1
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Doronin SA, Ilyin AA, Kononkova AD, Solovyev MA, Olenkina OM, Nenasheva VV, Mikhaleva EA, Lavrov SA, Ivannikova AY, Simonov RA, Fedotova AA, Khrameeva EE, Ulianov SV, Razin SV, Shevelyov YY. Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei. Commun Biol 2024; 7:783. [PMID: 38951619 PMCID: PMC11217421 DOI: 10.1038/s42003-024-06495-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 06/23/2024] [Indexed: 07/03/2024] Open
Abstract
Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Here, using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or with NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.
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Affiliation(s)
- Semen A Doronin
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Artem A Ilyin
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
- Department of Molecular Biosciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Anna D Kononkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026, Skolkovo, Russia
| | - Mikhail A Solovyev
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Oxana M Olenkina
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Valentina V Nenasheva
- Laboratory of Molecular Neurogenetics and Innate Immunity, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Elena A Mikhaleva
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Sergey A Lavrov
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Anna Y Ivannikova
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Ruslan A Simonov
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
| | - Anna A Fedotova
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia
- Department of Regulation of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 143026, Skolkovo, Russia.
| | - Sergey V Ulianov
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Sergey V Razin
- Department of Cellular Genomics, Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Yuri Y Shevelyov
- Laboratory of Analysis of Gene Regulation, Institute of Molecular Genetics of NRC "Kurchatov Institute", 123182, Moscow, Russia.
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2
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James C, Möller U, Spillner C, König S, Dybkov O, Urlaub H, Lenz C, Kehlenbach RH. Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis. EMBO Rep 2024; 25:2391-2417. [PMID: 38605278 PMCID: PMC11094025 DOI: 10.1038/s44319-024-00125-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
ELYS is a nucleoporin that localizes to the nuclear side of the nuclear pore complex (NPC) in interphase cells. In mitosis, it serves as an assembly platform that interacts with chromatin and then with nucleoporin subcomplexes to initiate post-mitotic NPC assembly. Here we identify ELYS as a major binding partner of the membrane protein VAPB during mitosis. In mitosis, ELYS becomes phosphorylated at many sites, including a predicted FFAT (two phenylalanines in an acidic tract) motif, which mediates interaction with the MSP (major sperm protein)-domain of VAPB. Binding assays using recombinant proteins or cell lysates and co-immunoprecipitation experiments show that VAPB binds the FFAT motif of ELYS in a phosphorylation-dependent manner. In anaphase, the two proteins co-localize to the non-core region of the newly forming nuclear envelope. Depletion of VAPB results in prolonged mitosis, slow progression from meta- to anaphase and in chromosome segregation defects. Together, our results suggest a role of VAPB in mitosis upon recruitment to or release from ELYS at the non-core region of the chromatin in a phosphorylation-dependent manner.
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Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Ulrike Möller
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Christiane Spillner
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Sabine König
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
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3
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Simon MN, Dubrana K, Palancade B. On the edge: how nuclear pore complexes rule genome stability. Curr Opin Genet Dev 2024; 84:102150. [PMID: 38215626 DOI: 10.1016/j.gde.2023.102150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/10/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
Nuclear organization has emerged as a critical layer in the coordination of DNA repair activities. Distinct types of DNA lesions have notably been shown to relocate at the vicinity of nuclear pore complexes (NPCs), where specific repair pathways are favored, ultimately safeguarding genome integrity. Here, we review the most recent progress in this field, notably highlighting the increasingly diverse types of DNA structures undergoing repositioning, and the signaling pathways involved. We further discuss our growing knowledge of the molecular mechanisms underlying the choice of repair pathways at NPCs, and their conservation - or divergences. Intriguingly, a series of recent findings suggest that DNA metabolism may be coupled to NPC biogenesis and specialization, challenging our initial vision of these processes.
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Affiliation(s)
- Marie-Noëlle Simon
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Equipe Labélisée Ligue, Aix Marseille University, Marseille, France. https://twitter.com/@IJMonod
| | - Karine Dubrana
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, F-92260 Fontenay-aux-Roses, France. https://twitter.com/@DubranaLab
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France.
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4
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Penzo A, Palancade B. Puzzling out nuclear pore complex assembly. FEBS Lett 2023; 597:2705-2727. [PMID: 37548888 DOI: 10.1002/1873-3468.14713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Nuclear pore complexes (NPCs) are sophisticated multiprotein assemblies embedded within the nuclear envelope and controlling the exchanges of molecules between the cytoplasm and the nucleus. In this review, we summarize the mechanisms by which these elaborate complexes are built from their subunits, the nucleoporins, based on our ever-growing knowledge of NPC structural organization and on the recent identification of additional features of this process. We present the constraints faced during the production of nucleoporins, their gathering into oligomeric complexes, and the formation of NPCs within nuclear envelopes, and review the cellular strategies at play, from co-translational assembly to the enrolment of a panel of cofactors. Remarkably, the study of NPCs can inform our perception of the biogenesis of multiprotein complexes in general - and vice versa.
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Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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5
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Capelson M. You are who your friends are-nuclear pore proteins as components of chromatin-binding complexes. FEBS Lett 2023; 597:2769-2781. [PMID: 37652464 PMCID: PMC11081553 DOI: 10.1002/1873-3468.14728] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023]
Abstract
Nuclear pore complexes are large multicomponent protein complexes that are embedded in the nuclear envelope, where they mediate nucleocytoplasmic transport. In addition to supporting transport, nuclear pore components, termed nucleoporins (Nups), can interact with chromatin and influence genome function. A subset of Nups can also localize to the nuclear interior and bind chromatin intranuclearly, providing an opportunity to investigate chromatin-associated functions of Nups outside of the transport context. This review focuses on the gene regulatory functions of such intranuclear Nups, with a particular emphasis on their identity as components of several chromatin regulatory complexes. Recent proteomic screens have identified Nups as interacting partners of active and repressive epigenetic machinery, architectural proteins, and DNA replication complexes, providing insight into molecular mechanisms via which Nups regulate gene expression programs. This review summarizes these interactions and discusses their potential functions in the broader framework of nuclear genome organization.
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Affiliation(s)
- Maya Capelson
- Cell and Molecular Biology Program, Department of Biology, San Diego State University, CA, USA
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6
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Kingsley G, Skagia A, Passaretti P, Fernandez-Cuesta C, Reynolds-Winczura A, Koscielniak K, Gambus A. DONSON facilitates Cdc45 and GINS chromatin association and is essential for DNA replication initiation. Nucleic Acids Res 2023; 51:9748-9763. [PMID: 37638758 PMCID: PMC10570026 DOI: 10.1093/nar/gkad694] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023] Open
Abstract
Faithful cell division is the basis for the propagation of life and DNA replication must be precisely regulated. DNA replication stress is a prominent endogenous source of genome instability that not only leads to ageing, but also neuropathology and cancer development in humans. Specifically, the issues of how vertebrate cells select and activate origins of replication are of importance as, for example, insufficient origin firing leads to genomic instability and mutations in replication initiation factors lead to the rare human disease Meier-Gorlin syndrome. The mechanism of origin activation has been well characterised and reconstituted in yeast, however, an equal understanding of this process in higher eukaryotes is lacking. The firing of replication origins is driven by S-phase kinases (CDKs and DDK) and results in the activation of the replicative helicase and generation of two bi-directional replication forks. Our data, generated from cell-free Xenopus laevis egg extracts, show that DONSON is required for assembly of the active replicative helicase (CMG complex) at origins during replication initiation. DONSON has previously been shown to be essential during DNA replication, both in human cells and in Drosophila, but the mechanism of DONSON's action was unknown. Here we show that DONSON's presence is essential for replication initiation as it is required for Cdc45 and GINS association with Mcm2-7 complexes and helicase activation. To fulfil this role, DONSON interacts with the initiation factor, TopBP1, in a CDK-dependent manner. Following its initiation role, DONSON also forms a part of the replisome during the elongation stage of DNA replication. Mutations in DONSON have recently been shown to lead to the Meier-Gorlin syndrome; this novel replication initiation role of DONSON therefore provides the explanation for the phenotypes caused by DONSON mutations in patients.
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Affiliation(s)
- Georgia Kingsley
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Aggeliki Skagia
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Paolo Passaretti
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Cyntia Fernandez-Cuesta
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Kinga Koscielniak
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, UK
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7
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Nobari P, Doye V, Boumendil C. Metazoan nuclear pore complexes in gene regulation and genome stability. DNA Repair (Amst) 2023; 130:103565. [PMID: 37696111 DOI: 10.1016/j.dnarep.2023.103565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
The nuclear pore complexes (NPCs), one of the hallmarks of eukaryotic nuclei, allow selective transport of macromolecules between the cytoplasm and the nucleus. Besides this canonical function, an increasing number of additional roles have been attributed to the NPCs and their constituents, the nucleoporins. Here we review recent insights into the mechanisms by which NPCs and nucleoporins affect transcription and DNA repair in metazoans. In the first part, we discuss how gene expression can be affected by the localization of genome-nucleoporin interactions at pores or "off-pores", by the role of nucleoporins in chromatin organization at different scales, or by the physical properties of nucleoporins. In the second part, we review the contribution of NPCs to genome stability, including transport-dependent and -independent functions and the role of positioning at NPCs in the repair of heterochromatic breaks and the regulation of replication stress.
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Affiliation(s)
- Parisa Nobari
- IGH, Université de Montpellier, CNRS, Montpellier, France
| | - Valérie Doye
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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8
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Zhao G, Liu S, Arun S, Renda F, Khodjakov A, Pellman D. A tubule-sheet continuum model for the mechanism of nuclear envelope assembly. Dev Cell 2023; 58:847-865.e10. [PMID: 37098350 PMCID: PMC10205699 DOI: 10.1016/j.devcel.2023.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/25/2023] [Accepted: 04/01/2023] [Indexed: 04/27/2023]
Abstract
Nuclear envelope (NE) assembly defects cause chromosome fragmentation, cancer, and aging. However, major questions about the mechanism of NE assembly and its relationship to nuclear pathology are unresolved. In particular, how cells efficiently assemble the NE starting from vastly different, cell type-specific endoplasmic reticulum (ER) morphologies is unclear. Here, we identify a NE assembly mechanism, "membrane infiltration," that defines one end of a continuum with another NE assembly mechanism, "lateral sheet expansion," in human cells. Membrane infiltration involves the recruitment of ER tubules or small sheets to the chromatin surface by mitotic actin filaments. Lateral sheet expansion involves actin-independent envelopment of peripheral chromatin by large ER sheets that then extend over chromatin within the spindle. We propose a "tubule-sheet continuum" model that explains the efficient NE assembly from any starting ER morphology, the cell type-specific patterns of nuclear pore complex (NPC) assembly, and the obligatory NPC assembly defect of micronuclei.
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Affiliation(s)
- Gengjing Zhao
- Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Shiwei Liu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sanjana Arun
- Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Fioranna Renda
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Alexey Khodjakov
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - David Pellman
- Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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9
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Huang G, Zeng C, Shi Y. Structure of the nuclear pore complex goes atomic. Curr Opin Struct Biol 2023; 78:102523. [PMID: 36641895 DOI: 10.1016/j.sbi.2022.102523] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 01/14/2023]
Abstract
The nuclear pore complex (NPC) is a supra-molecular assembly that mediates substance and information flow across the nuclear envelope (NE). Due to its extraordinary size and complexity, the NPC remains one of the most challenging tasks in structural elucidation at atomic resolution. Recent breakthroughs in cryo-electron microscopy (cryo-EM) reconstruction, Machine Learning empowered structure prediction and biochemical reconstitution have combined to yield molecular models of the NPC at unprecedented accuracy. Furthermore, in cellulo cryo-electron tomography (cryo-ET) structures reveal substantial structural dynamics of the NPC. These advances shed light on the organizational principles and functions of the NPC.
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Affiliation(s)
- Gaoxingyu Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China.
| | - Chao Zeng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China.
| | - Yigong Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Beijing Advanced Innovation Center for Structural Biology & Advanced Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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10
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Morgan KJ, Doggett K, Geng F, Mieruszynski S, Whitehead L, Smith KA, Hogan BM, Simons C, Baillie GJ, Molania R, Papenfuss AT, Hall TE, Ober EA, Stainier DYR, Gong Z, Heath JK. ahctf1 and kras mutations combine to amplify oncogenic stress and restrict liver overgrowth in a zebrafish model of hepatocellular carcinoma. eLife 2023; 12:73407. [PMID: 36648336 PMCID: PMC9897728 DOI: 10.7554/elife.73407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
The nucleoporin (NUP) ELYS, encoded by AHCTF1, is a large multifunctional protein with essential roles in nuclear pore assembly and mitosis. Using both larval and adult zebrafish models of hepatocellular carcinoma (HCC), in which the expression of an inducible mutant kras transgene (krasG12V) drives hepatocyte-specific hyperplasia and liver enlargement, we show that reducing ahctf1 gene dosage by 50% markedly decreases liver volume, while non-hyperplastic tissues are unaffected. We demonstrate that in the context of cancer, ahctf1 heterozygosity impairs nuclear pore formation, mitotic spindle assembly, and chromosome segregation, leading to DNA damage and activation of a Tp53-dependent transcriptional programme that induces cell death and cell cycle arrest. Heterozygous expression of both ahctf1 and ranbp2 (encoding a second nucleoporin), or treatment of heterozygous ahctf1 larvae with the nucleocytoplasmic transport inhibitor, Selinexor, completely blocks krasG12V-driven hepatocyte hyperplasia. Gene expression analysis of patient samples in the liver hepatocellular carcinoma (LIHC) dataset in The Cancer Genome Atlas shows that high expression of one or more of the transcripts encoding the 10 components of the NUP107-160 subcomplex, which includes AHCTF1, is positively correlated with worse overall survival. These results provide a strong and feasible rationale for the development of novel cancer therapeutics that target ELYS function and suggest potential avenues for effective combinatorial treatments.
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Affiliation(s)
- Kimberly J Morgan
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Karen Doggett
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Fansuo Geng
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Stephen Mieruszynski
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Lachlan Whitehead
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Centre for Dynamic Imaging, Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Kelly A Smith
- Department of Physiology, University of MelbourneParkvilleAustralia
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Benjamin M Hogan
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
- Peter MacCallum Cancer CentreMelbourneAustralia
| | - Cas Simons
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
- Murdoch Children's Research InstituteParkvilleAustralia
| | - Gregory J Baillie
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Ramyar Molania
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Anthony T Papenfuss
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Thomas E Hall
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Elke A Ober
- Danish Stem Cell Center, University of CopenhagenCopenhagenDenmark
| | - Didier YR Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Zhiyuan Gong
- Department of Biological Science, National University of SingaporeSingaporeSingapore
| | - Joan K Heath
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
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11
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Richards L, Lord CL, Benton ML, Capra JA, Nordman JT. Nucleoporins facilitate ORC loading onto chromatin. Cell Rep 2022; 41:111590. [PMID: 36351393 PMCID: PMC10040217 DOI: 10.1016/j.celrep.2022.111590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/10/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we perform immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we find that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis reveals that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, decreases ORC2 loading onto chromatin. Depleting Elys also sensitizes cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a connection between ORC, replication initiation, and nucleoporins, suggesting a function for nucleoporins in metazoan replication initiation.
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Affiliation(s)
- Logan Richards
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher L Lord
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | | | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA 94143, USA
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
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12
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Bley CJ, Nie S, Mobbs GW, Petrovic S, Gres AT, Liu X, Mukherjee S, Harvey S, Huber FM, Lin DH, Brown B, Tang AW, Rundlet EJ, Correia AR, Chen S, Regmi SG, Stevens TA, Jette CA, Dasso M, Patke A, Palazzo AF, Kossiakoff AA, Hoelz A. Architecture of the cytoplasmic face of the nuclear pore. Science 2022; 376:eabm9129. [PMID: 35679405 DOI: 10.1126/science.abm9129] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are generated by the circumscribed fusion of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) are the sole bidirectional gateways for nucleocytoplasmic transport. The ~110-MDa human NPC is an ~1000-protein assembly that comprises multiple copies of ~34 different proteins, collectively termed nucleoporins. The symmetric core of the NPC is composed of an inner ring encircling the central transport channel and outer rings formed by Y‑shaped coat nucleoporin complexes (CNCs) anchored atop both sides of the nuclear envelope. The outer rings are decorated with compartment‑specific asymmetric nuclear basket and cytoplasmic filament nucleoporins, which establish transport directionality and provide docking sites for transport factors and the small guanosine triphosphatase Ran. The cytoplasmic filament nucleoporins also play an essential role in the irreversible remodeling of messenger ribonucleoprotein particles (mRNPs) as they exit the central transport channel. Unsurprisingly, the NPC's cytoplasmic face represents a hotspot for disease‑associated mutations and is commonly targeted by viral virulence factors. RATIONALE Previous studies established a near-atomic composite structure of the human NPC's symmetric core by combining (i) biochemical reconstitution to elucidate the interaction network between symmetric nucleoporins, (ii) crystal and single-particle cryo-electron microscopy structure determination of nucleoporins and nucleoporin complexes to reveal their three-dimensional shape and the molecular details of their interactions, (iii) quantitative docking in cryo-electron tomography (cryo-ET) maps of the intact human NPC to uncover nucleoporin stoichiometry and positioning, and (iv) cell‑based assays to validate the physiological relevance of the biochemical and structural findings. In this work, we extended our approach to the cytoplasmic filament nucleoporins to reveal the near-atomic architecture of the cytoplasmic face of the human NPC. RESULTS Using biochemical reconstitution, we elucidated the protein-protein and protein-RNA interaction networks of the human and Chaetomium thermophilum cytoplasmic filament nucleoporins, establishing an evolutionarily conserved heterohexameric cytoplasmic filament nucleoporin complex (CFNC) held together by a central heterotrimeric coiled‑coil hub that tethers two separate mRNP‑remodeling complexes. Further biochemical analysis and determination of a series of crystal structures revealed that the metazoan‑specific cytoplasmic filament nucleoporin NUP358 is composed of 16 distinct domains, including an N‑terminal S‑shaped α‑helical solenoid followed by a coiled‑coil oligomerization element, numerous Ran‑interacting domains, an E3 ligase domain, and a C‑terminal prolyl‑isomerase domain. Physiologically validated quantitative docking into cryo-ET maps of the intact human NPC revealed that pentameric NUP358 bundles, conjoined by the oligomerization element, are anchored through their N‑terminal domains to the central stalk regions of the CNC, projecting flexibly attached domains as far as ~600 Å into the cytoplasm. Using cell‑based assays, we demonstrated that NUP358 is dispensable for the architectural integrity of the assembled interphase NPC and RNA export but is required for efficient translation. After NUP358 assignment, the remaining 4-shaped cryo‑ET density matched the dimensions of the CFNC coiled‑coil hub, in close proximity to an outer-ring NUP93. Whereas the N-terminal NUP93 assembly sensor motif anchors the properly assembled related coiled‑coil channel nucleoporin heterotrimer to the inner ring, biochemical reconstitution confirmed that the NUP93 assembly sensor is reused in anchoring the CFNC to the cytoplasmic face of the human NPC. By contrast, two C. thermophilum CFNCs are anchored by a divergent mechanism that involves assembly sensors located in unstructured portions of two CNC nucleoporins. Whereas unassigned cryo‑ET density occupies the NUP358 and CFNC binding sites on the nuclear face, docking of the nuclear basket component ELYS established that the equivalent position on the cytoplasmic face is unoccupied, suggesting that mechanisms other than steric competition promote asymmetric distribution of nucleoporins. CONCLUSION We have substantially advanced the biochemical and structural characterization of the asymmetric nucleoporins' architecture and attachment at the cytoplasmic and nuclear faces of the NPC. Our near‑atomic composite structure of the human NPC's cytoplasmic face provides a biochemical and structural framework for elucidating the molecular basis of mRNP remodeling, viral virulence factor interference with NPC function, and the underlying mechanisms of nucleoporin diseases at the cytoplasmic face of the NPC. [Figure: see text].
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Affiliation(s)
- Christopher J Bley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Si Nie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - George W Mobbs
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Stefan Petrovic
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Anna T Gres
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Xiaoyu Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sho Harvey
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Bonnie Brown
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Aaron W Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Emily J Rundlet
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Shane Chen
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saroj G Regmi
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Taylor A Stevens
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Claudia A Jette
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alina Patke
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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13
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Wesley NA, Skrajna A, Simmons HC, Budziszewski GR, Azzam DN, Cesmat AP, McGinty RK. Time Resolved-Fluorescence Resonance Energy Transfer platform for quantitative nucleosome binding and footprinting. Protein Sci 2022; 31:e4339. [PMID: 35634775 PMCID: PMC9134878 DOI: 10.1002/pro.4339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
Abstract
Quantitative analysis of chromatin protein-nucleosome interactions is essential to understand regulation of genome-templated processes. However, current methods to measure nucleosome interactions are limited by low throughput, low signal-to-noise, and/or the requirement for specialized instrumentation. Here, we report a Lanthanide Chelate Excite Time-Resolved Fluorescence Resonance Energy Transfer (LANCE TR-FRET) assay to efficiently quantify chromatin protein-nucleosome interactions. The system makes use of commercially available reagents, offers robust signal-to-noise with minimal sample requirements, uses a conventional fluorescence microplate reader, and can be adapted for high-throughput workflows. We determined the nucleosome-binding affinities of several chromatin proteins and complexes, which are consistent with measurements obtained through orthogonal biophysical methods. We also developed a TR-FRET competition assay for high-resolution footprinting of chromatin protein-nucleosome interactions. Finally, we set up a TR-FRET competition assay using the LANA peptide to quantitate nucleosome acidic patch binding. We applied this assay to establish a proof-of-principle for regulation of nucleosome acidic patch binding by methylation of chromatin protein arginine anchors. Overall, our TR-FRET assays allow facile, high-throughput quantification of chromatin interactions and are poised to complement mechanistic chromatin biochemistry, structural biology, and drug discovery programs.
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Affiliation(s)
- Nathaniel A. Wesley
- Department of Biochemistry and Biophysics, UNC School of MedicineThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Aleksandra Skrajna
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of PharmacyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Holly C. Simmons
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of PharmacyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Gabrielle R. Budziszewski
- Department of Biochemistry and Biophysics, UNC School of MedicineThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Dalal N. Azzam
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of PharmacyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Andrew P. Cesmat
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of PharmacyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Robert K. McGinty
- Department of Biochemistry and Biophysics, UNC School of MedicineThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of PharmacyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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14
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The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth. Cells 2022; 11:cells11091456. [PMID: 35563762 PMCID: PMC9100368 DOI: 10.3390/cells11091456] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/01/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the only transport channels that cross the nuclear envelope. Constructed from ~500–1000 nucleoporin proteins each, they are among the largest macromolecular assemblies in eukaryotic cells. Thanks to advances in structural analysis approaches, the construction principles and architecture of the NPC have recently been revealed at submolecular resolution. Although the overall structure and inventory of nucleoporins are conserved, NPCs exhibit significant compositional and functional plasticity even within single cells and surprising variability in their assembly pathways. Once assembled, NPCs remain seemingly unexchangeable in post-mitotic cells. There are a number of as yet unresolved questions about how the versatility of NPC assembly and composition is established, how cells monitor the functional state of NPCs or how they could be renewed. Here, we review current progress in our understanding of the key aspects of NPC architecture and lifecycle.
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15
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Raices M, D'Angelo MA. Structure, Maintenance, and Regulation of Nuclear Pore Complexes: The Gatekeepers of the Eukaryotic Genome. Cold Spring Harb Perspect Biol 2022; 14:a040691. [PMID: 34312247 PMCID: PMC8789946 DOI: 10.1101/cshperspect.a040691] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the genetic material is segregated inside the nucleus. This compartmentalization of the genome requires a transport system that allows cells to move molecules across the nuclear envelope, the membrane-based barrier that surrounds the chromosomes. Nuclear pore complexes (NPCs) are the central component of the nuclear transport machinery. These large protein channels penetrate the nuclear envelope, creating a passage between the nucleus and the cytoplasm through which nucleocytoplasmic molecule exchange occurs. NPCs are one of the largest protein assemblies of eukaryotic cells and, in addition to their critical function in nuclear transport, these structures also play key roles in many cellular processes in a transport-independent manner. Here we will review the current knowledge of the NPC structure, the cellular mechanisms that regulate their formation and maintenance, and we will provide a brief description of a variety of processes that NPCs regulate.
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Affiliation(s)
- Marcela Raices
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Maximiliano A D'Angelo
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
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16
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Huang G, Zhan X, Zeng C, Zhu X, Liang K, Zhao Y, Wang P, Wang Q, Zhou Q, Tao Q, Liu M, Lei J, Yan C, Shi Y. Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex. Cell Res 2022; 32:349-358. [PMID: 35177819 PMCID: PMC8976044 DOI: 10.1038/s41422-021-00610-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average resolution of 5.6 Å. The NR subunit comprises two 10-membered Y complexes, each with the nucleoporin ELYS closely associating with Nup160 and Nup37 of the long arm. Unlike the cytoplasmic ring (CR) or inner ring (IR), the NR subunit contains only one molecule each of Nup205 and Nup93. Nup205 binds both arms of the Y complexes and interacts with the stem of inner Y complex from the neighboring subunit. Nup93 connects the stems of inner and outer Y complexes within the same NR subunit, and places its N-terminal extended helix into the axial groove of Nup205 from the neighboring subunit. Together with other structural information, we have generated a composite atomic model of the central ring scaffold that includes the NR, IR, and CR. The IR is connected to the two outer rings mainly through Nup155. This model facilitates functional understanding of vertebrate NPC.
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Affiliation(s)
- Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China. .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China. .,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China.
| | - Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Chao Zeng
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Xuechen Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Ke Liang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Yanyu Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Pan Wang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Qifan Wang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Qiang Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Qinghua Tao
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Minhao Liu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yigong Shi
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang, China. .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, China. .,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China. .,Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China. .,Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China.
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17
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Chachoua I, Tzelepis I, Dai H, Lim JP, Lewandowska-Ronnegren A, Casagrande FB, Wu S, Vestlund J, Mallet de Lima CD, Bhartiya D, Scholz BA, Martino M, Mehmood R, Göndör A. Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site. Nat Commun 2022; 13:204. [PMID: 35017527 PMCID: PMC8752836 DOI: 10.1038/s41467-021-27868-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/19/2021] [Indexed: 01/21/2023] Open
Abstract
Abnormal WNT signaling increases MYC expression in colon cancer cells in part via oncogenic super-enhancer-(OSE)-mediated gating of the active MYC to the nuclear pore in a poorly understood process. We show here that the principal tenet of the WNT-regulated MYC gating, facilitating nuclear export of the MYC mRNA, is regulated by a CTCF binding site (CTCFBS) within the OSE to confer growth advantage in HCT-116 cells. To achieve this, the CTCFBS directs the WNT-dependent trafficking of the OSE to the nuclear pore from intra-nucleoplasmic positions in a stepwise manner. Once the OSE reaches a peripheral position, which is triggered by a CTCFBS-mediated CCAT1 eRNA activation, its final stretch (≤0.7 μm) to the nuclear pore requires the recruitment of AHCTF1, a key nucleoporin, to the CTCFBS. Thus, a WNT/ß-catenin-AHCTF1-CTCF-eRNA circuit enables the OSE to promote pathological cell growth by coordinating the trafficking of the active MYC gene within the 3D nuclear architecture. Gene-gating of a MYC oncogenic super-enhancer (OSE) increases its expression in colon cancer cells in a poorly understood process. Here the authors show that MYC gating requires a CTCF binding site (CTCFBS) within the OSE that directs the stepwise trafficking of the OSE to the nuclear pore to facilitate increased nuclear export of MYC mRNA, which results in a growth advantage.
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Affiliation(s)
- Ilyas Chachoua
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Ilias Tzelepis
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Hao Dai
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden.,Department of Breast Disease, Henan Breast Cancer Center, The affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Jia Pei Lim
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lewandowska-Ronnegren
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Felipe Beccaria Casagrande
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Shuangyang Wu
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Vestlund
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Diettrich Mallet de Lima
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Deeksha Bhartiya
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Barbara A Scholz
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Mirco Martino
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Rashid Mehmood
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden
| | - Anita Göndör
- Department of Oncology and Pathology, Bioclinicum, Karolinska University Hospital, U2, Akademiska Stråket 1, Karolinska Institutet, Stockholm, Sweden.
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18
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Holzer G, De Magistris P, Gramminger C, Sachdev R, Magalska A, Schooley A, Scheufen A, Lennartz B, Tatarek‐Nossol M, Lue H, Linder MI, Kutay U, Preisinger C, Moreno‐Andres D, Antonin W. The nucleoporin Nup50 activates the Ran guanine nucleotide exchange factor RCC1 to promote NPC assembly at the end of mitosis. EMBO J 2021; 40:e108788. [PMID: 34725842 PMCID: PMC8634129 DOI: 10.15252/embj.2021108788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
During mitotic exit, thousands of nuclear pore complexes (NPCs) assemble concomitant with the nuclear envelope to build a transport-competent nucleus. Here, we show that Nup50 plays a crucial role in NPC assembly independent of its well-established function in nuclear transport. RNAi-mediated downregulation in cells or immunodepletion of Nup50 protein in Xenopus egg extracts interferes with NPC assembly. We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and for NPC interaction. Surprisingly, neither NPC interaction nor binding of Nup50 to importin α/β, the GTPase Ran, or chromatin is crucial for its function in the assembly process. Instead, an N-terminal fragment of Nup50 can stimulate the Ran GTPase guanine nucleotide exchange factor RCC1 and NPC assembly, indicating that Nup50 acts via the Ran system in NPC reformation at the end of mitosis. In support of this conclusion, Nup50 mutants defective in RCC1 binding and stimulation cannot replace the wild-type protein in in vitro NPC assembly assays, whereas excess RCC1 can compensate the loss of Nup50.
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Affiliation(s)
- Guillaume Holzer
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Paola De Magistris
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
- Present address:
Department of BionanoscienceKavli Institute of NanoscienceDelftthe Netherlands
| | | | - Ruchika Sachdev
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Adriana Magalska
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Allana Schooley
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Anja Scheufen
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Birgitt Lennartz
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Marianna Tatarek‐Nossol
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Hongqi Lue
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Monika I Linder
- Institute of BiochemistryETH ZurichZurichSwitzerland
- Present address:
Department of PediatricsDr. von Hauner Children's Hospital and Gene CenterUniversity Hospital, LMUMunichGermany
| | - Ulrike Kutay
- Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Christian Preisinger
- Proteomics FacilityInterdisciplinary Centre for Clinical Research (IZKF)Medical SchoolRWTH Aachen UniversityAachenGermany
| | - Daniel Moreno‐Andres
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
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19
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Lund PJ, Lopes M, Sidoli S, Coradin M, Vitorino FNDL, da Cunha JPC, Garcia BA. FGF-2 induces a failure of cell cycle progression in cells harboring amplified K-Ras, revealing new insights into oncogene-induced senescence. Mol Omics 2021; 17:725-739. [PMID: 34636387 PMCID: PMC8511509 DOI: 10.1039/d1mo00019e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paradoxically, oncogenes that drive cell cycle progression may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells. Knowledge of how these pathways operate, and how tumor cells may evade these pathways, is important for understanding tumorigenesis. The Y1 cell line, which harbors an amplification of the proto-oncogene Ras, rapidly senesces in response to the mitogen fibroblast growth factor-2 (FGF-2). To gain a more complete picture of how FGF-2 promotes senescence, we employed a multi-omics approach to analyze histone modifications, mRNA and protein expression, and protein phosphorylation in Y1 cells treated with FGF-2. Compared to control cells treated with serum alone, FGF-2 caused a delayed accumulation of acetylation on histone H4 and higher levels of H3K27me3. Sequencing analysis revealed decreased expression of cell cycle-related genes with concomitant loss of H3K27ac. At the same time, FGF-2 promoted the expression of p21, various cytokines, and MAPK-related genes. Nuclear envelope proteins, particularly lamin B1, displayed increased phosphorylation in response to FGF-2. Proteome analysis suggested alterations in cellular metabolism, as evident by modulated expression of enzymes involved in purine biosynthesis, tRNA aminoacylation, and the TCA cycle. We propose that Y1 cells senesce due to an inability to progress through the cell cycle, which may stem from DNA damage or TGFb signaling. Altogether, the phenotype of Y1 cells is consistent with rapidly established oncogene-induced senescence, demonstrating the synergy between growth factors and oncogenes in driving senescence and bringing additional insight into this tumor suppressor mechanism.
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Affiliation(s)
- Peder J Lund
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mariana Lopes
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Francisca Nathália de Luna Vitorino
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo 05503-900, Brazil.
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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20
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Devlin L, Okletey J, Perkins G, Bowen JR, Nakos K, Montagna C, Spiliotis ET. Proteomic profiling of the oncogenic septin 9 reveals isoform-specific interactions in breast cancer cells. Proteomics 2021; 21:e2100155. [PMID: 34409731 DOI: 10.1002/pmic.202100155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/05/2021] [Indexed: 02/06/2023]
Abstract
Septins are a family of multimeric GTP-binding proteins, which are abnormally expressed in cancer. Septin 9 (SEPT9) is an essential and ubiquitously expressed septin with multiple isoforms, which have differential expression patterns and effects in breast cancer cells. It is unknown, however, if SEPT9 isoforms associate with different molecular networks and functions. Here, we performed a proteomic screen in MCF-7 breast cancer cells to identify the interactome of GFP-SEPT9 isoforms 1, 4 and 5, which vary significantly in their N-terminal extensions. While all three isoforms associated with SEPT2 and SEPT7, the truncated SEPT9_i4 and SEPT9_i5 interacted with septins of the SEPT6 group more promiscuously than SEPT9_i1, which bound predominately SEPT8. Spatial mapping and functional clustering of non-septin partners showed isoform-specific differences in interactions with proteins of distinct subcellular organelles (e.g., nuclei, centrosomes, cilia) and functions such as cell signalling and ubiquitination. The interactome of the full length SEPT9_i1 was more enriched in cytoskeletal regulators, while the truncated SEPT9_i4 and SEPT9_i5 exhibited preferential and isoform-specific interactions with nuclear, signalling, and ubiquitinating proteins. These data provide evidence for isoform-specific interactions, which arise from truncations in the N-terminal extensions of SEPT9, and point to novel roles in the pathogenesis of breast cancer.
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Affiliation(s)
- Louis Devlin
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA.,Sanofi Pasteur, Swiftwater, Pennsylvania, USA
| | - Joshua Okletey
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | | | - Jonathan R Bowen
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Konstantinos Nakos
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Cristina Montagna
- Department of Radiology & Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Elias T Spiliotis
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
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21
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Cavazza T, Takeda Y, Politi AZ, Aushev M, Aldag P, Baker C, Choudhary M, Bucevičius J, Lukinavičius G, Elder K, Blayney M, Lucas-Hahn A, Niemann H, Herbert M, Schuh M. Parental genome unification is highly error-prone in mammalian embryos. Cell 2021; 184:2860-2877.e22. [PMID: 33964210 PMCID: PMC8162515 DOI: 10.1016/j.cell.2021.04.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 02/05/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Most human embryos are aneuploid. Aneuploidy frequently arises during the early mitotic divisions of the embryo, but its origin remains elusive. Human zygotes that cluster their nucleoli at the pronuclear interface are thought to be more likely to develop into healthy euploid embryos. Here, we show that the parental genomes cluster with nucleoli in each pronucleus within human and bovine zygotes, and clustering is required for the reliable unification of the parental genomes after fertilization. During migration of intact pronuclei, the parental genomes polarize toward each other in a process driven by centrosomes, dynein, microtubules, and nuclear pore complexes. The maternal and paternal chromosomes eventually cluster at the pronuclear interface, in direct proximity to each other, yet separated. Parental genome clustering ensures the rapid unification of the parental genomes on nuclear envelope breakdown. However, clustering often fails, leading to chromosome segregation errors and micronuclei, incompatible with healthy embryo development.
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Affiliation(s)
- Tommaso Cavazza
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Yuko Takeda
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, NE1 4EP Newcastle upon Tyne, UK
| | - Antonio Z Politi
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Magomet Aushev
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, NE1 4EP Newcastle upon Tyne, UK
| | - Patrick Aldag
- Institute of Farm Animal Genetics, Biotechnology, Friedrich-Loeffler-Institute, Mariensee, 31535 Neustadt, Germany
| | | | - Meenakshi Choudhary
- Newcastle Fertility Centre at Life, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4EP Newcastle upon Tyne, UK
| | - Jonas Bucevičius
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | - Kay Elder
- Bourn Hall Clinic, CB23 2TN Cambridge, UK
| | | | - Andrea Lucas-Hahn
- Institute of Farm Animal Genetics, Biotechnology, Friedrich-Loeffler-Institute, Mariensee, 31535 Neustadt, Germany
| | - Heiner Niemann
- Institute of Farm Animal Genetics, Biotechnology, Friedrich-Loeffler-Institute, Mariensee, 31535 Neustadt, Germany
| | - Mary Herbert
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, NE1 4EP Newcastle upon Tyne, UK; Newcastle Fertility Centre at Life, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4EP Newcastle upon Tyne, UK
| | - Melina Schuh
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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22
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Shevelyov YY. The Role of Nucleoporin Elys in Nuclear Pore Complex Assembly and Regulation of Genome Architecture. Int J Mol Sci 2020; 21:ijms21249475. [PMID: 33322130 PMCID: PMC7764596 DOI: 10.3390/ijms21249475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/25/2022] Open
Abstract
For a long time, the nuclear lamina was thought to be the sole scaffold for the attachment of chromosomes to the nuclear envelope (NE) in metazoans. However, accumulating evidence indicates that nuclear pore complexes (NPCs) comprised of nucleoporins (Nups) participate in this process as well. One of the Nups, Elys, initiates NPC reassembly at the end of mitosis. Elys directly binds the decondensing chromatin and interacts with the Nup107–160 subcomplex of NPCs, thus serving as a seeding point for the subsequent recruitment of other NPC subcomplexes and connecting chromatin with the re-forming NE. Recent studies also uncovered the important functions of Elys during interphase where it interacts with chromatin and affects its compactness. Therefore, Elys seems to be one of the key Nups regulating chromatin organization. This review summarizes the current state of our knowledge about the participation of Elys in the post-mitotic NPC reassembly as well as the role that Elys and other Nups play in the maintenance of genome architecture.
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Affiliation(s)
- Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", 123182 Moscow, Russia
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23
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Liu S, Pellman D. The coordination of nuclear envelope assembly and chromosome segregation in metazoans. Nucleus 2020; 11:35-52. [PMID: 32208955 PMCID: PMC7289584 DOI: 10.1080/19491034.2020.1742064] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 01/25/2023] Open
Abstract
The nuclear envelope (NE) is composed of two lipid bilayer membranes that enclose the eukaryotic genome. In interphase, the NE is perforated by thousands of nuclear pore complexes (NPCs), which allow transport in and out of the nucleus. During mitosis in metazoans, the NE is broken down and then reassembled in a manner that enables proper chromosome segregation and the formation of a single nucleus in each daughter cell. Defects in coordinating NE reformation and chromosome segregation can cause aberrant nuclear architecture. This includes the formation of micronuclei, which can trigger a catastrophic mutational process commonly observed in cancers called chromothripsis. Here, we discuss the current understanding of the coordination of NE reformation with chromosome segregation during mitotic exit in metazoans. We review differing models in the field and highlight recent work suggesting that normal NE reformation and chromosome segregation are physically linked through the timing of mitotic spindle disassembly.
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Affiliation(s)
- Shiwei Liu
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Pellman
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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24
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Mehta SJK, Kumar V, Mishra RK. Drosophila ELYS regulates Dorsal dynamics during development. J Biol Chem 2020; 295:2421-2437. [PMID: 31941789 DOI: 10.1074/jbc.ra119.009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 01/13/2020] [Indexed: 11/06/2022] Open
Abstract
Embryonic large molecule derived from yolk sac (ELYS) is a constituent protein of nuclear pores. It initiates assembly of nuclear pore complexes into functional nuclear pores toward the end of mitosis. Using cellular, molecular, and genetic tools, including fluorescence and Electron microscopy, quantitative PCR, and RNAi-mediated depletion, we report here that the ELYS ortholog (dElys) plays critical roles during Drosophila development. dElys localized to the nuclear rim in interphase cells, but during mitosis it was absent from kinetochores and enveloped chromatin. We observed that RNAi-mediated dElys depletion leads to aberrant development and, at the cellular level, to defects in the nuclear pore and nuclear lamina assembly. Further genetic analyses indicated that dElys depletion re-activates the Dorsal (NF-κB) pathway during late larval stages. Re-activated Dorsal caused untimely expression of the Dorsal target genes in the post-embryonic stages. We also demonstrate that activated Dorsal triggers apoptosis during later developmental stages by up-regulating the pro-apoptotic genes reaper and hid The apoptosis induced by Reaper and Hid was probably the underlying cause for developmental abnormalities observed upon dElys depletion. Moreover, we noted that dElys has conserved structural features, but contains a noncanonical AT-hook-like motif through which it strongly binds to DNA. Together, our results uncover a novel epistatic interaction that regulates Dorsal dynamics by dElys during development.
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Affiliation(s)
- Saurabh Jayesh Kumar Mehta
- Nups and SUMO Biology Group, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India
| | - Vimlesh Kumar
- Laboratory of Neurogenetics, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India
| | - Ram Kumar Mishra
- Nups and SUMO Biology Group, Department of Biological Sciences, Academic Building 3, Indian Institute of Science Education and Research-Bhopal, Bhopal By-pass Road, Bhauri, Bhopal, Madhya Pradesh-462066, India.
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25
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Konishi HA, Yoshimura SH. Interactions between non‐structured domains of FG‐ and non‐FG‐nucleoporins coordinate the ordered assembly of the nuclear pore complex in mitosis. FASEB J 2019; 34:1532-1545. [DOI: 10.1096/fj.201901669r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/13/2019] [Accepted: 11/14/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Hide A. Konishi
- Laboratory of Plasma Membrane and Nuclear Signaling Graduate School of Biostudies Kyoto University Kyoto Japan
| | - Shige H. Yoshimura
- Laboratory of Plasma Membrane and Nuclear Signaling Graduate School of Biostudies Kyoto University Kyoto Japan
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26
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Scholz BA, Sumida N, de Lima CDM, Chachoua I, Martino M, Tzelepis I, Nikoshkov A, Zhao H, Mehmood R, Sifakis EG, Bhartiya D, Göndör A, Ohlsson R. WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating. Nat Genet 2019; 51:1723-1731. [DOI: 10.1038/s41588-019-0535-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/23/2019] [Indexed: 01/10/2023]
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27
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Gozalo A, Duke A, Lan Y, Pascual-Garcia P, Talamas JA, Nguyen SC, Shah PP, Jain R, Joyce EF, Capelson M. Core Components of the Nuclear Pore Bind Distinct States of Chromatin and Contribute to Polycomb Repression. Mol Cell 2019; 77:67-81.e7. [PMID: 31784359 DOI: 10.1016/j.molcel.2019.10.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/04/2019] [Accepted: 10/11/2019] [Indexed: 12/15/2022]
Abstract
Interactions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, in Drosophila cells. Our investigation uncovered differential binding of these NPC subunits, where Nup107 preferentially targets active genes while Nup93 associates primarily with Polycomb-silenced regions. Comparison to Lamin-associated domains (LADs) revealed that NPC binding sites can be found within LADs, demonstrating a linear binding of the genome along the nuclear envelope. Importantly, we identified a functional role of Nup93 in silencing of Polycomb target genes and in spatial folding of Polycomb domains. Our findings lend to a model where different nuclear pores bind different types of chromatin via interactions with specific NPC sub-complexes, and a subset of Polycomb domains is stabilized by interactions with Nup93.
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Affiliation(s)
- Alejandro Gozalo
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ashley Duke
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica A Talamas
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Son C Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Parisha P Shah
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajan Jain
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric F Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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28
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James C, Müller M, Goldberg MW, Lenz C, Urlaub H, Kehlenbach RH. Proteomic mapping by rapamycin-dependent targeting of APEX2 identifies binding partners of VAPB at the inner nuclear membrane. J Biol Chem 2019; 294:16241-16254. [PMID: 31519755 DOI: 10.1074/jbc.ra118.007283] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 08/05/2019] [Indexed: 11/06/2022] Open
Abstract
Vesicle-associated membrane protein-associated protein B (VAPB) is a tail-anchored protein that is present at several contact sites of the endoplasmic reticulum (ER). We now show by immunoelectron microscopy that VAPB also localizes to the inner nuclear membrane (INM). Using a modified enhanced ascorbate peroxidase 2 (APEX2) approach with rapamycin-dependent targeting of the peroxidase to a protein of interest, we searched for proteins that are in close proximity to VAPB, particularly at the INM. In combination with stable isotope labeling with amino acids in cell culture (SILAC), we confirmed many well-known interaction partners at the level of the ER with a clear distinction between specific and nonspecific hits. Furthermore, we identified emerin, TMEM43, and ELYS as potential interaction partners of VAPB at the INM and the nuclear pore complex, respectively.
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Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Marret Müller
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Martin W Goldberg
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center for Molecular Biosciences (GZMB), Georg August University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
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29
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Prorok P, Artufel M, Aze A, Coulombe P, Peiffer I, Lacroix L, Guédin A, Mergny JL, Damaschke J, Schepers A, Cayrou C, Teulade-Fichou MP, Ballester B, Méchali M. Involvement of G-quadruplex regions in mammalian replication origin activity. Nat Commun 2019; 10:3274. [PMID: 31332171 PMCID: PMC6646384 DOI: 10.1038/s41467-019-11104-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Genome-wide studies of DNA replication origins revealed that origins preferentially associate with an Origin G-rich Repeated Element (OGRE), potentially forming G-quadruplexes (G4). Here, we functionally address their requirements for DNA replication initiation in a series of independent approaches. Deletion of the OGRE/G4 sequence strongly decreased the corresponding origin activity. Conversely, the insertion of an OGRE/G4 element created a new replication origin. This element also promoted replication of episomal EBV vectors lacking the viral origin, but not if the OGRE/G4 sequence was deleted. A potent G4 ligand, PhenDC3, stabilized G4s but did not alter the global origin activity. However, a set of new, G4-associated origins was created, whereas suppressed origins were largely G4-free. In vitro Xenopus laevis replication systems showed that OGRE/G4 sequences are involved in the activation of DNA replication, but not in the pre-replication complex formation. Altogether, these results converge to the functional importance of OGRE/G4 elements in DNA replication initiation.
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Affiliation(s)
- Paulina Prorok
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | | | - Antoine Aze
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Philippe Coulombe
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Isabelle Peiffer
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Laurent Lacroix
- Balasubramanian group, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac, 33607, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), Pessac, 33607, France.,Institut Curie, CNRS UMR9187, Inserm U1196, Universite Paris Saclay, Orsay, France
| | - Julia Damaschke
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Marchioninistraße 25, 81377, Munich, Germany
| | - Aloys Schepers
- Research Unit Gene Vectors, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Marchioninistraße 25, 81377, Munich, Germany.,Monoclonal Antibody Core Facility & Research Group, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstädter Landstrasse, 85764, Neuherberg, Germany
| | - Christelle Cayrou
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France.,Centre de Recherche en Cancérologie de Marseille 27 Boulevard Lei Roure, 13273, Marseille, France
| | | | | | - Marcel Méchali
- Institute of Human Genetics, CNRS-University of Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France.
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30
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Jevtić P, Schibler AC, Wesley CC, Pegoraro G, Misteli T, Levy DL. The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity. EMBO Rep 2019; 20:embr.201847283. [PMID: 31085625 DOI: 10.15252/embr.201847283] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
How intracellular organelles acquire their characteristic sizes is a fundamental question in cell biology. Given stereotypical changes in nuclear size in cancer, it is important to understand the mechanisms that control nuclear size in human cells. Using a high-throughput imaging RNAi screen, we identify and mechanistically characterize ELYS, a nucleoporin required for post-mitotic nuclear pore complex (NPC) assembly, as a determinant of nuclear size in mammalian cells. ELYS knockdown results in small nuclei, reduced nuclear lamin B2 localization, lower NPC density, and decreased nuclear import. Increasing nuclear import by importin α overexpression rescues nuclear size and lamin B2 import, while inhibiting importin α/β-mediated nuclear import decreases nuclear size. Conversely, ELYS overexpression increases nuclear size, enriches nuclear lamin B2 at the nuclear periphery, and elevates NPC density and nuclear import. Consistent with these observations, knockdown or inhibition of exportin 1 increases nuclear size. Thus, we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | | | - Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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31
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Kobayashi W, Takizawa Y, Aihara M, Negishi L, Ishii H, Kurumizaka H. Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding. Commun Biol 2019; 2:163. [PMID: 31069272 PMCID: PMC6499780 DOI: 10.1038/s42003-019-0385-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
The nuclear pore complex embedded within the nuclear envelope is the essential architecture for trafficking macromolecules, such as proteins and RNAs, between the cytoplasm and nucleus. The nuclear pore complex assembly occurs on chromatin in the post-mitotic phase of the cell cycle. ELYS (MEL-28/AHCTF1) binds to the nucleosome, which is the basic chromatin unit, and promotes assembly of the complex around the chromosomes in cells. Here we show that the Arg-Arg-Lys (RRK) stretch of the C-terminal ELYS region plays an essential role in the nucleosome binding. The cryo-EM structure and the crosslinking mass spectrometry reveal that the ELYS C-terminal region directly binds to the acidic patch of the nucleosome. These results provide mechanistic insight into the ELYS-nucleosome interaction, which promotes the post-mitotic nuclear pore complex formation around chromosomes in cells.
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Affiliation(s)
- Wataru Kobayashi
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Yoshimasa Takizawa
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
| | - Maya Aihara
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Lumi Negishi
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
| | - Hajime Ishii
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Hitoshi Kurumizaka
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
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32
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Priego Moreno S, Jones RM, Poovathumkadavil D, Scaramuzza S, Gambus A. Mitotic replisome disassembly depends on TRAIP ubiquitin ligase activity. Life Sci Alliance 2019; 2:2/2/e201900390. [PMID: 30979826 PMCID: PMC6464043 DOI: 10.26508/lsa.201900390] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
Analysis of the mitotic replisome disassembly pathway in X. laevis egg extract shows that any replisomes retained on chromatin past S-phase are unloaded through formation of K6- and K63-linked ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and p97/VCP activity. We have shown previously that the process of replication machinery (replisome) disassembly at the termination of DNA replication forks in the S-phase is driven through polyubiquitylation of one of the replicative helicase subunits (Mcm7) by Cul2LRR1 ubiquitin ligase. Interestingly, upon inhibition of this pathway in Caenorhabditis elegans embryos, the replisomes retained on chromatin were unloaded in the subsequent mitosis. Here, we show that this mitotic replisome disassembly pathway exists in Xenopus laevis egg extract and we determine the first elements of its regulation. The mitotic disassembly pathway depends on the formation of K6- and K63-linked ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and the activity of p97/VCP protein segregase. Unlike in lower eukaryotes, however, it does not require SUMO modifications. Importantly, we also show that this process can remove all replisomes from mitotic chromatin, including stalled ones, which indicates a wide application for this pathway over being just a “backup” for terminated replisomes. Finally, we characterise the composition of the replisome retained on chromatin until mitosis.
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Affiliation(s)
- Sara Priego Moreno
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rebecca M Jones
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Divyasree Poovathumkadavil
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Shaun Scaramuzza
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Agnieszka Gambus
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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33
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Moura M, Conde C. Phosphatases in Mitosis: Roles and Regulation. Biomolecules 2019; 9:E55. [PMID: 30736436 PMCID: PMC6406801 DOI: 10.3390/biom9020055] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023] Open
Abstract
Mitosis requires extensive rearrangement of cellular architecture and of subcellular structures so that replicated chromosomes can bind correctly to spindle microtubules and segregate towards opposite poles. This process originates two new daughter nuclei with equal genetic content and relies on highly-dynamic and tightly regulated phosphorylation of numerous cell cycle proteins. A burst in protein phosphorylation orchestrated by several conserved kinases occurs as cells go into and progress through mitosis. The opposing dephosphorylation events are catalyzed by a small set of protein phosphatases, whose importance for the accuracy of mitosis is becoming increasingly appreciated. This review will focus on the established and emerging roles of mitotic phosphatases, describe their structural and biochemical properties, and discuss recent advances in understanding the regulation of phosphatase activity and function.
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Affiliation(s)
- Margarida Moura
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde da Universidade do Porto, 4200-135, Porto, Portugal.
- Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
| | - Carlos Conde
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde da Universidade do Porto, 4200-135, Porto, Portugal.
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34
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Kane M, Rebensburg SV, Takata MA, Zang TM, Yamashita M, Kvaratskhelia M, Bieniasz PD. Nuclear pore heterogeneity influences HIV-1 infection and the antiviral activity of MX2. eLife 2018; 7:e35738. [PMID: 30084827 PMCID: PMC6101944 DOI: 10.7554/elife.35738] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
HIV-1 accesses the nuclear DNA of interphase cells via a poorly defined process involving functional interactions between the capsid protein (CA) and nucleoporins (Nups). Here, we show that HIV-1 CA can bind multiple Nups, and that both natural and manipulated variation in Nup levels impacts HIV-1 infection in a manner that is strikingly dependent on cell-type, cell-cycle, and cyclophilin A (CypA). We also show that Nups mediate the function of the antiviral protein MX2, and that MX2 can variably inhibit non-viral NLS function. Remarkably, both enhancing and inhibiting effects of cyclophilin A and MX2 on various HIV-1 CA mutants could be induced or abolished by manipulating levels of the Nup93 subcomplex, the Nup62 subcomplex, NUP88, NUP214, RANBP2, or NUP153. Our findings suggest that several Nup-dependent 'pathways' are variably exploited by HIV-1 to target host DNA in a cell-type, cell-cycle, CypA and CA-sequence dependent manner, and are differentially inhibited by MX2.
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Affiliation(s)
- Melissa Kane
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Stephanie V Rebensburg
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Matthew A Takata
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Trinity M Zang
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Mamuka Kvaratskhelia
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Paul D Bieniasz
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
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35
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Genetic Analyses of Elys Mutations in Drosophila Show Maternal-Effect Lethality and Interactions with Nucleoporin Genes. G3-GENES GENOMES GENETICS 2018; 8:2421-2431. [PMID: 29773558 PMCID: PMC6027884 DOI: 10.1534/g3.118.200361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ELYS determines the subcellular localizations of Nucleoporins (Nups) during interphase and mitosis. We made loss-of-function mutations of Elys in Drosophila melanogaster and found that ELYS is dispensable for zygotic viability and male fertility but the maternal supply is necessary for embryonic development. Subsequent to fertilization, mitotic progression of the embryos produced by the mutant females is severely disrupted at the first cleavage division, accompanied by irregular behavior of mitotic centrosomes. The Nup160 introgression from D. simulans shows close resemblance to that of the Elys mutations, suggesting a common role for those proteins in the first cleavage division. Our genetic experiments indicated critical interactions between ELYS and three Nup107-160 subcomplex components; hemizygotes of either Nup37, Nup96 or Nup160 were lethal in the genetic background of the Elys mutation. Not only Nup96 and Nup160 but also Nup37 of D. simulans behave as recessive hybrid incompatibility genes with D. melanogaster An evolutionary analysis indicated positive natural selection in the ELYS-like domain of ELYS. Here we propose that genetic incompatibility between Elys and Nups may lead to reproductive isolation between D. melanogaster and D. simulans, although direct evidence is necessary.
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36
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Abstract
Transcriptional enhancers constitute a subclass of regulatory elements that facilitate transcription. Such regions are generally organized by short stretches of DNA enriched in transcription factor-binding sites but also can include very large regions containing clusters of enhancers, termed super-enhancers. These regions increase the probability or the rate (or both) of transcription generally in
cis and sometimes over very long distances by altering chromatin states and the activity of Pol II machinery at promoters. Although enhancers were discovered almost four decades ago, their inner workings remain enigmatic. One important opening into the underlying principle has been provided by observations that enhancers make physical contacts with their target promoters to facilitate the loading of the RNA polymerase complex. However, very little is known about how such chromatin loops are regulated and how they govern transcription in the three-dimensional context of the nuclear architecture. Here, we present current themes of how enhancers may boost gene expression in three dimensions and we identify currently unresolved key questions.
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Affiliation(s)
- Anita Göndör
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Rolf Ohlsson
- Department of Oncology and Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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37
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Platani M, Samejima I, Samejima K, Kanemaki MT, Earnshaw WC. Seh1 targets GATOR2 and Nup153 to mitotic chromosomes. J Cell Sci 2018; 131:jcs.213140. [PMID: 29618633 PMCID: PMC5992584 DOI: 10.1242/jcs.213140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/23/2018] [Indexed: 12/27/2022] Open
Abstract
In metazoa, the Nup107 complex (also known as the nucleoporin Y-complex) plays a major role in formation of the nuclear pore complex in interphase and is localised to kinetochores in mitosis. The Nup107 complex shares a single highly conserved subunit, Seh1 (also known as SEH1L in mammals) with the GATOR2 complex, an essential activator of mTORC1 kinase. mTORC1/GATOR2 has a central role in the coordination of cell growth and proliferation. Here, we use chemical genetics and quantitative chromosome proteomics to study the role of the Seh1 protein in mitosis. Surprisingly, Seh1 is not required for the association of the Nup107 complex with mitotic chromosomes, but it is essential for the association of both the GATOR2 complex and nucleoporin Nup153 with mitotic chromosomes. Our analysis also reveals a role for Seh1 at human centromeres, where it is required for efficient localisation of the chromosomal passenger complex (CPC). Furthermore, this analysis detects a functional interaction between the Nup107 complex and the small kinetochore protein SKAP (also known as KNSTRN). Highlighted Article: The nucleoporin Seh1 is essential for the association of both the GATOR2 complex and the nucleoporin Nup153, but not the Nup107 complex, with mitotic chromosomes.
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Affiliation(s)
- Melpomeni Platani
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Itaru Samejima
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kumiko Samejima
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, ROIS, and Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
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38
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Zhang W, Neuner A, Rüthnick D, Sachsenheimer T, Lüchtenborg C, Brügger B, Schiebel E. Brr6 and Brl1 locate to nuclear pore complex assembly sites to promote their biogenesis. J Cell Biol 2018; 217:877-894. [PMID: 29439116 PMCID: PMC5839787 DOI: 10.1083/jcb.201706024] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/21/2017] [Accepted: 01/10/2018] [Indexed: 12/30/2022] Open
Abstract
The conserved paralogous Brr6 and Brl1 promote NPC biogenesis in an unclear manner. Here, Zhang et al. show that both transmembrane proteins transiently associate with NPC assembly intermediates and directly promote NPC biogenesis. The paralogous Brr6 and Brl1 are conserved integral membrane proteins of the nuclear envelope (NE) with an unclear role in nuclear pore complex (NPC) biogenesis. Here, we analyzed double-degron mutants of Brr6/Brl1 to understand this function. Depletion of Brr6 and Brl1 caused defects in NPC biogenesis, whereas the already assembled NPCs remained unaffected. This NPC biogenesis defect was not accompanied by a change in lipid composition. However, Brl1 interacted with Ndc1 and Nup188 by immunoprecipitation, and with transmembrane and outer and inner ring NPC components by split yellow fluorescent protein analysis, indicating a direct role in NPC biogenesis. Consistently, we found that Brr6 and Brl1 associated with a subpopulation of NPCs and emerging NPC assembly sites. Moreover, BRL1 overexpression affected NE morphology without a change in lipid composition and completely suppressed the nuclear pore biogenesis defect of nup116Δ and gle2Δ cells. We propose that Brr6 and Brl1 transiently associate with NPC assembly sites where they promote NPC biogenesis.
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Affiliation(s)
- Wanlu Zhang
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Diana Rüthnick
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | | | | | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
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39
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Aze A, Fragkos M, Bocquet S, Cau J, Méchali M. RNAs coordinate nuclear envelope assembly and DNA replication through ELYS recruitment to chromatin. Nat Commun 2017; 8:2130. [PMID: 29242643 PMCID: PMC5730577 DOI: 10.1038/s41467-017-02180-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 11/13/2017] [Indexed: 12/17/2022] Open
Abstract
Upon fertilisation, the sperm pronucleus acquires the competence to replicate the genome through a cascade of events that link chromatin remodelling to nuclear envelope formation. The factors involved have been partially identified and are poorly characterised. Here, using Xenopus laevis egg extracts we show that RNAs are required for proper nuclear envelope assembly following sperm DNA decondensation. Although chromatin remodelling and pre-replication complex formation occur normally, RNA-depleted extracts show a defect in pre-RC activation. The nuclear processes affected by RNA-depletion included ELYS recruitment, which accounts for the deficiency in nuclear pore complex assembly. This results in failure in chromatin relaxation as well as in the import and proper nuclear concentration of the S-phase kinases necessary for DNA replication activation. Our results highlight a translation-independent RNA function necessary for the parental genome progression towards the early embryonic cell cycle programme. The factors that link chromatin remodelling to nuclear envelope formation in the sperm pronucleus are not fully characterised. Here, the authors show that in RNA-depleted Xenopus laevis egg extracts, ELYS recruitment and nuclear pore complex formation are impaired, resulting in defective nuclear processes.
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Affiliation(s)
- Antoine Aze
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Michalis Fragkos
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France.,Institut Gustave Roussy, Genetic Stability and Oncogenesis Department, 39 rue Camille Desmoulins, 94805, Villejuif, France
| | - Stéphane Bocquet
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Julien Cau
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Montpellier RIO Imaging, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Marcel Méchali
- Institute of Human Genetics, UMR 9002, CNRS and the University of Montpellier, Replication and Genome Dynamics, 141 rue de la Cardonille, 34396, Montpellier, France.
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40
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Suresh S, Markossian S, Osmani AH, Osmani SA. Mitotic nuclear pore complex segregation involves Nup2 in Aspergillus nidulans. J Cell Biol 2017; 216:2813-2826. [PMID: 28747316 PMCID: PMC5584150 DOI: 10.1083/jcb.201610019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 05/11/2017] [Accepted: 07/06/2017] [Indexed: 01/20/2023] Open
Abstract
Transport through nuclear pore complexes (NPCs) during interphase is facilitated by the nucleoporin Nup2 via its importin α- and Ran-binding domains. However, Aspergillus nidulans and vertebrate Nup2 also locate to chromatin during mitosis, suggestive of mitotic functions. In this study, we report that Nup2 is required for mitotic NPC inheritance in A. nidulans Interestingly, the role of Nup2 during mitotic NPC segregation is independent of its importin α- and Ran-binding domains but relies on a central targeting domain that is necessary for localization and viability. To test whether mitotic chromatin-associated Nup2 might function to bridge NPCs with chromatin during segregation, we provided an artificial link between NPCs and chromatin via Nup133 and histone H1. Using this approach, we bypassed the requirement of Nup2 for NPC segregation. This indicates that A. nidulans cells ensure accurate mitotic NPC segregation to daughter nuclei by linking mitotic DNA and NPC segregation via the mitotic specific chromatin association of Nup2.
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Affiliation(s)
- Subbulakshmi Suresh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH.,Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Sarine Markossian
- Department of Molecular Genetics, The Ohio State University, Columbus, OH
| | - Aysha H Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH
| | - Stephen A Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH
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41
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Hattersley N, Cheerambathur D, Moyle M, Stefanutti M, Richardson A, Lee KY, Dumont J, Oegema K, Desai A. A Nucleoporin Docks Protein Phosphatase 1 to Direct Meiotic Chromosome Segregation and Nuclear Assembly. Dev Cell 2017; 38:463-77. [PMID: 27623381 DOI: 10.1016/j.devcel.2016.08.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/10/2016] [Accepted: 08/13/2016] [Indexed: 12/31/2022]
Abstract
During M-phase entry in metazoans with open mitosis, the concerted action of mitotic kinases disassembles nuclei and promotes assembly of kinetochores-the primary microtubule attachment sites on chromosomes. At M-phase exit, these major changes in cellular architecture must be reversed. Here, we show that the conserved kinetochore-localized nucleoporin MEL-28/ELYS docks the catalytic subunit of protein phosphatase 1 (PP1c) to direct kinetochore disassembly-dependent chromosome segregation during oocyte meiosis I and nuclear assembly during the transition from M phase to interphase. During oocyte meiosis I, MEL-28-PP1c disassembles kinetochores in a timely manner to promote elongation of the acentrosomal spindles that segregate homologous chromosomes. During nuclear assembly, MEL-28 recruits PP1c to the periphery of decondensed chromatin, where it directs formation of a functional nuclear compartment. Thus, a pool of phosphatase activity associated with a kinetochore-localized nucleoporin contributes to two key events that occur during M-phase exit in metazoans: kinetochore disassembly and nuclear reassembly.
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Affiliation(s)
- Neil Hattersley
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Dhanya Cheerambathur
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Mark Moyle
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Marine Stefanutti
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Amelia Richardson
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Kian-Yong Lee
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Julien Dumont
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Karen Oegema
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Arshad Desai
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA.
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42
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Yang Y, Wang W, Chu Z, Zhu JK, Zhang H. Roles of Nuclear Pores and Nucleo-cytoplasmic Trafficking in Plant Stress Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:574. [PMID: 28446921 PMCID: PMC5388774 DOI: 10.3389/fpls.2017.00574] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 03/30/2017] [Indexed: 05/29/2023]
Abstract
The nuclear pore complex (NPC) is a large protein complex that controls the exchange of components between the nucleus and the cytoplasm. In plants, the NPC family components play critical roles not only in essential growth and developmental processes, but also in plant responses to various environmental stress conditions. The involvement of NPC components in plant stress responses is mainly attributed to different mechanisms including control of mRNA/protein nucleo-cytoplasmic trafficking and transcriptional gene regulation. This mini review summarizes current knowledge of the NPC-mediated plant stress responses and provides an overview of the underlying molecular mechanisms.
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Affiliation(s)
- Yu Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West LafayetteIN, USA
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
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43
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Gómez-Saldivar G, Fernandez A, Hirano Y, Mauro M, Lai A, Ayuso C, Haraguchi T, Hiraoka Y, Piano F, Askjaer P. Identification of Conserved MEL-28/ELYS Domains with Essential Roles in Nuclear Assembly and Chromosome Segregation. PLoS Genet 2016; 12:e1006131. [PMID: 27341616 PMCID: PMC4920428 DOI: 10.1371/journal.pgen.1006131] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/26/2016] [Indexed: 11/19/2022] Open
Abstract
Nucleoporins are the constituents of nuclear pore complexes (NPCs) and are essential regulators of nucleocytoplasmic transport, gene expression and genome stability. The nucleoporin MEL-28/ELYS plays a critical role in post-mitotic NPC reassembly through recruitment of the NUP107-160 subcomplex, and is required for correct segregation of mitotic chromosomes. Here we present a systematic functional and structural analysis of MEL-28 in C. elegans early development and human ELYS in cultured cells. We have identified functional domains responsible for nuclear envelope and kinetochore localization, chromatin binding, mitotic spindle matrix association and chromosome segregation. Surprisingly, we found that perturbations to MEL-28’s conserved AT-hook domain do not affect MEL-28 localization although they disrupt MEL-28 function and delay cell cycle progression in a DNA damage checkpoint-dependent manner. Our analyses also uncover a novel meiotic role of MEL-28. Together, these results show that MEL-28 has conserved structural domains that are essential for its fundamental roles in NPC assembly and chromosome segregation. Most animal cells have a nucleus that contains the genetic material: the chromosomes. The nucleus is enclosed by the nuclear envelope, which provides a physical barrier between the chromosomes and the surrounding cytoplasm, and enables precisely controlled transport of proteins into and out of the nucleus. Transport occurs through nuclear pore complexes, which consist of multiple copies of ~30 different proteins called nucleoporins. Although the composition of nuclear pore complexes is known, the mechanisms of their assembly and function are still unclear. We have analyzed the nucleoporin MEL-28/ELYS through a systematic dissection of functional domains both in the nematode Caenorhabditis elegans and in human cells. Interestingly, MEL-28/ELYS localizes not only to nuclear pore complexes, but is also associated with chromosomal structures known as kinetochores during cell division. Our studies have revealed that even small perturbations in MEL-28/ELYS can have dramatic consequences on nuclear pore complex assembly as well as on separation of chromosomes during cell division. Surprisingly, inhibition of MEL-28/ELYS causes cell-cycle delay, suggesting activation of a cellular surveillance system for chromosomal damages. Finally, we conclude that the structural domains of MEL-28/ELYS are conserved from nematodes to humans.
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Affiliation(s)
- Georgina Gómez-Saldivar
- Andalusian Center for Developmental Biology (CABD), CSIC/Junta de Andalucia/Universidad Pablo de Olavide, Seville, Spain
| | - Anita Fernandez
- Biology Department, Fairfield University, Fairfield, Connecticut, United States of America
- * E-mail: (AF); (PA)
| | - Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Michael Mauro
- Biology Department, Fairfield University, Fairfield, Connecticut, United States of America
| | - Allison Lai
- Biology Department, Fairfield University, Fairfield, Connecticut, United States of America
| | - Cristina Ayuso
- Andalusian Center for Developmental Biology (CABD), CSIC/Junta de Andalucia/Universidad Pablo de Olavide, Seville, Spain
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Fabio Piano
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- New York University, Abu Dhabi, United Arab Emirates
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/Junta de Andalucia/Universidad Pablo de Olavide, Seville, Spain
- * E-mail: (AF); (PA)
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44
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Gillespie PJ, Neusiedler J, Creavin K, Chadha GS, Blow JJ. Cell Cycle Synchronization in Xenopus Egg Extracts. Methods Mol Biol 2016; 1342:101-47. [PMID: 26254920 DOI: 10.1007/978-1-4939-2957-3_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many important discoveries in cell cycle research have been made using cell-free extracts prepared from the eggs of the South African clawed frog Xenopus laevis. These extracts efficiently support the key nuclear functions of the eukaryotic cell cycle in vitro under apparently the same controls that exist in vivo. The Xenopus cell-free system is therefore uniquely suited to the study of the mechanisms, dynamics and integration of cell cycle regulated processes at a biochemical level. Here, we describe methods currently in use in our laboratory for the preparation of Xenopus egg extracts and demembranated sperm nuclei. We detail how these extracts can be used to study the key transitions of the eukaryotic cell cycle and describe conditions under which these transitions can be manipulated by addition of drugs that either retard or advance passage. In addition, we describe in detail essential techniques that provide a practical starting point for investigating the function of proteins involved in the operation of the eukaryotic cell cycle.
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Affiliation(s)
- Peter J Gillespie
- Centre for Gene Regulation & Expression, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
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45
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Raghunayakula S, Subramonian D, Dasso M, Kumar R, Zhang XD. Molecular Characterization and Functional Analysis of Annulate Lamellae Pore Complexes in Nuclear Transport in Mammalian Cells. PLoS One 2015; 10:e0144508. [PMID: 26642330 PMCID: PMC4671610 DOI: 10.1371/journal.pone.0144508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/19/2015] [Indexed: 01/26/2023] Open
Abstract
Annulate lamellae are cytoplasmic organelles containing stacked sheets of membranes embedded with pore complexes. These cytoplasmic pore complexes at annulate lamellae are morphologically similar to nuclear pore complexes at the nuclear envelope. Although annulate lamellae has been observed in nearly all types of cells, their biological functions are still largely unknown. Here we show that SUMO1-modification of the Ran GTPase-activating protein RanGAP1 not only target RanGAP1 to its known sites at nuclear pore complexes but also to annulate lamellae pore complexes through interactions with the Ran-binding protein RanBP2 and the SUMO-conjugating enzyme Ubc9 in mammalian cells. Furthermore, upregulation of annulate lamellae, which decreases the number of nuclear pore complexes and concurrently increases that of annulate lamellae pore complexes, causes a redistribution of nuclear transport receptors including importin α/β and the exportin CRM1 from nuclear pore complexes to annulate lamellae pore complexes and also reduces the rates of nuclear import and export. Moreover, our results reveal that importin α/β-mediated import complexes initially accumulate at annulate lamellae pore complexes upon the activation of nuclear import and subsequently disassociate for nuclear import through nuclear pore complexes in cells with upregulation of annulate lamellae. Lastly, CRM1-mediated export complexes are concentrated at both nuclear pore complexes and annulate lamellae pore complexes when the disassembly of these export complexes is inhibited by transient expression of a Ran GTPase mutant arrested in its GTP-bound form, suggesting that RanGAP1/RanBP2-activated RanGTP hydrolysis at these pore complexes is required for the dissociation of the export complexes. Hence, our findings provide a foundation for further investigation of how upregulation of annulate lamellae decreases the rates of nuclear transport and also for elucidation of the biological significance of the interaction between annulate lamellae pore complexes and nuclear transport complexes in mammalian cells.
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Affiliation(s)
- Sarita Raghunayakula
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Divya Subramonian
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Mary Dasso
- Laboratory of Gene Regulation and Development, National Institute for Child Health and Human Development, NIH, Bethesda, Maryland, United States of America
| | - Rita Kumar
- Departments of Emergency Medicine and Physiology, Wayne State University, Detroit, Michigan, United States of America
| | - Xiang-Dong Zhang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
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46
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Abstract
Breuer and Ohkura propose a negative regulatory loop within the nuclear pore complex (NPC) controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. The nuclear pore complex (NPC) tethers chromatin to create an environment for gene regulation, but little is known about how this activity is regulated to avoid excessive tethering of the genome. Here we propose a negative regulatory loop within the NPC controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. Depletion of Nup62 severely disrupts chromatin distribution in the nuclei of female germlines and somatic cells, which can be reversed by codepleting Nup155. Thus, this universal regulatory system within the NPC is crucial to control large-scale chromatin organization in the nucleus.
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Affiliation(s)
- Manuel Breuer
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Hiroyuki Ohkura
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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47
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Schwartz M, Travesa A, Martell SW, Forbes DJ. Analysis of the initiation of nuclear pore assembly by ectopically targeting nucleoporins to chromatin. Nucleus 2015; 6:40-54. [PMID: 25602437 PMCID: PMC4615246 DOI: 10.1080/19491034.2015.1004260] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Nuclear pore complexes (NPCs) form the gateway to the nucleus, mediating virtually all nucleocytoplasmic trafficking. Assembly of a nuclear pore complex requires the organization of many soluble sub-complexes into a final massive structure embedded in the nuclear envelope. By use of a LacI/LacO reporter system, we were able to assess nucleoporin (Nup) interactions, show that they occur with a high level of specificity, and identify nucleoporins sufficient for initiation of the complex process of NPC assembly in vivo. Eleven nucleoporins from different sub-complexes were fused to LacI-CFP and transfected separately into a human cell line containing a stably integrated LacO DNA array. The LacI-Nup fusion proteins, which bound to the array, were examined for their ability to recruit endogenous nucleoporins to the intranuclear LacO site. Many could recruit nucleoporins of the same sub-complex and a number could also recruit other sub-complexes. Strikingly, Nup133 and Nup107 of the Nup107/160 subcomplex and Nup153 and Nup50 of the nuclear pore basket recruited a near full complement of nucleoporins to the LacO array. Furthermore, Nup133 and Nup153 efficiently targeted the LacO array to the nuclear periphery. Our data support a hierarchical, seeded assembly pathway and identify Nup133 and Nup153 as effective “seeds” for NPC assembly. In addition, we show that this system can be applied to functional studies of individual nucleoporin domains as well as to specific nucleoporin disease mutations. We find that the R391H cardiac arrhythmia/sudden death mutation of Nup155 prevents both its subcomplex assembly and nuclear rim targeting of the LacO array.
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Affiliation(s)
- Michal Schwartz
- a Section of Cell and Developmental Biology; Division of Biological Sciences 0347; University of California-San Diego ; La Jolla , CA USA
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48
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Yokoyama H, Koch B, Walczak R, Ciray-Duygu F, González-Sánchez JC, Devos DP, Mattaj IW, Gruss OJ. The nucleoporin MEL-28 promotes RanGTP-dependent γ-tubulin recruitment and microtubule nucleation in mitotic spindle formation. Nat Commun 2015; 5:3270. [PMID: 24509916 DOI: 10.1038/ncomms4270] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/16/2014] [Indexed: 01/11/2023] Open
Abstract
The GTP-bound form of the Ran GTPase (RanGTP), produced around chromosomes, drives nuclear envelope and nuclear pore complex (NPC) re-assembly after mitosis. The nucleoporin MEL-28/ELYS binds chromatin in a RanGTP-regulated manner and acts to seed NPC assembly. Here we show that, upon mitotic NPC disassembly, MEL-28 dissociates from chromatin and re-localizes to spindle microtubules and kinetochores. MEL-28 directly binds microtubules in a RanGTP-regulated way via its C-terminal chromatin-binding domain. Using Xenopus egg extracts, we demonstrate that MEL-28 is essential for RanGTP-dependent microtubule nucleation and spindle assembly, independent of its function in NPC assembly. Specifically, MEL-28 interacts with the γ-tubulin ring complex and recruits it to microtubule nucleation sites. Our data identify MEL-28 as a RanGTP target that functions throughout the cell cycle. Its cell cycle-dependent binding to chromatin or microtubules discriminates MEL-28 functions in interphase and mitosis, and ensures that spindle assembly occurs only after NPC breakdown.
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Affiliation(s)
- Hideki Yokoyama
- 1] Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany [2] European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Birgit Koch
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rudolf Walczak
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Fulya Ciray-Duygu
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | - Damien P Devos
- Centre for Organismal Studies (COS), Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Iain W Mattaj
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Oliver J Gruss
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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49
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Schellhaus AK, De Magistris P, Antonin W. Nuclear Reformation at the End of Mitosis. J Mol Biol 2015; 428:1962-85. [PMID: 26423234 DOI: 10.1016/j.jmb.2015.09.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 12/17/2022]
Abstract
Cells have developed highly sophisticated ways to accurately pass on their genetic information to the daughter cells. In animal cells, which undergo open mitosis, the nuclear envelope breaks down at the beginning of mitosis and the chromatin massively condenses to be captured and segregated by the mitotic spindle. These events have to be reverted in order to allow the reformation of a nucleus competent for DNA transcription and replication, as well as all other nuclear processes occurring in interphase. Here, we summarize our current knowledge of how, in animal cells, the highly compacted mitotic chromosomes are decondensed at the end of mitosis and how a nuclear envelope, including functional nuclear pore complexes, reassembles around these decondensing chromosomes.
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Affiliation(s)
| | - Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany.
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50
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Schooley A, Moreno-Andrés D, De Magistris P, Vollmer B, Antonin W. The lysine demethylase LSD1 is required for nuclear envelope formation at the end of mitosis. J Cell Sci 2015. [PMID: 26224877 DOI: 10.1242/jcs.173013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The metazoan nucleus breaks down and reassembles during each cell division. Upon mitotic exit, the successful reestablishment of an interphase nucleus requires the coordinated reorganization of chromatin and formation of a functional nuclear envelope. Here, we report that the histone demethylase LSD1 (also known as KDM1A) plays a crucial role in nuclear assembly at the end of mitosis. Downregulation of LSD1 in cells extends telophase and impairs nuclear pore complex assembly. In vitro, LSD1 demethylase activity is required for the recruitment of MEL28 (also known as ELYS and AHCTF1) and nuclear envelope precursor vesicles to chromatin, crucial steps in nuclear reassembly. Accordingly, the formation of a closed nuclear envelope and nuclear pore complex assembly are impaired upon depletion of LSD1 or inhibition of its activity. Our results identify histone demethylation by LSD1 as a new regulatory mechanism linking the chromatin state and nuclear envelope formation at the end of mitosis.
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Affiliation(s)
- Allana Schooley
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Daniel Moreno-Andrés
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Benjamin Vollmer
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
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