl
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
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14
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Arrojo E Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer MW. Age Mosaicism across Multiple Scales in Adult Tissues. Cell Metab 2019; 30:343-351.e3. [PMID: 31178361 PMCID: PMC7289515 DOI: 10.1016/j.cmet.2019.05.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/18/2018] [Accepted: 05/11/2019] [Indexed: 12/22/2022]
Abstract
Most neurons are not replaced during an animal's lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.
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Affiliation(s)
- Rafael Arrojo E Drigo
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory (MCBL), La Jolla, CA, USA
| | - Varda Lev-Ram
- Department of Pharmacology, University of California, San Diego School of Medicine (UCSD), La Jolla, CA, USA
| | - Swati Tyagi
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory (MCBL), La Jolla, CA, USA
| | - Ranjan Ramachandra
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Thomas Deerinck
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Eric Bushong
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Victoria Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Claude Lechene
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark H Ellisman
- Department of Pharmacology, University of California, San Diego School of Medicine (UCSD), La Jolla, CA, USA; Department of Neurosciences, University of California, San Diego School of Medicine (UCSD), La Jolla, CA, USA
| | - Martin W Hetzer
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory (MCBL), La Jolla, CA, USA.
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15
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Abstract
The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing.
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Affiliation(s)
- Abigail Buchwalter
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Jeanae M Kaneshiro
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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16
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Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer MW, Navlakha S. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biol 2018; 19:221. [PMID: 30567591 PMCID: PMC6300908 DOI: 10.1186/s13059-018-1599-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/29/2018] [Indexed: 12/03/2022] Open
Abstract
Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients.
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Affiliation(s)
- Jason G Fleischer
- Integrative Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Roberta Schulte
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Hsiao H Tsai
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Swati Tyagi
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Maxim N Shokhirev
- Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Ling Huang
- Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Saket Navlakha
- Integrative Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
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17
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Toyama BH, Arrojo E Drigo R, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene C, Ellisman MH, Hetzer MW. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. J Cell Biol 2018; 218:433-444. [PMID: 30552100 PMCID: PMC6363465 DOI: 10.1083/jcb.201809123] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/12/2018] [Accepted: 11/26/2018] [Indexed: 12/26/2022] Open
Abstract
Toyama et al. monitor the replacement of long-lived components of nuclear pore complexes (NPCs) and nucleosomes in postmitotic cells. They describe age mosaicism at the level of chromatin organization and find that NPCs are maintained by piecemeal replacement in postmitotic nondividing cells but by entire complex replacement in an ESCRT-dependent manner in nondividing, starved quiescent cells. Many adult tissues contain postmitotic cells as old as the host organism. The only organelle that does not turn over in these cells is the nucleus, and its maintenance represents a formidable challenge, as it harbors regulatory proteins that persist throughout adulthood. Here we developed strategies to visualize two classes of such long-lived proteins, histones and nucleoporins, to understand the function of protein longevity in nuclear maintenance. Genome-wide mapping of histones revealed specific enrichment of long-lived variants at silent gene loci. Interestingly, nuclear pores are maintained by piecemeal replacement of subunits, resulting in mosaic complexes composed of polypeptides with vastly different ages. In contrast, nondividing quiescent cells remove old nuclear pores in an ESCRT-dependent manner. Our findings reveal distinct molecular strategies of nuclear maintenance, linking lifelong protein persistence to gene regulation and nuclear integrity.
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Affiliation(s)
- Brandon H Toyama
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA
| | - Rafael Arrojo E Drigo
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA
| | - Varda Lev-Ram
- Department of Pharmacology, University of California, San Diego, La Jolla, CA
| | - Ranjan Ramachandra
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California, San Diego, La Jolla, CA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California, San Diego, La Jolla, CA
| | - Claude Lechene
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California, San Diego, La Jolla, CA.,Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA
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18
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Abstract
In this study, McCloskey et al. investigated the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope. Their results show that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types and provide insight into a critical role of the nucleoporin Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus. The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.
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Affiliation(s)
- Asako McCloskey
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92130, USA
| | - Arkaitz Ibarra
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92130, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92130, USA
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19
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Franks TM, McCloskey A, Shokirev MN, Benner C, Rathore A, Hetzer MW. Nup98 recruits the Wdr82-Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes Dev 2017; 31:2222-2234. [PMID: 29269482 PMCID: PMC5769767 DOI: 10.1101/gad.306753.117] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/21/2017] [Indexed: 12/26/2022]
Abstract
In this study, Franks et al. investigated the mechanisms underlying how Nup98 regulates gene expression. They show that in hematopoietic cells, Nup98 binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS complex, which is required for deposition of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark, and expression of a Nup98 fusion protein implicated in aggressive AML causes mislocalization of H3K4me3 at aberrant regions and up-regulation of associated genes due to aberrant Wdr82/Set1A activity. Recent studies have shown that a subset of nucleoporins (Nups) can detach from the nuclear pore complex and move into the nuclear interior to regulate transcription. One such dynamic Nup, called Nup98, has been implicated in gene activation in healthy cells and has been shown to drive leukemogenesis when mutated in patients with acute myeloid leukemia (AML). Here we show that in hematopoietic cells, Nup98 binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS (complex of proteins associated with Set1) complex, which is required for deposition of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark. Depletion of Nup98 or Wdr82 abolishes Set1A recruitment to chromatin and subsequently ablates H3K4me3 at adjacent promoters. Furthermore, expression of a Nup98 fusion protein implicated in aggressive AML causes mislocalization of H3K4me3 at abnormal regions and up-regulation of associated genes. Our findings establish a function of Nup98 in hematopoietic gene activation and provide mechanistic insight into which Nup98 leukemic fusion proteins promote AML.
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Affiliation(s)
- Tobias M Franks
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Asako McCloskey
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Maxim Nikolaievich Shokirev
- The Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Chris Benner
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA.,Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Annie Rathore
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Martin W Hetzer
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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20
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Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer MW, Gage FH. Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells. Cell Stem Cell 2017; 21:618-634.e7. [PMID: 28919367 DOI: 10.1016/j.stem.2017.08.012] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/17/2017] [Accepted: 08/16/2017] [Indexed: 12/14/2022]
Abstract
Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that changes during differentiation. Nucleoporins are linked with cell-type-specific gene regulation, coupling physical changes in nuclear structure to transcriptional output; but, whether and how they coordinate with key fate-determining transcription factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2 in adult NeuPCs, where it is indispensable for their maintenance and controls neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional end sites correlates with increased or decreased gene expression, respectively, and inhibiting Nup153 expression alters open chromatin configurations at its target genes, disrupts genomic localization of Sox2, and promotes differentiation in vitro and a gliogenic fate switch in vivo. Together, these findings reveal that nuclear structural proteins may exert bimodal transcriptional effects to control cell fate.
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Affiliation(s)
- Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jonathan Y Hsu
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lauren Hu
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Filipe V Jacinto
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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21
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Abstract
Premature aging disorders provide an opportunity to study the mechanisms that drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins. We sought to investigate protein homeostasis in this disease. Here, we report a widespread increase in protein turnover in HGPS-derived cells compared to normal cells. We determine that global protein synthesis is elevated as a consequence of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts. Depleting normal lamin A or inducing mutant lamin A expression are each sufficient to drive nucleolar expansion. We further show that nucleolar size correlates with donor age in primary fibroblasts derived from healthy individuals and that ribosomal RNA production increases with age, indicating that nucleolar size and activity can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan in several systems, we show that increased ribosome biogenesis and activity are a hallmark of premature aging. HGPS is a premature aging disease caused by mutations in the nuclear protein lamin A. Here, the authors show that cells from patients with HGPS have expanded nucleoli and increased protein synthesis, and report that nucleoli also expand as aging progresses in cells derived from healthy individuals.
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Affiliation(s)
- Abigail Buchwalter
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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22
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Franks TM, Benner C, Narvaiza I, Marchetto MC, Young JM, Malik HS, Gage FH, Hetzer MW. Corrigendum: Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes Dev 2017; 31:845. [DOI: 10.1101/gad.300699.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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van de Ven RA, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer MW, Sahai E, Derksen PW. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nat Commun 2016; 7:13874. [PMID: 28004812 PMCID: PMC5192218 DOI: 10.1038/ncomms13874] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/07/2016] [Indexed: 02/07/2023] Open
Abstract
Spatiotemporal activation of RhoA and actomyosin contraction underpins cellular adhesion and division. Loss of cell-cell adhesion and chromosomal instability are cardinal events that drive tumour progression. Here, we show that p120-catenin (p120) not only controls cell-cell adhesion, but also acts as a critical regulator of cytokinesis. We find that p120 regulates actomyosin contractility through concomitant binding to RhoA and the centralspindlin component MKLP1, independent of cadherin association. In anaphase, p120 is enriched at the cleavage furrow where it binds MKLP1 to spatially control RhoA GTPase cycling. Binding of p120 to MKLP1 during cytokinesis depends on the N-terminal coiled-coil domain of p120 isoform 1A. Importantly, clinical data show that loss of p120 expression is a common event in breast cancer that strongly correlates with multinucleation and adverse patient survival. In summary, our study identifies p120 loss as a driver event of chromosomal instability in cancer.
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Affiliation(s)
- Robert A.H. van de Ven
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jolien S. de Groot
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Danielle Park
- Tumour Cell Biology Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Robert van Domselaar
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Danielle de Jong
- Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
| | - Elsken van der Wall
- Department of Internal Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - H. Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Paul J. van Diest
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Martin W. Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Erik Sahai
- Tumour Cell Biology Laboratory, Cancer Research UK London Research Institute, 44 Lincoln’s Inn Fields, London WC2A 3LY, UK
| | - Patrick W.B. Derksen
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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24
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Abstract
Here, Ibarra et al. investigate the contribution of nuclear envelope components to the regulation of cell type-specific gene expression and show a role for NPC components in the regulation of cell type-specific gene expression The authors found that nucleoporin-associated superenhancers localize preferentially to the nuclear periphery, and, in the absence of nucleoporins, transcriptional changes of SE-associated genes were observed. The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.
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Affiliation(s)
- Arkaitz Ibarra
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Chris Benner
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Swati Tyagi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jonah Cool
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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25
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Abstract
Hatch and Hetzer show that nuclear envelope rupture in cancer cells is caused by defects in lamina organization, resulting in an increase in intranuclear pressure from actin-based nucleus confinement. Repeated rounds of nuclear envelope (NE) rupture and repair have been observed in laminopathy and cancer cells and result in intermittent loss of nucleus compartmentalization. Currently, the causes of NE rupture are unclear. Here, we show that NE rupture in cancer cells relies on the assembly of contractile actin bundles that interact with the nucleus via the linker of nucleoskeleton and cytoskeleton (LINC) complex. We found that the loss of actin bundles or the LINC complex did not rescue nuclear lamina defects, a previously identified determinant of nuclear membrane stability, but did decrease the number and size of chromatin hernias. Finally, NE rupture inhibition could be rescued in cells treated with actin-depolymerizing drugs by mechanically constraining nucleus height. These data suggest a model of NE rupture where weak membrane areas, caused by defects in lamina organization, rupture because of an increase in intranuclear pressure from actin-based nucleus confinement.
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Affiliation(s)
- Emily M Hatch
- Department of Basic Sciences, The Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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26
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Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer MW. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes Dev 2016; 30:1155-71. [PMID: 27198230 PMCID: PMC4888837 DOI: 10.1101/gad.280941.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/26/2016] [Indexed: 11/24/2022]
Abstract
Franks et al. identify a widely expressed variant of the transmembrane nucleoporin Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. Instead of localizing to the NPC, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic transport, recent research suggests that certain NPC proteins have additionally acquired the role of affecting gene expression at the nuclear periphery and in the nucleoplasm in metazoans. Here we identify a widely expressed variant of the transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Interestingly, sPom121 transcripts appear independently in several mammalian species, suggesting convergent innovation of Nup-mediated transcription regulation during mammalian evolution. Our findings implicate alternate transcription initiation as a mechanism to increase the functional diversity of NPC components.
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Affiliation(s)
- Tobias M Franks
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Chris Benner
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Iñigo Narvaiza
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Maria C N Marchetto
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Janet M Young
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Harmit S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, USA; Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California 92093, USA
| | - Martin W Hetzer
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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27
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Affiliation(s)
- Emily M Hatch
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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28
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Mertens J, Paquola ACM, Ku M, Hatch E, Böhnke L, Ladjevardi S, McGrath S, Campbell B, Lee H, Herdy JR, Gonçalves JT, Toda T, Kim Y, Winkler J, Yao J, Hetzer MW, Gage FH. Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects. Cell Stem Cell 2015; 17:705-718. [PMID: 26456686 DOI: 10.1016/j.stem.2015.09.001] [Citation(s) in RCA: 472] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/18/2015] [Accepted: 09/02/2015] [Indexed: 02/09/2023]
Abstract
Aging is a major risk factor for many human diseases, and in vitro generation of human neurons is an attractive approach for modeling aging-related brain disorders. However, modeling aging in differentiated human neurons has proved challenging. We generated neurons from human donors across a broad range of ages, either by iPSC-based reprogramming and differentiation or by direct conversion into induced neurons (iNs). While iPSCs and derived neurons did not retain aging-associated gene signatures, iNs displayed age-specific transcriptional profiles and revealed age-associated decreases in the nuclear transport receptor RanBP17. We detected an age-dependent loss of nucleocytoplasmic compartmentalization (NCC) in donor fibroblasts and corresponding iNs and found that reduced RanBP17 impaired NCC in young cells, while iPSC rejuvenation restored NCC in aged cells. These results show that iNs retain important aging-related signatures, thus allowing modeling of the aging process in vitro, and they identify impaired NCC as an important factor in human aging.
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Affiliation(s)
- Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Apuã C M Paquola
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Manching Ku
- Next Generation Sequencing Core, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emily Hatch
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lena Böhnke
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shauheen Ladjevardi
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sean McGrath
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Benjamin Campbell
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hyungjun Lee
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joseph R Herdy
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - J Tiago Gonçalves
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yongsung Kim
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jürgen Winkler
- Department of Molecular Neurology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Jun Yao
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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29
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Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell Syst 2015; 1:224-37. [PMID: 27135913 PMCID: PMC4802414 DOI: 10.1016/j.cels.2015.08.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/21/2015] [Accepted: 08/26/2015] [Indexed: 12/29/2022]
Abstract
Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats. An integrated approach identifies molecular alterations between young and old rats Changes in translation output explain the majority of the altered protein abundances Key protein complexes are altered in abundance and composition We provide a rich data resource to stimulate further studies of aging
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Affiliation(s)
- Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Brandon H Toyama
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael S Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thomas Bock
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Murat Iskar
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany; Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany.
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30
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Abstract
Human cancer cells bear complex chromosome rearrangements that can be potential drivers of cancer development. However, the molecular mechanisms underlying these rearrangements have been unclear. Zhang et al. use a new technique combining live-cell imaging and single-cell sequencing to demonstrate that chromosomes mis-segregated to micronuclei frequently undergo chromothripsis-like rearrangements in the subsequent cell cycle.
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Affiliation(s)
- Emily M Hatch
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, 92037 CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, 92037 CA, USA.
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31
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Jacinto FV, Benner C, Hetzer MW. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes Dev 2015; 29:1224-38. [PMID: 26080816 PMCID: PMC4495395 DOI: 10.1101/gad.260919.115] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/27/2015] [Indexed: 11/24/2022]
Abstract
Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that mediate nuclear transport across the nuclear envelope. Recent evidence suggests that several Nups have additional roles in controlling the activation and silencing of developmental genes; however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the derepression of developmental genes and induction of early differentiation. This loss of stem cell identity is not associated with defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds around the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its target loci. Our results demonstrate a chromatin-associated role of Nup153 in maintaining stem cell pluripotency by functioning in mammalian epigenetic gene silencing.
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Affiliation(s)
- Filipe V Jacinto
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, 92037 California, USA
| | - Chris Benner
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, 92037 California, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, 92037 California, USA
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32
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Abstract
The luminal domain of Nup210 that lacks NPC sorting signals is sufficient for myogenesis, which suggests that Nup210 may operate within the nuclear envelope/ER lumen during differentiation. Previously, we identified the nucleoporin gp210/Nup210 as a critical regulator of muscle and neuronal differentiation, but how this nucleoporin exerts its function and whether it modulates nuclear pore complex (NPC) activity remain unknown. Here, we show that gp210/Nup210 mediates muscle cell differentiation in vitro via its conserved N-terminal domain that extends into the perinuclear space. Removal of the C-terminal domain, which partially mislocalizes gp210/Nup210 away from NPCs, efficiently rescues the differentiation defect caused by the knockdown of endogenous gp210/Nup210. Unexpectedly, a gp210/Nup210 mutant lacking the NPC-targeting transmembrane and C-terminal domains is sufficient for C2C12 myoblast differentiation. We demonstrate that the endoplasmic reticulum (ER) stress-specific caspase cascade is exacerbated during Nup210 depletion and that blocking ER stress-mediated apoptosis rescues differentiation of Nup210-deficient cells. Our results suggest that the role of gp210/Nup210 in cell differentiation is mediated by its large luminal domain, which can act independently of NPC association and appears to play a pivotal role in the maintenance of nuclear envelope/ER homeostasis.
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Affiliation(s)
- J Sebastian Gomez-Cavazos
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037 Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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33
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Abstract
Nup50 is a mobile nucleoporin with a pronounced presence both at the nuclear pore complex and in the nucleoplasm that can move between these different localizations. The dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II. The nuclear pore complex (NPC) plays a critical role in gene expression by mediating import of transcription regulators into the nucleus and export of RNA transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating transport, a subset of nucleoporins (Nups) engage in transcriptional activation and elongation at genomic loci that are not associated with NPCs. The underlying mechanism and regulation of Nup mobility on and off nuclear pores remain unclear. Here we show that Nup50 is a mobile Nup with a pronounced presence both at the NPC and in the nucleoplasm that can move between these different localizations. Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II and requires the N-terminal half of the protein, which contains importin α– and Nup153-binding domains. However, Nup50 dynamics are independent of importin α, Nup153, and Nup98, even though the latter two proteins also exhibit transcription-dependent mobility. Of interest, depletion of Nup50 from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation into myotubes. Taken together, our results suggest a transport-independent role for Nup50 in chromatin biology that occurs away from the NPC.
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Affiliation(s)
- Abigail L Buchwalter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Yun Liang
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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34
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Abstract
The spindle assembly checkpoint prevents separation of sister chromatids until each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report that the nuclear pore complex scaffolds spindle assembly checkpoint signaling in interphase, providing a store of inhibitory signals that limits the speed of the subsequent mitosis.
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Affiliation(s)
- Abigail Buchwalter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, 92037 CA, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, 92037 CA, USA.
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35
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Hatch EM, Fischer AH, Deerinck TJ, Hetzer MW. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell 2013; 154:47-60. [PMID: 23827674 DOI: 10.1016/j.cell.2013.06.007] [Citation(s) in RCA: 482] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 04/24/2013] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
Abstract
During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy.
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Affiliation(s)
- Emily M Hatch
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
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36
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Abstract
Neoplastic cells are often characterized by specific morphological abnormalities of the nuclear envelope (NE), which have been used for cancer diagnosis for more than a century. The NE is a double phospholipid bilayer that encapsulates the nuclear genome, regulates all nuclear trafficking of RNAs and proteins and prevents the passive diffusion of macromolecules between the nucleoplasm and the cytoplasm. Whether there is a consequence to the proper functioning of the cell and loss of structural integrity of the nucleus remains unclear. Using live cell imaging, we characterize a phenomenon wherein nuclei of several proliferating human cancer cell lines become temporarily ruptured during interphase. Strikingly, NE rupturing was associated with the mislocalization of nucleoplasmic and cytoplasmic proteins and, in the most extreme cases, the entrapment of cytoplasmic organelles in the nuclear interior. In addition, we observed the formation of micronuclei-like structures during interphase and the movement of chromatin out of the nuclear space. The frequency of these NE rupturing events was higher in cells in which the nuclear lamina, a network of intermediate filaments providing mechanical support to the NE, was not properly formed. Our data uncover the existence of a NE instability that has the potential to change the genomic landscape of cancer cells.
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Affiliation(s)
- Jesse D Vargas
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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37
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Gomez-Cavazos JS, Hetzer MW. Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. Curr Opin Cell Biol 2012; 24:775-83. [PMID: 22995343 DOI: 10.1016/j.ceb.2012.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/07/2012] [Accepted: 08/20/2012] [Indexed: 11/29/2022]
Abstract
The Nuclear Envelope (NE) contains over 100 different proteins that associate with nuclear components such as chromatin, the lamina and the transcription machinery. Mutations in genes encoding NE proteins have been shown to result in tissue-specific defects and disease, suggesting cell-type specific differences in NE composition and function. Consistent with these observations, recent studies have revealed unexpected functions for numerous NE associated proteins during cell differentiation and development. Here we review the latest insights into the roles played by the NE in cell differentiation, development, disease and aging, focusing primarily on inner nuclear membrane (INM) proteins and nuclear pore components.
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Affiliation(s)
- J Sebastian Gomez-Cavazos
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, 10010N. Torrey Pines Road, La Jolla, 92037 CA, United States
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38
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Abstract
Nuclear export of mRNAs is thought to occur exclusively through nuclear pore complexes. In this issue of Cell, Speese et al. identify an alternate pathway for mRNA export in muscle cells where ribonucleoprotein complexes involved in forming neuromuscular junctions transit the nuclear envelope by fusing with and budding through the nuclear membrane.
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Affiliation(s)
- Emily M Hatch
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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39
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Abstract
To combat the functional decline of the proteome, cells use the process of protein turnover to replace potentially impaired polypeptides with new functional copies. We found that extremely long-lived proteins (ELLPs) did not turn over in postmitotic cells of the rat central nervous system. These ELLPs were associated with chromatin and the nuclear pore complex, the central transport channels that mediate all molecular trafficking in and out of the nucleus. The longevity of these proteins would be expected to expose them to potentially harmful metabolites, putting them at risk of accumulating damage over extended periods of time. Thus, it is possible that failure to maintain proper levels and functional integrity of ELLPs in nonproliferative cells might contribute to age-related deterioration in cell and tissue function.
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Affiliation(s)
- Jeffrey N Savas
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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40
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D'Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer MW. A change in nuclear pore complex composition regulates cell differentiation. Dev Cell 2012; 22:446-58. [PMID: 22264802 DOI: 10.1016/j.devcel.2011.11.021] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/06/2011] [Accepted: 11/14/2011] [Indexed: 12/11/2022]
Abstract
Nuclear pore complexes (NPCs) are built from ∼30 different proteins called nucleoporins or Nups. Previous studies have shown that several Nups exhibit cell-type-specific expression and that mutations in NPC components result in tissue-specific diseases. Here we show that a specific change in NPC composition is required for both myogenic and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in proliferating myoblasts and embryonic stem cells (ESCs) but becomes expressed and incorporated into NPCs during cell differentiation. Preventing Nup210 production by RNAi blocks myogenesis and the differentiation of ESCs into neuroprogenitors. We found that the addition of Nup210 to NPCs does not affect nuclear transport but is required for the induction of genes that are essential for cell differentiation. Our results identify a single change in NPC composition as an essential step in cell differentiation and establish a role for Nup210 in gene expression regulation and cell fate determination.
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Affiliation(s)
- Maximiliano A D'Angelo
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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41
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Abstract
POM121 and Sun1, but not the Nup107–160 complex, are required for fusion of the inner and outer nuclear membrane during nuclear pore assembly in interphase of the cell cycle. Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear envelope (NE) reformation and into an intact NE as cells progress through interphase. Although recent studies have shown that NPC formation occurs by two different molecular mechanisms at two distinct cell cycle stages, little is known about the molecular players that mediate the fusion of the outer and inner nuclear membranes to form pores. In this paper, we provide evidence that the transmembrane nucleoporin (Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the INM and ONM. Additionally, Sun1, an INM protein that is known to interact with the cytoskeleton, was specifically required for interphase assembly and localized with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact transiently to promote early steps of interphase NPC assembly.
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Affiliation(s)
- Jessica A Talamas
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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42
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Abstract
Eukaryotic cell function depends on the physical separation of nucleoplasmic and cytoplasmic components by the nuclear envelope (NE). Molecular communication between the two compartments involves active, signal-mediated trafficking, a function that is exclusively performed by nuclear pore complexes (NPCs). The individual NPC components and the mechanisms that are involved in nuclear trafficking are well documented and have become textbook knowledge. However, in addition to their roles as nuclear gatekeepers, NPC components-nucleoporins-have been shown to have critical roles in chromatin organization and gene regulation. These findings have sparked new enthusiasm to study the roles of this multiprotein complex in nuclear organization and explore novel functions that in some cases appear to go beyond a role in transport. Here, we discuss our present view of NPC biogenesis, which is tightly linked to proper cell cycle progression and cell differentiation. In addition, we summarize new data suggesting that NPCs represent dynamic hubs for the integration of gene regulation and nuclear transport processes.
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Affiliation(s)
- M Capelson
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, La Jolla, California 92037, USA
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43
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Abstract
As the gatekeepers of the eukaryotic cell nucleus, nuclear pore complexes (NPCs) mediate all molecular trafficking between the nucleoplasm and the cytoplasm. In recent years, transport-independent functions of NPC components, nucleoporins, have been identified including roles in chromatin organization and gene regulation. Here, we summarize our current view of the NPC as a dynamic hub for the integration of chromatin regulation and nuclear trafficking and discuss the functional interplay between nucleoporins and the nuclear genome.
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Affiliation(s)
- Yun Liang
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, 10010 N. Torrey Pines Road, La Jolla, CA 92037, United States
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44
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Abstract
The nuclear envelope (NE) is a highly regulated membrane barrier that separates the nucleus from the cytoplasm in eukaryotic cells. It contains a large number of different proteins that have been implicated in chromatin organization and gene regulation. Although the nuclear membrane enables complex levels of gene expression, it also poses a challenge when it comes to cell division. To allow access of the mitotic spindle to chromatin, the nucleus of metazoans must completely disassemble during mitosis, generating the need to re-establish the nuclear compartment at the end of each cell division. Here, I summarize our current understanding of the dynamic remodeling of the NE during the cell cycle.
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Affiliation(s)
- Martin W Hetzer
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, La Jolla, California 92037, USA.
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45
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Doucet CM, Hetzer MW. Nuclear pore biogenesis into an intact nuclear envelope. Chromosoma 2010; 119:469-77. [DOI: 10.1007/s00412-010-0289-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/15/2010] [Accepted: 07/19/2010] [Indexed: 10/19/2022]
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46
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Doucet CM, Talamas JA, Hetzer MW. Cell cycle-dependent differences in nuclear pore complex assembly in metazoa. Cell 2010; 141:1030-41. [PMID: 20550937 DOI: 10.1016/j.cell.2010.04.036] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 02/15/2010] [Accepted: 04/06/2010] [Indexed: 12/21/2022]
Abstract
In metazoa, nuclear pore complexes (NPCs) assemble from disassembled precursors into a reforming nuclear envelope (NE) at the end of mitosis and into growing intact NEs during interphase. Here, we show via RNAi-mediated knockdown that ELYS, a nucleoporin critical for the recruitment of the essential Nup107/160 complex to chromatin, is required for NPC assembly at the end of mitosis but not during interphase. Conversely, the transmembrane nucleoporin POM121 is critical for the incorporation of the Nup107/160 complex into new assembly sites specifically during interphase. Strikingly, recruitment of the Nup107/160 complex to an intact NE involves a membrane curvature-sensing domain of its constituent Nup133, which is not required for postmitotic NPC formation. Our results suggest that in organisms with open mitosis, NPCs assemble via two distinct mechanisms to accommodate cell cycle-dependent differences in NE topology.
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Affiliation(s)
- Christine M Doucet
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, 10010 North Torrey Pines Road, La Jolla, 92037 CA, USA
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47
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Affiliation(s)
- Martin W Hetzer
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, La Jolla, CA 92037, USA.
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48
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Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer MW. Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 2010; 140:372-83. [PMID: 20144761 DOI: 10.1016/j.cell.2009.12.054] [Citation(s) in RCA: 331] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 10/06/2009] [Accepted: 12/29/2009] [Indexed: 11/16/2022]
Abstract
Nuclear pore complexes have recently been shown to play roles in gene activation; however their potential involvement in metazoan transcription remains unclear. Here we show that the nucleoporins Sec13, Nup98, and Nup88, as well as a group of FG-repeat nucleoporins, bind to the Drosophila genome at functionally distinct loci that often do not represent nuclear envelope contact sites. Whereas Nup88 localizes to silent loci, Sec13, Nup98, and a subset of FG-repeat nucleoporins bind to developmentally regulated genes undergoing transcription induction. Strikingly, RNAi-mediated knockdown of intranuclear Sec13 and Nup98 specifically inhibits transcription of their target genes and prevents efficient reactivation of transcription after heat shock, suggesting an essential role of NPC components in regulating complex gene expression programs of multicellular organisms.
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Affiliation(s)
- Maya Capelson
- Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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49
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Abstract
Over the last decade, the nuclear envelope (NE) has emerged as a key component in the organization and function of the nuclear genome. As many as 100 different proteins are thought to specifically localize to this double membrane that separates the cytoplasm and the nucleoplasm of eukaryotic cells. Selective portals through the NE are formed at sites where the inner and outer nuclear membranes are fused, and the coincident assembly of approximately 30 proteins into nuclear pore complexes occurs. These nuclear pore complexes are essential for the control of nucleocytoplasmic exchange. Many of the NE and nuclear pore proteins are thought to play crucial roles in gene regulation and thus are increasingly linked to human diseases.
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Affiliation(s)
- Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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50
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Anderson DJ, Vargas JD, Hsiao JP, Hetzer MW. Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. J Biophys Biochem Cytol 2009. [PMCID: PMC2753155 DOI: 10.1083/jcb.20090110620090903c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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