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Kono Y, Shimi T. Crosstalk between mitotic reassembly and repair of the nuclear envelope. Nucleus 2024; 15:2352203. [PMID: 38780365 PMCID: PMC11123513 DOI: 10.1080/19491034.2024.2352203] [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: 09/01/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
In eukaryotic cells, the nuclear envelope (NE) is a membrane partition between the nucleus and the cytoplasm to compartmentalize nuclear contents. It plays an important role in facilitating nuclear functions including transcription, DNA replication and repair. In mammalian cells, the NE breaks down and then reforms during cell division, and in interphase it is restored shortly after the NE rupture induced by mechanical force. In this way, the partitioning effect is regulated through dynamic processes throughout the cell cycle. A failure in rebuilding the NE structure triggers the mixing of nuclear and cytoplasmic contents, leading to catastrophic consequences for the nuclear functions. Whereas the precise details of molecular mechanisms for NE reformation during cell division and NE restoration in interphase are still being investigated, here, we mostly focus on mammalian cells to describe key aspects that have been identified and to discuss the crosstalk between them.
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Affiliation(s)
- Yohei Kono
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeshi Shimi
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
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2
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Campos-Díaz A, Morejón-García P, Monte-Serrano E, Ros-Pardo D, Marcos-Alcalde I, Gómez-Puertas P, Lazo PA. Pathogenic effects of Leu200Pro and Arg387His VRK1 protein variants on phosphorylation targets and H4K16 acetylation in distal hereditary motor neuropathy. J Mol Med (Berl) 2024; 102:801-817. [PMID: 38554151 PMCID: PMC11106162 DOI: 10.1007/s00109-024-02442-8] [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: 11/20/2023] [Revised: 03/07/2024] [Accepted: 03/21/2024] [Indexed: 04/01/2024]
Abstract
Rare recessive variants in the human VRK1 gene are associated with several motor neuron diseases (MND), such as amyotrophic lateral sclerosis, spinal muscular atrophy, or distal hereditary motor neuropathies (dHMN). A case with dHMN carrying two novel VRK1 gene variants, expressing Leu200Pro (L200P) and Arg387His (R387H) variant proteins, identified that these protein variants are functionally different. The Leu200Pro variant shares with several variants in the catalytic domain the loss of the kinase activity on different substrates, such as histones, p53, or coilin. However, the distal Arg387His variant and the distal Trp375* (W375X) chinese variant, both located at the end of the low complexity C-terminal region and proximal to the termination codon, retain their catalytic activity on some substrates, and mechanistically their functional impairment is different. The L200P variant, as well as most VRK1 pathogenic variants, impairs the phosphorylation of BAF and histone H4K16 acetylation, which are required for DNA attachment to the nuclear envelope and chromatin accessibility to DNA repair mechanisms, respectively. The R387H variant impairs phosphorylation of H2AX, an early step in different types of DNA damage responses. The functional variability of VRK1 protein variants and their different combinations are a likely contributor to the clinical phenotypic heterogeneity of motor neuron and neurological diseases associated with rare VRK1 pathogenic variants. KEY MESSAGES: VRK1 variants implicated in motor neuron diseases are functionally different. The L200P variant is kinase inactive, and the R387H variant is partially active. VRK1 variants alter H4K16 acetylation and loss of coilin and BAF phosphorylation. VRK1 variants alter Cajal bodies and DNA damage responses. VRK1 variant combination determines the neurological phenotype heterogeneity.
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Affiliation(s)
- Aurora Campos-Díaz
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Patricia Morejón-García
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Eva Monte-Serrano
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - David Ros-Pardo
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28040, Madrid, Spain
| | - Iñigo Marcos-Alcalde
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28040, Madrid, Spain
| | - Paulino Gómez-Puertas
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28040, Madrid, Spain
| | - Pedro A Lazo
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007, Salamanca, Spain.
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007, Salamanca, Spain.
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3
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Bunner S, Prince K, Srikrishna K, Pujadas EM, McCarthy AA, Kuklinski A, Jackson O, Pellegrino P, Jagtap S, Eweka I, Lawlor C, Eastin E, Yas G, Aiello J, LaPointe N, von Blucher IS, Hardy J, Chen J, Backman V, Janssen A, Packard M, Dorfman K, Almassalha L, Bahiru MS, Stephens AD. DNA density is a better indicator of a nuclear bleb than lamin B loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579152. [PMID: 38370828 PMCID: PMC10871186 DOI: 10.1101/2024.02.06.579152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Nuclear blebs are herniations of the nucleus that occur in diseased nuclei that cause nuclear rupture leading to cellular dysfunction. Chromatin and lamins are two of the major structural components of the nucleus that maintain its shape and function, but their relative roles in nuclear blebbing remain elusive. Lamin B is reported to be lost in blebs by qualitative data while quantitative studies reveal a spectrum of lamin B levels in nuclear blebs dependent on perturbation and cell type. Chromatin has been reported to be decreased or de-compacted in nuclear blebs, but again the data are not conclusive. To determine the composition of nuclear blebs, we compared the immunofluorescence intensity of lamin B and DNA in the main nucleus body and nuclear bleb across cell types and perturbations. Lamin B nuclear bleb levels varied drastically across MEF wild type and chromatin or lamins perturbations, HCT116 lamin B1-GFP imaging, and human disease model cells of progeria and prostate cancer. However, DNA concentration was consistently decreased to about half that of the main nucleus body across all measured conditions. Using Partial Wave Spectroscopic (PWS) microscopy to measure chromatin density in the nuclear bleb vs body we find similar results that DNA is consistently less dense in nuclear blebs. Thus, our data spanning many different cell types and perturbations supports that decreased DNA is a better marker of a nuclear bleb than lamin B levels that vary widely.
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Affiliation(s)
- Samantha Bunner
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Kelsey Prince
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Karan Srikrishna
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Emily Marie Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | | | - Anna Kuklinski
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Olivia Jackson
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Pedro Pellegrino
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Shrushti Jagtap
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Imuetiyan Eweka
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Colman Lawlor
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Emma Eastin
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Griffin Yas
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Julianna Aiello
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Nathan LaPointe
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | | | - Jillian Hardy
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Jason Chen
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Anne Janssen
- School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Mary Packard
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Katherine Dorfman
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Luay Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Michael Seifu Bahiru
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
- Program in Neuroscience and Behavior, University of Massachusetts, Amherst, MA 01003, USA
| | - A. D. Stephens
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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4
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van Heerden D, Klima S, van den Bout I. How nuclear envelope dynamics can direct laminopathy phenotypes. Curr Opin Cell Biol 2024; 86:102290. [PMID: 38048657 DOI: 10.1016/j.ceb.2023.102290] [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: 06/30/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023]
Abstract
The nuclear envelope separates the genome from the cytoplasmic environment. However, the nuclear envelope is also physically associated with the genome and exerts influence on gene expression and genome modification. The nucleus is dynamic, changing shape and responding to cell movement, disassembling and assembling during cell division, and undergoing rupture and repair. These dynamics can be impacted by genetic disease, leading to a family of diseases called laminopathies. Their disparate phenotypes suggest that multiple processes are affected. We highlight three such processes here, which we believe can be used to classify most of the laminopathies. While much still needs to be learned, some commonalities between these processes, such as proteins involved in nuclear envelope formation and rupture repair, may drive a variety of laminopathies. Here we review the latest information regarding nuclear dynamics and its role in laminopathies related to mutations in the nuclear lamina and linker of nucleoskeleton and cytoskeleton complex (LINC) proteins.
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Affiliation(s)
- David van Heerden
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, South Africa; Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Stefanie Klima
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, South Africa; Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Iman van den Bout
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, South Africa; Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, South Africa.
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5
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Sobo JM, Alagna NS, Sun SX, Wilson KL, Reddy KL. Lamins: The backbone of the nucleocytoskeleton interface. Curr Opin Cell Biol 2024; 86:102313. [PMID: 38262116 DOI: 10.1016/j.ceb.2023.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024]
Abstract
The nuclear lamina (NL) is a crucial component of the inner nuclear membrane (INM) and consists of lamin filaments and associated proteins. Lamins are type V intermediate filament proteins essential for maintaining the integrity and mechanical properties of the nucleus. In human cells, 'B-type' lamins (lamin B1 and lamin B2) are ubiquitously expressed, while 'A-type' lamins (lamin A, lamin C, and minor isoforms) are expressed in a tissue- and development-specific manner. Lamins homopolymerize to form filaments that localize primarily near the INM, but A-type lamins also localize to and function in the nucleoplasm. Lamins play central roles in the assembly, structure, positioning, and mechanics of the nucleus, modulating cell signaling and influencing development, differentiation, and other activities. This review highlights recent findings on the structure and regulation of lamin filaments, providing insights into their multifaceted functions, including their role as "mechanosensors", delving into the emerging significance of lamin filaments as vital links between cytoskeletal and nuclear structures, chromatin organization, and the genome.
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Affiliation(s)
- Joan M Sobo
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Nicholas S Alagna
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sean X Sun
- Department of Mechanical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherine L Wilson
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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6
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Halfmann CT, Scott KL, Sears RM, Roux KJ. Mechanisms by which barrier-to-autointegration factor regulates dynamics of nucleocytoplasmic leakage and membrane repair following nuclear envelope rupture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572811. [PMID: 38187776 PMCID: PMC10769424 DOI: 10.1101/2023.12.21.572811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The nuclear envelope (NE) creates a barrier between the cytosol and nucleus during interphase that is key for cellular compartmentalization and protecting genomic DNA. NE rupture can expose genomic DNA to the cytosol and allow admixture of the nuclear and cytosolic constituents, a proposed mechanism of cancer and NE-associated diseases. Barrier-to-autointegration factor (BAF) is a DNA-binding protein that localizes to NE ruptures where it recruits LEM-domain proteins, A-type lamins, and participates in rupture repair. To further reveal the mechanisms by which BAF responds to and aids in repairing NE ruptures, we investigated known properties of BAF including LEM domain binding, lamin binding, compartmentalization, phosphoregulation of DNA binding, and BAF dimerization. We demonstrate that it is the cytosolic population of BAF that functionally repairs NE ruptures, and phosphoregulation of BAF's DNA-binding that enables its ability to facilitate that repair. Interestingly, BAF's LEM or lamin binding activity appears dispensable for its role in functional repair. Furthermore, we demonstrate that BAF functions to reduce the extent of leakage though NE ruptures, suggesting that BAF effectively forms a diffusion barrier prior to NE repair. Collectively, these results enhances our knowledge of the mechanisms by which BAF responds to NE ruptures and facilitates their repair.
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Affiliation(s)
| | - Kelsey L. Scott
- Enabling Technologies Group, Sanford Research, Sioux Falls SD
| | - Rhiannon M. Sears
- Enabling Technologies Group, Sanford Research, Sioux Falls SD
- Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD
| | - Kyle J. Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls SD
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls SD
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7
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Yao X, Xu X, Hu K, Yang Z, Deng S. BANF1 promotes glutamate-induced apoptosis of HT-22 hippocampal neurons. Mol Biol Rep 2023; 50:9441-9452. [PMID: 37838622 DOI: 10.1007/s11033-023-08889-1] [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: 04/13/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Glutamate exposure was fatal to HT-22 neuronal cells that derived from mouse hippocampus. This is often used as a model for hippocampus neurodegeneration in vitro. The targets relevant to glutamate-induced neuronal toxicity is not fully understood. In this study, we aimed to identify crucial factors associated with glutamate-induced cytotoxicity in HT-22 cells. METHODS HT-22 cells were treated with 7.5 mM glutamate for 24 h and isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis conducted to identify the differentially expressed proteins. Differential proteins were subjected to Gene Ontology analyses. Upregulation of barrier to autointegration factor (BANF1/BANF1) protein was confirmed by RT-qPCR and western blotting. Cell viability was measured by CKK-8 and MTT assays. Cell apoptosis rates and intracellular reactive oxygen species (ROS) levels were detected using flow cytometry. RESULTS A total of 5811 proteins were quantified by iTRAQ, 50 of which were recognized as significantly differential proteins (fold change ≥ 1.5 and P ≤ 0.05); 26 proteins were up-regulated and 24 were down-regulated after exposure to glutamate. GO enrichment analysis showed that the apoptotic signaling pathway was involved in cell death induced by glutamate. BANF1 expression level was markedly increased in HT-22 cells after glutamate treatment. Further, knockdown of BANF1 alleviated glutamate-mediated cell death with lower ROS levels. CONCLUSIONS In conclusion, we successfully filtered out differential proteins relevant to glutamate-mediated cytotoxicity. BANF1 upregulation promoted glutamate-induced apoptosis of HT-22 cells by enhancing ROS generation.
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Affiliation(s)
- Xinyu Yao
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Xiaoyi Xu
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, Guangdong, China
| | - Kunhua Hu
- Proteomics Research Center, Sun Yat-Sen Medical College of Sun Yat-Sen University, Guangzhou, 510080, China
| | - Zhaoshou Yang
- The First Affiliated Hospital/School of Clinical Medicine of Guangdong Pharmaceutical University, Guangdong Pharmaceutical University, Guangzhou, 510080, China.
| | - Shaodong Deng
- The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan, 523710, Guangdong, China.
- Scientific Research Platform, The Second Clinical Medical College, Guangdong Medical University, Dongguan, 523808, China.
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8
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Bastianello G, Foiani M. Mechanisms controlling the mechanical properties of the nuclei. Curr Opin Cell Biol 2023; 84:102222. [PMID: 37619290 DOI: 10.1016/j.ceb.2023.102222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/26/2023]
Abstract
The mechanical properties of the nucleus influence different cellular and nuclear functions and have relevant implications for several human diseases. The nucleus protects genetic information while acting as a mechano-sensory hub in response to internal and external forces. Cells have evolved mechano-transduction signaling to respond to physical cellular and nuclear perturbations and adopted a multitude of molecular pathways to maintain nuclear shape stability and prevent morphological abnormalities of the nucleus. Here we describe those key biological processes that control nuclear mechanics and discuss emerging perspectives on the mechanobiology of the nucleus as a diagnostic tool and clinical target.
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Affiliation(s)
- Giulia Bastianello
- IFOM, The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Oncology and Haemato-Oncology Department, University of Milan, Milan 20122, Italy.
| | - Marco Foiani
- IFOM, The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Oncology and Haemato-Oncology Department, University of Milan, Milan 20122, Italy.
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9
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A De Novo Sequence Variant in Barrier-to-Autointegration Factor Is Associated with Dominant Motor Neuronopathy. Cells 2023; 12:cells12060847. [PMID: 36980188 PMCID: PMC10099716 DOI: 10.3390/cells12060847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/12/2023] Open
Abstract
Barrier-to-autointegration factor (BAF) is an essential component of the nuclear lamina. Encoded by BANF1, this DNA binding protein contributes to the regulation of gene expression, cell cycle progression, and nuclear integrity. A rare recessive BAF variant, Ala12Thr, causes the premature aging syndrome, Néstor–Guillermo progeria syndrome (NGPS). Here, we report the first dominant pathogenic BAF variant, Gly16Arg, identified in a patient presenting with progressive neuromuscular weakness. Although disease variants carry nearby amino acid substitutions, cellular and biochemical properties are distinct. In contrast to NGPS, Gly16Arg patient fibroblasts show modest changes in nuclear lamina structure and increases in repressive marks associated with heterochromatin. Structural studies reveal that the Gly16Arg substitution introduces a salt bridge between BAF monomers, reducing the conformation ensemble available to BAF. We show that this structural change increases the double-stranded DNA binding affinity of BAF Gly16Arg. Together, our findings suggest that BAF Gly16Arg has an increased chromatin occupancy that leads to epigenetic changes and impacts nuclear functions. These observations provide a new example of how a missense mutation can change a protein conformational equilibrium to cause a dominant disease and extend our understanding of mechanisms by which BAF function impacts human health.
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10
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Duan T, Thyagarajan S, Amoiroglou A, Rogers GC, Geyer PK. Analysis of a rare progeria variant of Barrier-to-autointegration factor in Drosophila connects centromere function to tissue homeostasis. Cell Mol Life Sci 2023; 80:73. [PMID: 36842139 PMCID: PMC9968693 DOI: 10.1007/s00018-023-04721-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/27/2023]
Abstract
Barrier-to-autointegration factor (BAF/BANF) is a nuclear lamina protein essential for nuclear integrity, chromatin structure, and genome stability. Whereas complete loss of BAF causes lethality in multiple organisms, the A12T missense mutation of the BANF1 gene in humans causes a premature aging syndrome, called Néstor-Guillermo Progeria Syndrome (NGPS). Here, we report the first in vivo animal investigation of progeroid BAF, using CRISPR editing to introduce the NGPS mutation into the endogenous Drosophila baf gene. Progeroid BAF adults are born at expected frequencies, demonstrating that this BAF variant retains some function. However, tissue homeostasis is affected, supported by studies of the ovary, a tissue that depends upon BAF for stem cell survival and continuous oocyte production. We find that progeroid BAF causes defects in germline stem cell mitosis that delay anaphase progression and compromise chromosome segregation. We link these defects to decreased recruitment of centromeric proteins of the kinetochore, indicating dysfunction of cenBAF, a localized pool of dephosphorylated BAF produced by Protein Phosphatase PP4. We show that DNA damage increases in progenitor germ cells, which causes germ cell death due to activation of the DNA damage transducer kinase Chk2. Mitotic defects appear widespread, as aberrant chromosome segregation and increased apoptosis occur in another tissue. Together, these data highlight the importance of BAF in establishing centromeric structures critical for mitosis. Further, these studies link defects in cenBAF function to activation of a checkpoint that depletes progenitor reserves critical for tissue homeostasis, aligning with phenotypes of NGPS patients.
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Affiliation(s)
- Tingting Duan
- Department of Biochemistry and Molecular Biology, University of Iowa, 3135E MERF, Iowa City, IA, 52242, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Srikantha Thyagarajan
- Department of Biochemistry and Molecular Biology, University of Iowa, 3135E MERF, Iowa City, IA, 52242, USA
| | - Anastasia Amoiroglou
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Gregory C Rogers
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Pamela K Geyer
- Department of Biochemistry and Molecular Biology, University of Iowa, 3135E MERF, Iowa City, IA, 52242, USA.
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11
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The Conformation of the Intrinsically Disordered N-Terminal Region of Barrier-to-Autointegration Factor (BAF) is Regulated by pH and Phosphorylation. J Mol Biol 2023; 435:167888. [PMID: 36402223 DOI: 10.1016/j.jmb.2022.167888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022]
Abstract
Barrier-to-Autointegration Factor (BAF) is a highly conserved DNA binding protein important for genome integrity. Its localization and function are regulated through phosphorylation. Previously reported structures of BAF suggested that it is fully ordered, but our recent NMR analysis revealed that its N-terminal region is flexible in solution and that S4/T3 di-phosphorylation by VRK1 reduces this flexibility. Here, molecular dynamics (MD) simulation was used to unveil the conformational ensembles accessible to the N-terminal region of BAF either unphosphorylated, mono-phosphorylated on S4 or di-phosphorylated on S4/T3 (pBAF) and to reveal the interactions that contribute to define these ensembles. We show that the intrinsic flexibility observed in the N-terminal region of BAF is reduced by S4 phosphorylation and to a larger extent by S4/T3 di-phosphorylation. Thanks to the atomic description offered by MD supported by the NMR study of several BAF mutants, we identified the dynamic network of salt bridge interactions responsible for the conformational restriction involving pS4 and pT3 with residues located in helix α1 and α6. Using MD, we showed that the flexibility in the N-terminal region of BAF depends on the ionic strength and on the pH. We show that the presence of two negative charges of the phosphoryl groups is required for a substantial decrease in flexibility in pBAF. Using MD supported by NMR, we also showed that H7 deprotonation reduces the flexibility in the N-terminal region of BAF. Thus, the conformation of the intrinsically disordered N-terminal region of BAF is highly tunable, likely related to its diverse functions.
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