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Lazarte J, Jurgens SJ, Choi SH, Khurshid S, Morrill VN, Weng LC, Nauffal V, Pirruccello JP, Halford JL, Hegele RA, Ellinor PT, Lunetta KL, Lubitz SA. LMNA Variants and Risk of Adult-Onset Cardiac Disease. J Am Coll Cardiol 2022; 80:50-59. [PMID: 35772917 PMCID: PMC11071053 DOI: 10.1016/j.jacc.2022.04.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Genetic variants in LMNA may cause cardiac disease, but population-level contributions of variants to cardiac disease burden are not well-characterized. OBJECTIVES We sought to determine the frequency and contribution of rare LMNA variants to cardiomyopathy and arrhythmia risk among ambulatory adults. METHODS We included 185,990 UK Biobank participants with whole-exome sequencing. We annotated rare loss-of-function and missense LMNA variants for functional effect using 30 in silico prediction tools. We assigned a predicted functional effect weight to each variant and calculated a score for each carrier. We tested associations between the LMNA score and arrhythmia (atrial fibrillation, bradyarrhythmia, ventricular arrhythmia) or cardiomyopathy outcomes (dilated cardiomyopathy and heart failure). We also examined associations for variants located upstream vs downstream of the nuclear localization signal. RESULTS Overall, 1,167 (0.63%) participants carried an LMNA variant and 15,079 (8.11%) had an arrhythmia or cardiomyopathy event during a median follow-up of 10.9 years. The LMNA score was associated with arrhythmia or cardiomyopathy (OR: 2.21; P < 0.001) and the association was more significant when restricted to variants upstream of the nuclear localization signal (OR: 5.05; P < 0.001). The incidence rate of arrhythmia or cardiomyopathy was 8.43 per 1,000 person-years (95% CI: 6.73-10.12 per 1,000 person-years) among LMNA variant carriers and 6.38 per 1,000 person-years (95% CI: 6.27-6.50 per 1,000 person-years) among noncarriers. Only 3 (1.2%) of the variants were reported as pathogenic in ClinVar. CONCLUSIONS Middle-aged adult carriers of rare missense or loss-of-function LMNA variants are at increased risk for arrhythmia and cardiomyopathy.
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Affiliation(s)
- Julieta Lazarte
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada. https://twitter.com/Juliet_Lazarte
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shaan Khurshid
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Valerie N Morrill
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lu-Chen Weng
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Victor Nauffal
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Cardiovascular Medicine Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - James P Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jennifer L Halford
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Robert A Hegele
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kathryn L Lunetta
- National Heart, Lung, and Blood Institute and Boston University's Framingham Heart Study, Framingham, Massachusetts, USA; Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Steven A Lubitz
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, Massachusetts, USA.
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2
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Sebestyén E, Marullo F, Lucini F, Petrini C, Bianchi A, Valsoni S, Olivieri I, Antonelli L, Gregoretti F, Oliva G, Ferrari F, Lanzuolo C. SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome. Nat Commun 2020; 11:6274. [PMID: 33293552 PMCID: PMC7722762 DOI: 10.1038/s41467-020-20048-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome is a genetic disease caused by an aberrant form of Lamin A resulting in chromatin structure disruption, in particular by interfering with lamina associated domains. Early molecular alterations involved in chromatin remodeling have not been identified thus far. Here, we present SAMMY-seq, a high-throughput sequencing-based method for genome-wide characterization of heterochromatin dynamics. Using SAMMY-seq, we detect early stage alterations of heterochromatin structure in progeria primary fibroblasts. These structural changes do not disrupt the distribution of H3K9me3 in early passage cells, thus suggesting that chromatin rearrangements precede H3K9me3 alterations described at later passages. On the other hand, we observe an interplay between changes in chromatin accessibility and Polycomb regulation, with site-specific H3K27me3 variations and transcriptional dysregulation of bivalent genes. We conclude that the correct assembly of lamina associated domains is functionally connected to the Polycomb repression and rapidly lost in early molecular events of progeria pathogenesis.
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Affiliation(s)
- Endre Sebestyén
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Fabrizia Marullo
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
| | - Federica Lucini
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | | | - Andrea Bianchi
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
- IRCCS Santa Lucia Foundation, Rome, Italy
| | - Sara Valsoni
- IRCCS Santa Lucia Foundation, Rome, Italy
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Ilaria Olivieri
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
| | - Laura Antonelli
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Francesco Gregoretti
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Gennaro Oliva
- Institute for High Performance Computing and Networking, National Research Council, Naples, Italy
| | - Francesco Ferrari
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.
- Institute of Molecular Genetics, National Research Council, Pavia, Italy.
| | - Chiara Lanzuolo
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.
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3
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Cejas RB, Garay YC, de la Fuente S, Lardone RD, Irazoqui FJ. Core 1 O-N-acetylgalactosamine (O-GalNAc) glycosylation in the human cell nucleus. Biol Chem 2020; 401:1041-1051. [PMID: 32297877 DOI: 10.1515/hsz-2019-0448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/07/2020] [Indexed: 11/15/2022]
Abstract
Glycosylation is a very frequent post-translational modification in proteins, and the initiation of O-N-acetylgalactosamine (O-GalNAc) glycosylation has been recently described on relevant nuclear proteins. Here we evaluated the nuclear incorporation of a second sugar residue in the biosynthesis pathway of O-GalNAc glycans to yield the terminal core 1 glycan (C1G, Galβ3GalNAcαSer/Thr). Using confocal microscopy, enzymatic assay, affinity chromatography, and mass spectrometry, we analyzed intact cells, purified nuclei and soluble nucleoplasms to identify the essential factors for C1G biosynthesis in the cell nucleus. The enzyme C1GalT1 responsible for C1G synthesis was detected inside the nucleus, while catalytic activity of C1Gal-transferase was present in nucleoplasm and purified nuclei. In addition, C1G were detected in the nucleus inside of intact cells, and nuclear proteins exposing C1G were also identified. These evidences represent the first demonstration of core 1 O-GalNAc glycosylation of proteins in the human cell nucleus. These findings reveal a novel post-translational modification on nuclear proteins, with relevant repercussion in epigenetic and chemical biology areas.
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Affiliation(s)
- Romina B Cejas
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Yohana C Garay
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Sofia de la Fuente
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Ricardo D Lardone
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Fernando J Irazoqui
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
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4
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Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions. Cells 2020; 9:cells9071633. [PMID: 32645958 PMCID: PMC7407374 DOI: 10.3390/cells9071633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022] Open
Abstract
The molecular architecture and assembly mechanism of intermediate filaments have been enigmatic for decades. Among those, lamin filaments are of particular interest due to their universal role in cell nucleus and numerous disease-related mutations. Filament assembly is driven by specific interactions of the elementary dimers, which consist of the central coiled-coil rod domain flanked by non-helical head and tail domains. We aimed to investigate the longitudinal 'head-to-tail' interaction of lamin dimers (the so-called ACN interaction), which is crucial for filament assembly. To this end, we prepared a series of recombinant fragments of human lamin A centred around the N- and C-termini of the rod. The fragments were stabilized by fusions to heterologous capping motifs which provide for a correct formation of parallel, in-register coiled-coil dimers. As a result, we established crystal structures of two N-terminal fragments one of which highlights the propensity of the coiled-coil to open up, and one C-terminal rod fragment. Additional studies highlighted the capacity of such N- and C-terminal fragments to form specific complexes in solution, which were further characterized using chemical cross-linking. These data yielded a molecular model of the ACN complex which features a 6.5 nm overlap of the rod ends.
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5
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Sankaran JS, Sen B, Dudakovic A, Paradise CR, Perdue T, Xie Z, McGrath C, Styner M, Newberg J, Uzer G, van Wijnen AJ, Rubin J. Knockdown of formin mDia2 alters lamin B1 levels and increases osteogenesis in stem cells. Stem Cells 2020; 38:102-117. [PMID: 31648392 PMCID: PMC6993926 DOI: 10.1002/stem.3098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/03/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023]
Abstract
Nuclear actin plays a critical role in mediating mesenchymal stem cell (MSC) fate commitment. In marrow-derived MSCs, the principal diaphanous-related formin Diaph3 (mDia2) is present in the nucleus and regulates intranuclear actin polymerization, whereas Diaph1 (mDia1) is localized to the cytoplasm and controls cytoplasmic actin polymerization. We here show that mDia2 can be used as a tool to query actin-lamin nucleoskeletal structure. Silencing mDia2 affected the nucleoskeletal lamin scaffold, altering nuclear morphology without affecting cytoplasmic actin cytoskeleton, and promoted MSC differentiation. Attempting to target intranuclear actin polymerization by silencing mDia2 led to a profound loss in lamin B1 nuclear envelope structure and integrity, increased nuclear height, and reduced nuclear stiffness without compensatory changes in other actin nucleation factors. Loss of mDia2 with the associated loss in lamin B1 promoted Runx2 transcription and robust osteogenic differentiation and suppressed adipogenic differentiation. Hence, mDia2 is a potent tool to query intranuclear actin-lamin nucleoskeletal structure, and its presence serves to retain multipotent stromal cells in an undifferentiated state.
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Affiliation(s)
- Jeyantt S. Sankaran
- Department of Medicine, University of North Carolina Chapel
Hill, Chapel Hill, North Carolina
| | - Buer Sen
- Department of Medicine, University of North Carolina Chapel
Hill, Chapel Hill, North Carolina
| | - Amel Dudakovic
- Department of Orthopedic Surgery and Biochemistry and
Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Christopher R. Paradise
- Graduate School of Biomedical Sciences and Center for
Regenerative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Tony Perdue
- Department of Biology, University of North Carolina Chapel
Hill, Chapel Hill, North Carolina
| | - Zhihui Xie
- Department of Medicine, University of North Carolina Chapel
Hill, Chapel Hill, North Carolina
| | - Cody McGrath
- Department of Medicine, University of North Carolina Chapel
Hill, Chapel Hill, North Carolina
| | - Maya Styner
- Department of Medicine, University of North Carolina Chapel
Hill, Chapel Hill, North Carolina
| | - Joshua Newberg
- Department of Mechanical and Biomedical Engineering, Boise
State University, Boise, Idaho
| | - Gunes Uzer
- Department of Mechanical and Biomedical Engineering, Boise
State University, Boise, Idaho
| | - Andre J. van Wijnen
- Department of Orthopedic Surgery and Biochemistry and
Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Janet Rubin
- Department of Medicine, University of North Carolina Chapel
Hill, Chapel Hill, North Carolina
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6
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Briand N, Collas P. Laminopathy-causing lamin A mutations reconfigure lamina-associated domains and local spatial chromatin conformation. Nucleus 2019. [PMID: 29517398 PMCID: PMC5973257 DOI: 10.1080/19491034.2018.1449498] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The nuclear lamina contributes to the regulation of gene expression and to chromatin organization. Mutations in A-type nuclear lamins cause laminopathies, some of which are associated with a loss of heterochromatin at the nuclear periphery. Until recently however, little if any information has been provided on where and how lamin A interacts with the genome and on how disease-causing lamin A mutations may rearrange genome conformation. Here, we review aspects of nuclear lamin association with the genome. We highlight recent evidence of reorganization of lamin A-chromatin interactions in cellular models of laminopathies, and implications on the 3-dimensional rearrangement of chromatin in these models, including patient cells. We discuss how a hot-spot lipodystrophic lamin A mutation alters chromatin conformation and epigenetic patterns at an anti-adipogenic locus, and conclude with remarks on links between lamin A, Polycomb and the pathophysiology of laminopathies. The recent findings presented here collectively argue towards a deregulation of large-scale and local spatial genome organization by a subset of lamin A mutations causing laminopathies.
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Affiliation(s)
- Nolwenn Briand
- a Department of Molecular Medicine , Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo , Norway
| | - Philippe Collas
- a Department of Molecular Medicine , Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo , Oslo , Norway.,b Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine , Oslo University Hospital , Oslo , Norway
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7
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Bianchi A, Manti PG, Lucini F, Lanzuolo C. Mechanotransduction, nuclear architecture and epigenetics in Emery Dreifuss Muscular Dystrophy: tous pour un, un pour tous. Nucleus 2019; 9:276-290. [PMID: 29619865 PMCID: PMC5973142 DOI: 10.1080/19491034.2018.1460044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The alteration of the several roles that Lamin A/C plays in the mammalian cell leads to a broad spectrum of pathologies that – all together – are named laminopathies. Among those, the Emery Dreifuss Muscular Dystrophy (EDMD) is of particular interest as, despite the several known mutations of Lamin A/C, the genotype–phenotype correlation still remains poorly understood; this suggests that the epigenetic background of patients might play an important role during the time course of the disease. Historically, both a mechanical role of Lamin A/C and a regulative one have been suggested as the driving force of laminopathies; however, those two hypotheses are not mutually exclusive. Recent scientific evidence shows that Lamin A/C sustains the correct gene expression at the epigenetic level thanks to the Lamina Associated Domains (LADs) reorganization and the crosstalk with the Polycomb Group of Proteins (PcG). Furthermore, the PcG-dependent histone mark H3K27me3 increases under mechanical stress, finally pointing out the link between the mechano-properties of the nuclear lamina and epigenetics. Here, we summarize the emerging mechanisms that could explain the high variability seen in Emery Dreifuss muscular dystrophy.
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Affiliation(s)
- Andrea Bianchi
- a CNR Institute of Cell Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia , Rome , Italy.,b Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy
| | | | - Federica Lucini
- b Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy
| | - Chiara Lanzuolo
- a CNR Institute of Cell Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia , Rome , Italy.,b Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy.,c Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia , Rome , Italy
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8
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Salvarani N, Crasto S, Miragoli M, Bertero A, Paulis M, Kunderfranco P, Serio S, Forni A, Lucarelli C, Dal Ferro M, Larcher V, Sinagra G, Vezzoni P, Murry CE, Faggian G, Condorelli G, Di Pasquale E. The K219T-Lamin mutation induces conduction defects through epigenetic inhibition of SCN5A in human cardiac laminopathy. Nat Commun 2019; 10:2267. [PMID: 31118417 PMCID: PMC6531493 DOI: 10.1038/s41467-019-09929-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 04/06/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in LMNA, which encodes the nuclear proteins Lamin A/C, can cause cardiomyopathy and conduction disorders. Here, we employ induced pluripotent stem cells (iPSCs) generated from human cells carrying heterozygous K219T mutation on LMNA to develop a disease model. Cardiomyocytes differentiated from these iPSCs, and which thus carry K219T-LMNA, have altered action potential, reduced peak sodium current and diminished conduction velocity. Moreover, they have significantly downregulated Nav1.5 channel expression and increased binding of Lamin A/C to the promoter of SCN5A, the channel's gene. Coherently, binding of the Polycomb Repressive Complex 2 (PRC2) protein SUZ12 and deposition of the repressive histone mark H3K27me3 are increased at SCN5A. CRISPR/Cas9-mediated correction of the mutation re-establishes sodium current density and SCN5A expression. Thus, K219T-LMNA cooperates with PRC2 in downregulating SCN5A, leading to decreased sodium current density and slower conduction velocity. This mechanism may underlie the conduction abnormalities associated with LMNA-cardiomyopathy.
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Affiliation(s)
- Nicolò Salvarani
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Silvia Crasto
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Michele Miragoli
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
- Department of Medicine and Surgery, University of Parma, Parma, 43121, Italy
| | - Alessandro Bertero
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, 98109, WA, USA
| | - Marianna Paulis
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Paolo Kunderfranco
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Simone Serio
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Alberto Forni
- Division of Cardiac Surgery, University of Verona, Verona, 37129, Italy
| | - Carla Lucarelli
- Division of Cardiac Surgery, University of Verona, Verona, 37129, Italy
| | - Matteo Dal Ferro
- Cardiovascular Department, "Ospedali Riuniti" and University of Trieste, Trieste, 34129, Italy
| | - Veronica Larcher
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Gianfranco Sinagra
- Cardiovascular Department, "Ospedali Riuniti" and University of Trieste, Trieste, 34129, Italy
| | - Paolo Vezzoni
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, 98109, WA, USA
| | - Giuseppe Faggian
- Division of Cardiac Surgery, University of Verona, Verona, 37129, Italy
| | - Gianluigi Condorelli
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy.
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy.
- Humanitas University, Rozzano (MI), 20089, Italy.
| | - Elisa Di Pasquale
- Institute of Genetic and Biomedical Research (IRGB), UOS of Milan, National Research Council of Italy, Milan, 20138, Italy.
- Department of Cardiovascular Medicine and Laboratory of Medical Biotechnology, Humanitas Clinical and Research Center - IRCCS, Rozzano (MI), 20089, Italy.
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9
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Cejas RB, Lorenz V, Garay YC, Irazoqui FJ. Biosynthesis of O-N-acetylgalactosamine glycans in the human cell nucleus. J Biol Chem 2019; 294:2997-3011. [PMID: 30591584 PMCID: PMC6398145 DOI: 10.1074/jbc.ra118.005524] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/20/2018] [Indexed: 12/16/2022] Open
Abstract
Biological functions of nuclear proteins are regulated by post-translational modifications (PTMs) that modulate gene expression and cellular physiology. However, the role of O-linked glycosylation (O-GalNAc) as a PTM of nuclear proteins in the human cell has not been previously reported. Here, we examined in detail the initiation of O-GalNAc glycan biosynthesis, representing a novel PTM of nuclear proteins in the nucleus of human cells, with an emphasis on HeLa cells. Using soluble nuclear fractions from purified nuclei, enzymatic assays, fluorescence microscopy, affinity chromatography, MS, and FRET analyses, we identified all factors required for biosynthesis of O-GalNAc glycans in nuclei: the donor substrate (UDP-GalNAc), nuclear polypeptide GalNAc -transferase activity, and a GalNAc transferase (polypeptide GalNAc-T3). Moreover, we identified O-GalNAc glycosylated proteins in the nucleus and present solid evidence for O-GalNAc glycan synthesis in this organelle. The demonstration of O-GalNAc glycosylation of nuclear proteins in mammalian cells reported here has important implications for cell and chemical biology.
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Affiliation(s)
- Romina B Cejas
- From the Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Virginia Lorenz
- From the Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Yohana C Garay
- From the Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Fernando J Irazoqui
- From the Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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10
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Ho R, Hegele RA. Complex effects of laminopathy mutations on nuclear structure and function. Clin Genet 2018; 95:199-209. [DOI: 10.1111/cge.13455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Rosettia Ho
- Departments of Biochemistry and Medicine, and Robarts Research Institute; Schulich School of Medicine and Dentistry, Western University; London Ontario Canada
| | - Robert A. Hegele
- Departments of Biochemistry and Medicine, and Robarts Research Institute; Schulich School of Medicine and Dentistry, Western University; London Ontario Canada
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11
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Stover PJ, James WPT, Krook A, Garza C. Emerging concepts on the role of epigenetics in the relationships between nutrition and health. J Intern Med 2018; 284:37-49. [PMID: 29706028 DOI: 10.1111/joim.12768] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the physiological and metabolic underpinnings that confer individual differences in responses to diet and diet-related chronic disease is essential to advance the field of nutrition. This includes elucidating the differences in gene expression that are mediated through programming of the genome through epigenetic chromatin modifications. Epigenetic landscapes are influenced by age, genetics, toxins and other environmental factors, including dietary exposures and nutritional status. Epigenetic modifications influence transcription and genome stability are established during development with life-long consequences. They can be inherited from one generation to the next. The covalent modifications of chromatin, which include methylation and acetylation, on DNA nucleotide bases, histone proteins and RNA are derived from intermediates of one-carbon metabolism and central metabolism. They influence key physiological processes throughout life, and together with inherited DNA primary sequence, contribute to responsiveness to environmental stresses, diet and risk for age-related chronic disease. Revealing diet-epigenetic relationships has the potential to transform nutrition science by increasing our fundamental understanding of: (i) the role of nutrients in biological systems, (ii) the resilience of living organisms in responding to environmental perturbations, and (iii) the development of dietary patterns that programme physiology for life-long health. Epigenetics may also enable the classification of individuals with chronic disease for specific dietary management and/or for efficacious diet-pharmaceutical combination therapies. These new emerging concepts at the interface of nutrition and epigenetics were discussed, and future research needs identified by leading experts at the 26th Marabou Symposium entitled 'Nutrition, Epigenetics, Genetics: Impact on Health and Disease'. For a compilation of the general discussion at the marabou symposium, click here http://www.marabousymposium.org/.
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Affiliation(s)
- P J Stover
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - W P T James
- Department of Population Health, Nutrition Group, London School of Hygiene and Tropical Medicine, London, UK
| | - A Krook
- Department of Physiology and Pharmacology, Section for Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - C Garza
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
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12
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Qin L, Jiang X, Dong Z, Huang J, Chen X. Identification of two integration sites in favor of transgene expression in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:142. [PMID: 29796083 PMCID: PMC5956788 DOI: 10.1186/s13068-018-1139-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/02/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND The ascomycete fungus Trichoderma reesei was widely used as a biotechnological workhorse for production of cellulases and recombinant proteins due to its large capacity of protein secretion. Transgenesis by random integration of a gene of interest (GOI) into the genome of T. reesei can generate series of strains that express different levels of the indicated transgene. The insertion site of the GOI plays an important role in the ultimate production of the targeted proteins. However, so far no systematic studies have been made to identify transgene integration loci for optimal expression of the GOI in T. reesei. Currently, only the locus of exocellobiohydrolases I encoding gene (cbh1) is widely used as a promising integration site to lead to high expression level of the GOI. No additional sites associated with efficient gene expression have been characterized. RESULTS To search for gene integration sites that benefit for the secreted expression of GOI, the food-and-mouth disease virus 2A protein was applied for co-expression of an Aspergillus niger lipA gene and Discosoma sp. DsRed1 gene in T. reesei, by random integration of the expression cassette into the genome. We demonstrated that the fluorescent intensity of RFP (red fluorescent protein) inside of the cell was well correlated with the secreted lipase yields, based on which, we successfully developed a high-throughput screening method to screen strains with relatively higher secreted expression of the GOI (in this study, lipase). The copy number and the insertion sites of the transgene were investigated among the selected highly expressed strains. Eventually, in addition to cbh1 gene locus, two other genome insertion loci that efficiently facilitate gene expression in T. reesei were identified. CONCLUSIONS We have successfully developed a high-throughput screening method to screen strains with optimal expression of the indicated secreted proteins in T. reesei. Moreover, we identified two optimal genome loci for transgene expression, which could provide new approach to modulate gene expression levels while retaining the indicated promoter and culture conditions.
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Affiliation(s)
- Lina Qin
- National and Local Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Qishan Campus, No.1 Keji Road, Shangjie, Minhou, Fuzhou, 350117 Fujian China
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117 Fujian China
| | - Xianzhang Jiang
- National and Local Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Qishan Campus, No.1 Keji Road, Shangjie, Minhou, Fuzhou, 350117 Fujian China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jianzhong Huang
- National and Local Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Qishan Campus, No.1 Keji Road, Shangjie, Minhou, Fuzhou, 350117 Fujian China
| | - Xiuzhen Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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13
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Abstract
Chrom3D is a computational platform for 3D genome modeling that simulates the spatial positioning of chromosome domains relative to each other and relative to the nuclear periphery. In Chrom3D, chromosomes are modeled as chains of contiguous beads, in which each bead represents a genomic domain. In this protocol, a bead represents a topologically associated domain (TAD) mapped from ensemble Hi-C data. Chrom3D takes as input data significant pairwise TAD-TAD interactions determined from a Hi-C contact matrix, and TAD interactions with the nuclear periphery, determined by ChIP-sequencing of nuclear lamins to define lamina-associated domains (LADs). Chrom3D is based on Monte Carlo simulations initiated from a starting random bead configuration. During the optimization process, TAD-TAD interactions constrain bead positions relative to each other, whereas LAD information constrains the corresponding bead toward the nuclear periphery. Optimization can be repeated many times to generate an ensemble of 3D genome models. Analyses of the models enable estimations of the radial positioning of genomic sites in the nucleus across cells in a population. Chrom3D provides opportunities to reveal spatial relationships between TADs and LADs. More generally, predictions from Chrom3D models can be experimentally tested in the laboratory. We describe the entire Chrom3D protocol for modeling a 3D diploid human genome, from the creation of input files to the final rendering of 3D genome structures. The procedure takes ∼18 h. Chrom3D is freely available on GitHub.
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14
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Spitalieri P, Talarico RV, Caioli S, Murdocca M, Serafino A, Girasole M, Dinarelli S, Longo G, Pucci S, Botta A, Novelli G, Zona C, Mango R, Sangiuolo F. Modelling the pathogenesis of Myotonic Dystrophy type 1 cardiac phenotype through human iPSC-derived cardiomyocytes. J Mol Cell Cardiol 2018; 118:95-109. [PMID: 29551391 DOI: 10.1016/j.yjmcc.2018.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 12/20/2022]
Abstract
Myotonic Dystrophy type 1 (DM1) is a multisystemic disease, autosomal dominant, caused by a CTG repeat expansion in DMPK gene. We assessed the appropriateness of patient-specific induced pluripotent stem cell-derived cardiomyocytes (CMs) as a model to recapitulate some aspects of the pathogenetic mechanism involving cardiac manifestations in DM1 patients. Once obtained in vitro, CMs have been characterized for their morphology and their functionality. CMs DM1 show intranuclear foci and transcript markers abnormally spliced respect to WT ones, as well as several irregularities in nuclear morphology, probably caused by an unbalanced lamin A/C ratio. Electrophysiological characterization evidences an abnormal profile only in CMs DM1 such that the administration of antiarrythmic drugs to these cells highlights even more the functional defect linked to the disease. Finally, Atomic Force Measurements reveal differences in the biomechanical behaviour of CMs DM1, in terms of frequencies and synchronicity of the beats. Altogether the complex phenotype described in this work, strongly reproduces some aspects of the human DM1 cardiac phenotype. Therefore, the present study provides an in vitro model suggesting novel insights into the mechanisms leading to the development of arrhythmogenesis and dilatative cardiomyopathy to consider when approaching to DM1 patients, especially for the risk assessment of sudden cardiac death (SCD). These data could be also useful in identifying novel biomarkers effective in clinical settings and patient-tailored therapies.
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Affiliation(s)
- Paola Spitalieri
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Rosa V Talarico
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | | | - Michela Murdocca
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | | | | | | | | | - Sabina Pucci
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Annalisa Botta
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Giuseppe Novelli
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Cristina Zona
- I.R.C.C.S. S. Lucia, Rome, Italy; Dept of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Federica Sangiuolo
- Dept of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy.
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15
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Cicchillitti L, Manni I, Mancone C, Regazzo G, Spagnuolo M, Alonzi T, Carlomosti F, Dell'Anna ML, Dell'Omo G, Picardo M, Ciana P, Capogrossi MC, Tripodi M, Magenta A, Rizzo MG, Gurtner A, Piaggio G. The laminA/NF-Y protein complex reveals an unknown transcriptional mechanism on cell proliferation. Oncotarget 2018; 8:2628-2646. [PMID: 27793050 PMCID: PMC5356829 DOI: 10.18632/oncotarget.12914] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/10/2016] [Indexed: 12/02/2022] Open
Abstract
Lamin A is a component of the nuclear matrix that also controls proliferation by largely unknown mechanisms. NF-Y is a ubiquitous protein involved in cell proliferation composed of three subunits (-YA -YB -YC) all required for the DNA binding and transactivation activity. To get clues on new NF-Y partner(s) we performed a mass spectrometry screening of proteins that co-precipitate with the regulatory subunit of the complex, NF-YA. By this screening we identified lamin A as a novel putative NF-Y interactor. Co-immunoprecipitation experiments and confocal analysis confirmed the interaction between the two endogenous proteins. Interestingly, this association occurs on euchromatin regions, too. ChIP experiments demonstrate lamin A enrichment in several promoter regions of cell cycle related genes in a NF-Y dependent manner. Gain and loss of function experiments reveal that lamin A counteracts NF-Y transcriptional activity. Taking advantage of a recently generated transgenic reporter mouse, called MITO-Luc, in which an NF-Y–dependent promoter controls luciferase expression, we demonstrate that lamin A counteracts NF-Y transcriptional activity not only in culture cells but also in living animals. Altogether, our data demonstrate the occurrence of lamin A/NF-Y interaction and suggest a possible role of this protein complex in regulation of NF-Y function in cell proliferation.
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Affiliation(s)
- Lucia Cicchillitti
- Department of Research, Advanced Diagnostics and Technological Innovation, SAFU Unit, Translational Research Area, Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Isabella Manni
- Department of Research, Advanced Diagnostics and Technological Innovation, SAFU Unit, Translational Research Area, Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Carmine Mancone
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Department of Epidemiology and Preclinical Research, 00149 Rome, Italy.,Department of Cellular Biotechnologies and Haematology, Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy
| | - Giulia Regazzo
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, Regina Elena National Cancer Institute, Rome, Italy
| | - Manuela Spagnuolo
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, Regina Elena National Cancer Institute, Rome, Italy
| | - Tonino Alonzi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Department of Epidemiology and Preclinical Research, 00149 Rome, Italy
| | - Fabrizio Carlomosti
- Fondazione Luigi Maria Monti, Istituto Dermopatico dell'Immacolata-IRCCS, Laboratorio di Patologia Vascolare, 00167 Rome, Italy
| | - Maria Lucia Dell'Anna
- Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatologic Institute, IRCCS, 00144 Rome, Italy
| | - Giulia Dell'Omo
- Department of Oncology and Hemato-Oncology and Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
| | - Mauro Picardo
- Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatologic Institute, IRCCS, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Paolo Ciana
- Center of Excellence on Neurodegenerative Diseases, Department of Oncology and Hemato-Oncology, University of Milan, 20133 Milan, Italy
| | - Maurizio C Capogrossi
- Fondazione Luigi Maria Monti, Istituto Dermopatico dell'Immacolata-IRCCS, Laboratorio di Patologia Vascolare, Via dei Monti di Creta 104, Rome 00167, Italy Rome, Italy
| | - Marco Tripodi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Department of Epidemiology and Preclinical Research, 00149 Rome, Italy.,Department of Cellular Biotechnologies and Haematology, Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy
| | - Alessandra Magenta
- Fondazione Luigi Maria Monti, Istituto Dermopatico dell'Immacolata-IRCCS, Laboratorio di Patologia Vascolare, Via dei Monti di Creta 104, Rome 00167, Italy Rome, Italy
| | - Maria Giulia Rizzo
- Department of Research, Advanced Diagnostics and Technological Innovation, Genomic and Epigenetic Unit, Translational Research Area, Regina Elena National Cancer Institute, Rome, Italy
| | - Aymone Gurtner
- Department of Research, Advanced Diagnostics and Technological Innovation, SAFU Unit, Translational Research Area, Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Giulia Piaggio
- Department of Research, Advanced Diagnostics and Technological Innovation, SAFU Unit, Translational Research Area, Regina Elena National Cancer Institute, 00144 Rome, Italy
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16
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Schoen I, Aires L, Ries J, Vogel V. Nanoscale invaginations of the nuclear envelope: Shedding new light on wormholes with elusive function. Nucleus 2017; 8:506-514. [PMID: 28686487 DOI: 10.1080/19491034.2017.1337621] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Recent advances in fluorescence microscopy have opened up new possibilities to investigate chromosomal and nuclear 3D organization on the nanoscale. We here discuss their potential for elucidating topographical details of the nuclear lamina. Single molecule localization microscopy (SMLM) in combination with immunostainings of lamina proteins readily reveals tube-like invaginations with a diameter of 100-500 nm. Although these invaginations have been established as a frequent and general feature of interphase nuclei across different cell types, their formation mechanism and function have remained largely elusive. We critically review the current state of research, propose possible connections to lamina associated domains (LADs), and revisit the discussion about the potential role of these invaginations for accelerating mRNA nuclear export. Illustrative studies using 3D super-resolution imaging are shown and will be instrumental to decipher the physiological role of these nanoscale invaginations.
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Affiliation(s)
- Ingmar Schoen
- a ETH Zurich, Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology , Zurich , Switzerland
| | - Lina Aires
- a ETH Zurich, Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology , Zurich , Switzerland
| | - Jonas Ries
- b European Molecular Biology Laboratory, Cell Biology and Biophysics Unit , Heidelberg , Germany
| | - Viola Vogel
- a ETH Zurich, Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology , Zurich , Switzerland
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17
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Distinct Fiber Type Signature in Mouse Muscles Expressing a Mutant Lamin A Responsible for Congenital Muscular Dystrophy in a Patient. Cells 2017; 6:cells6020010. [PMID: 28441765 PMCID: PMC5492014 DOI: 10.3390/cells6020010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 01/21/2023] Open
Abstract
Specific mutations in LMNA, which encodes nuclear intermediate filament proteins lamins A/C, affect skeletal muscle tissues. Early-onset LMNA myopathies reveal different alterations of muscle fibers, including fiber type disproportion or prominent dystrophic and/or inflammatory changes. Recently, we identified the p.R388P LMNA mutation as responsible for congenital muscular dystrophy (L-CMD) and lipodystrophy. Here, we asked whether viral-mediated expression of mutant lamin A in murine skeletal muscles would be a pertinent model to reveal specific muscle alterations. We found that the total amount and size of muscle fibers as well as the extent of either inflammation or muscle regeneration were similar to wildtype or mutant lamin A. In contrast, the amount of fast oxidative muscle fibers containing myosin heavy chain IIA was lower upon expression of mutant lamin A, in correlation with lower expression of genes encoding transcription factors MEF2C and MyoD. These data validate this in vivo model for highlighting distinct muscle phenotypes associated with different lamin contexts. Additionally, the data suggest that alteration of muscle fiber type identity may contribute to the mechanisms underlying physiopathology of L-CMD related to R388P mutant lamin A.
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18
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Rohde M, Sievers E, Janzer A, Willmann D, Egert A, Schorle H, Schüle R, Kirfel J. Overexpression of histone demethylase Fbxl10 leads to enhanced migration in mouse embryonic fibroblasts. Exp Cell Res 2016; 348:123-131. [DOI: 10.1016/j.yexcr.2016.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 02/04/2023]
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19
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Landeen EL, Muirhead CA, Wright L, Meiklejohn CD, Presgraves DC. Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline. PLoS Biol 2016; 14:e1002499. [PMID: 27404402 PMCID: PMC4942098 DOI: 10.1371/journal.pbio.1002499] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower—approximately 3-fold or more—for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked genes in the male germline and its evolutionary consequences. Using transgenes and transpositions, we show that most endogenous X-linked genes, not just testis-specific ones, are transcriptionally suppressed several-fold specifically in the Drosophila male germline. In wild-type testes, this sex chromosome-wide transcriptional suppression is generally undetectable, being effectively compensated by the gene-by-gene evolutionary recruitment of strong promoters on the X chromosome. We identify and experimentally validate a promoter element sequence motif that is enriched upstream of the transcription start sites of hundreds of testis-expressed genes; evolutionarily conserved across species; associated with strong gene expression levels in testes; and overrepresented on the X chromosome. These findings show that the expression of X-linked genes in the Drosophila testes reflects a balance between chromosome-wide epigenetic transcriptional suppression and long-term compensatory adaptation by sex-linked genes. Our results have broad implications for the evolution of gene expression in the Drosophila male germline and for genome evolution. Expression of sex-linked genes in the Drosophila male germline reflects a balance between an X chromosome-wide transcriptional suppression and long-term, gene-wise evolutionary recruitment of strong, compensatory promoter elements. The evolution of different sex chromosomes (e.g., X and Y) has occurred many times in animals and plants. One consequence of having different chromosome copy numbers between the sexes (XY males and XX females) is the evolution of sex chromosome-specific regulation, both in the soma (i.e., X chromosome dosage compensation) and in the male germline (i.e., meiotic sex chromosome inactivation). Understanding how the X is regulated in the male germline has implications for gene expression, the evolution of sex chromosome-specific gene content, and speciation. Surprisingly, how the X chromosome is regulated in the Drosophila melanogaster male germline remains unclear. We have characterized X suppression, a novel form of X chromosome transcriptional regulation specific to the Drosophila male germline. Our results reveal that transcription of the X is suppressed 2- to 4-fold for endogenous genes. We show that the X chromosome has evolved strong testis-specific promoters via the gene-by-gene recruitment of sequence elements that counteract transcriptional suppression of the X chromosome. These findings reveal a novel form of X chromosome regulation and lead to a new model for the control of gene expression in the Drosophila male germline.
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Affiliation(s)
- Emily L. Landeen
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (ELL); (DCP)
| | - Christina A. Muirhead
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- The Ronin Institute, Montclair, New Jersey, United States of America
| | - Lori Wright
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Colin D. Meiklejohn
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Daven C. Presgraves
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (ELL); (DCP)
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20
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21
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Marullo F, Cesarini E, Antonelli L, Gregoretti F, Oliva G, Lanzuolo C. Nucleoplasmic Lamin A/C and Polycomb group of proteins: An evolutionarily conserved interplay. Nucleus 2016; 7:103-11. [PMID: 26930442 PMCID: PMC4916880 DOI: 10.1080/19491034.2016.1157675] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Nuclear lamins are the main components of the nuclear lamina at the nuclear periphery, providing mechanical support to the nucleus. However, recent findings suggest that lamins also reside in the nuclear interior, as a distinct and dynamic pool with critical roles in transcriptional regulation. In our work we found a functional and evolutionary conserved crosstalk between Lamin A/C and the Polycomb group (PcG) of proteins, this being required for the maintenance of the PcG repressive functions. Indeed, Lamin A/C knock-down causes PcG foci dispersion and defects in PcG-mediated higher order structures, thereby leading to impaired PcG mediated transcriptional repression. By using ad-hoc algorithms for image analysis and PLA approaches we hereby show that PcG proteins are preferentially located in the nuclear interior where they interact with nucleoplasmic Lamin A/C. Taken together, our findings suggest that nuclear components, such as Lamin A/C, functionally interact with epigenetic factors to ensure the correct transcriptional program maintenance.
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Affiliation(s)
- F Marullo
- a CNR Institute of Cell Biology and Neurobiology, IRCCS Santa Lucia Foundation , Rome , Italy
| | - E Cesarini
- a CNR Institute of Cell Biology and Neurobiology, IRCCS Santa Lucia Foundation , Rome , Italy
| | - L Antonelli
- b CNR Institute for High Performance Computing and Networking (ICAR) , Naples, Italy
| | - F Gregoretti
- b CNR Institute for High Performance Computing and Networking (ICAR) , Naples, Italy
| | - G Oliva
- b CNR Institute for High Performance Computing and Networking (ICAR) , Naples, Italy
| | - C Lanzuolo
- a CNR Institute of Cell Biology and Neurobiology, IRCCS Santa Lucia Foundation , Rome , Italy.,c Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi , Milan , Italy
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22
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Cesarini E, Mozzetta C, Marullo F, Gregoretti F, Gargiulo A, Columbaro M, Cortesi A, Antonelli L, Di Pelino S, Squarzoni S, Palacios D, Zippo A, Bodega B, Oliva G, Lanzuolo C. Lamin A/C sustains PcG protein architecture, maintaining transcriptional repression at target genes. J Cell Biol 2016; 211:533-51. [PMID: 26553927 PMCID: PMC4639869 DOI: 10.1083/jcb.201504035] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Reduction of lamin A/C, which is evolutionarily required for the modulation of Polycomb group (PcG) protein–dependent transcriptional repression by sustaining PcG protein nuclear architecture, leads to PcG protein diffusion and to muscle differentiation. Beyond its role in providing structure to the nuclear envelope, lamin A/C is involved in transcriptional regulation. However, its cross talk with epigenetic factors—and how this cross talk influences physiological processes—is still unexplored. Key epigenetic regulators of development and differentiation are the Polycomb group (PcG) of proteins, organized in the nucleus as microscopically visible foci. Here, we show that lamin A/C is evolutionarily required for correct PcG protein nuclear compartmentalization. Confocal microscopy supported by new algorithms for image analysis reveals that lamin A/C knock-down leads to PcG protein foci disassembly and PcG protein dispersion. This causes detachment from chromatin and defects in PcG protein–mediated higher-order structures, thereby leading to impaired PcG protein repressive functions. Using myogenic differentiation as a model, we found that reduced levels of lamin A/C at the onset of differentiation led to an anticipation of the myogenic program because of an alteration of PcG protein–mediated transcriptional repression. Collectively, our results indicate that lamin A/C can modulate transcription through the regulation of PcG protein epigenetic factors.
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Affiliation(s)
- Elisa Cesarini
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Chiara Mozzetta
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Fabrizia Marullo
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Francesco Gregoretti
- Consiglio Nazionale delle Ricerche Institute for High Performance Computing and Networking, 80131 Naples, Italy
| | - Annagiusi Gargiulo
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Marta Columbaro
- Struttura Complessa Laboratorio Biologia Cellulare Muscoloscheletrica, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Alice Cortesi
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Laura Antonelli
- Consiglio Nazionale delle Ricerche Institute for High Performance Computing and Networking, 80131 Naples, Italy
| | - Simona Di Pelino
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Stefano Squarzoni
- Struttura Complessa Laboratorio Biologia Cellulare Muscoloscheletrica, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy Consiglio Nazionale delle Ricerche Institute of Molecular Genetics, 40136 Bologna, Italy
| | - Daniela Palacios
- Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
| | - Alessio Zippo
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Beatrice Bodega
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Gennaro Oliva
- Consiglio Nazionale delle Ricerche Institute for High Performance Computing and Networking, 80131 Naples, Italy
| | - Chiara Lanzuolo
- Consiglio Nazionale delle Ricerche Institute of Cellular Biology and Neurobiology, Istituto di Ricovero e Cura a Carattere Scientifico Fondazione Santa Lucia, 00143 Rome, Italy
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23
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Mapping Nuclear Lamin-Genome Interactions by Chromatin Immunoprecipitation of Nuclear Lamins. Methods Mol Biol 2016; 1411:315-24. [PMID: 27147051 DOI: 10.1007/978-1-4939-3530-7_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The nuclear lamina is a meshwork of A- and B-type lamins which interact with chromatin and regulate many nuclear functions. Recent studies have reported the discovery of chromatin domains interacting with nuclear lamins by chromatin immunoprecipitation (ChIP) of lamin A/C or B1 and identification of the associated DNA sequences by microarray or high-throughput sequencing. ChIP has been used over many years to get a snapshot of interactions between DNA and proteins in cells, including modified histones, transcription factors, chromatin remodelers, and recently, structural proteins such as nuclear lamins. We describe here the procedure we have established in our laboratory for ChIP of lamin A/C and lamin B1 from human cultured cells. The protocol is compatible with polymerase chain reaction and high-throughput sequencing analysis of the co-immunoprecipitated DNA.
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24
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Zhang PY, Li G, Deng ZJ, Liu LY, Chen L, Tang JZ, Wang YQ, Cao ST, Fang YX, Wen F, Xu Y, Chen X, Shi KQ, Li WF, Xie C, Tang KF. Dicer interacts with SIRT7 and regulates H3K18 deacetylation in response to DNA damaging agents. Nucleic Acids Res 2015; 44:3629-42. [PMID: 26704979 PMCID: PMC4856966 DOI: 10.1093/nar/gkv1504] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 12/10/2015] [Indexed: 01/14/2023] Open
Abstract
Dicer participates in heterochromatin formation in fission yeast and plants. However, whether it has a similar role in mammals remains controversial. Here we showed that the human Dicer protein interacts with SIRT7, an NAD+-dependent H3K18Ac (acetylated lysine 18 of histone H3) deacetylase, and holds a proportion of SIRT7 in the cytoplasm. Dicer knockdown led to an increase of chromatin-associated SIRT7 and simultaneously a decrease of cytoplasmic SIRT7, while its overexpression induced SIRT7 reduction in the chromatin-associated fraction and increment in the cytoplasm. Furthermore, DNA damaging agents promoted Dicer expression, leading to decreased level of chromatin-associated SIRT7 and increased level of H3K18Ac, which can be alleviated by Dicer knockdown. Taken together with that H3K18Ac was exclusively associated with the chromatin, our findings suggest that Dicer induction by DNA damaging treatments prevents H3K18Ac deacetylation, probably by trapping more SIRT7 in the cytoplasm.
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Affiliation(s)
- Pei-Ying Zhang
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Cancer Center, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Guiling Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Zhu-Jun Deng
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Cancer Center, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Li-Yuan Liu
- Department of Infection and Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Li Chen
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Cancer Center, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Jun-Zhou Tang
- Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Yu-Qun Wang
- Department of Infection and Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Su-Ting Cao
- Department of Infection and Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Yu-Xiao Fang
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Cancer Center, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Fuping Wen
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Yunsheng Xu
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Department of Dermato-Venereology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Xiaoming Chen
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Department of Pediatric Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Ke-Qing Shi
- Department of Infection and Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Wen-Feng Li
- Department of Radiation Oncology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Congying Xie
- Department of Radiation Oncology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
| | - Kai-Fu Tang
- Institute of Translational Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Cancer Center, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325015, Zhejiang, P.R. China
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25
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Fitzgerald S, Dillon SC, Chao TC, Wiencko HL, Hokamp K, Cameron ADS, Dorman CJ. Re-engineering cellular physiology by rewiring high-level global regulatory genes. Sci Rep 2015; 5:17653. [PMID: 26631971 PMCID: PMC4668568 DOI: 10.1038/srep17653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023] Open
Abstract
Knowledge of global regulatory networks has been exploited to rewire the gene control programmes of the model bacterium Salmonella enterica serovar Typhimurium. The product is an organism with competitive fitness that is superior to that of the wild type but tuneable under specific growth conditions. The paralogous hns and stpA global regulatory genes are located in distinct regions of the chromosome and control hundreds of target genes, many of which contribute to stress resistance. The locations of the hns and stpA open reading frames were exchanged reciprocally, each acquiring the transcription control signals of the other. The new strain had none of the compensatory mutations normally associated with alterations to hns expression in Salmonella; instead it displayed rescheduled expression of the stress and stationary phase sigma factor RpoS and its regulon. Thus the expression patterns of global regulators can be adjusted artificially to manipulate microbial physiology, creating a new and resilient organism.
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Affiliation(s)
- Stephen Fitzgerald
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.,Department of Biology, University of Regina, Saskatchewan, Canada
| | - Shane C Dillon
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Tzu-Chiao Chao
- Department of Biology, University of Regina, Saskatchewan, Canada
| | - Heather L Wiencko
- Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Karsten Hokamp
- Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin 2, Ireland
| | | | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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26
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Lund EG, Duband-Goulet I, Oldenburg A, Buendia B, Collas P. Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin. Nucleus 2015; 6:30-9. [PMID: 25602132 DOI: 10.4161/19491034.2014.990855] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The nuclear lamina has been shown to interact with the genome through lamina-associated domains (LADs). LADs have been identified by DamID, a proximity labeling assay, and more recently by chromatin immunoprecipitation-sequencing (ChIP-seq) of A- and B-type lamins. LADs form megabase-size domains at the nuclear periphery, they are gene-poor and mostly heterochromatic. Here, we show that the mode of chromatin fragmentation for ChIP, namely bath sonication or digestion with micrococcal nuclease (MNase), leads to the discovery of common but also distinct sets of lamin-interacting domains, or LiDs. Using ChIP-seq, we show the existence of lamin A/C (LMNA) LiDs with distinct gene contents, histone composition enrichment and relationships to lamin B1-interacting domains. The extent of genome coverage of lamin A/C (LMNA) LiDs in sonicated or MNase-digested chromatin is similar (∼730 megabases); however over half of these domains are uniquely detected in sonicated or MNase-digested chromatin. Sonication-specific LMNA LiDs are gene-poor and devoid of a broad panel of histone modifications, while MNase-specific LMNA LiDs are of higher gene density and are enriched in H3K9me3, H3K27me3 and in histone variant H2A.Z. LMNB1 LiDs are gene-poor and show no or little enrichment in these marks. Comparison of published LMNB1 DamID LADs with LMNB1 and LMNA LiDs identified here by ChIP-seq further shows that LMNA can associate with 'open' chromatin domains displaying euchromatin characteristics, and which are not associated with LMNB1. The differential genomic and epigenetic properties of lamin-interacting domains reflect the existence of distinct LiD populations identifiable in different chromatin contexts, including nuclease-accessible regions presumably localized in the nuclear interior.
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Affiliation(s)
- Eivind G Lund
- a Department of Molecular Medicine, Institute of Basic Medical Sciences ; University of Oslo, and Norwegian Center for Stem Cell Research , Oslo , Norway
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27
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Aliper AM, Csoka AB, Buzdin A, Jetka T, Roumiantsev S, Moskalev A, Zhavoronkov A. Signaling pathway activation drift during aging: Hutchinson-Gilford Progeria Syndrome fibroblasts are comparable to normal middle-age and old-age cells. Aging (Albany NY) 2015; 7:26-37. [PMID: 25587796 PMCID: PMC4350323 DOI: 10.18632/aging.100717] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
For the past several decades, research in understanding the molecular basis of human aging has progressed significantly with the analysis of premature aging syndromes. Progerin, an altered form of lamin A, has been identified as the cause of premature aging in Hutchinson-Gilford Progeria Syndrome (HGPS), and may be a contributing causative factor in normal aging. However, the question of whether HGPS actually recapitulates the normal aging process at the cellular and organismal level, or simply mimics the aging phenotype is widely debated. In the present study we analyzed publicly available microarray datasets for fibroblasts undergoing cellular aging in culture, as well as fibroblasts derived from young, middle-age, and old-age individuals, and patients with HGPS. Using GeroScope pathway analysis and drug discovery platform we analyzed the activation states of 65 major cellular signaling pathways. Our analysis reveals that signaling pathway activation states in cells derived from chronologically young patients with HGPS strongly resemble cells taken from normal middle-aged and old individuals. This clearly indicates that HGPS may truly represent accelerated aging, rather than being just a simulacrum. Our data also points to potential pathways that could be targeted to develop drugs and drug combinations for both HGPS and normal aging.
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Affiliation(s)
- Alexander M Aliper
- Insilico Medicine, Inc., Johns Hopkins University, ETC, B301, MD 21218, USA.,Federal Clinical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Antonei Benjamin Csoka
- Vision Genomics LLC, Washington DC 20011, USA.,Epigenetics Laboratory, Dept. of Anatomy, Howard University, Washington DC 20059, USA
| | - Anton Buzdin
- Insilico Medicine, Inc., Johns Hopkins University, ETC, B301, MD 21218, USA.,Pathway Pharmaceuticals, Limited, Wan Chai, Hong Kong
| | - Tomasz Jetka
- Institute of Fundamental Technological Research, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Sergey Roumiantsev
- Insilico Medicine, Inc., Johns Hopkins University, ETC, B301, MD 21218, USA.,Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141700, Russia
| | - Alexy Moskalev
- Insilico Medicine, Inc., Johns Hopkins University, ETC, B301, MD 21218, USA.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141700, Russia.,George Mason University, Fairfax, VA 22030, USA
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., Johns Hopkins University, ETC, B301, MD 21218, USA.,Federal Clinical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141700, Russia.,The Biotechnology Research Foundation, BGRF, London W1J 5NE, UK
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28
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Abstract
The intermediate filament proteins, A- and B-type lamins, form the nuclear lamina scaffold adjacent to the inner nuclear membrane. Lamins also contribute to chromatin regulation and various signaling pathways affecting gene expression. In this review, Osmanagic-Myers et al. focus on the role of nuclear lamins in mechanosensing and also discuss how disease-linked lamin mutants may impair the response of cells to mechanical stimuli and influence the properties of the extracellular matrix. The intermediate filament proteins, A- and B-type lamins, form the nuclear lamina scaffold adjacent to the inner nuclear membrane. B-type lamins confer elasticity, while A-type lamins lend viscosity and stiffness to nuclei. Lamins also contribute to chromatin regulation and various signaling pathways affecting gene expression. The mechanical roles of lamins and their functions in gene regulation are often viewed as independent activities, but recent findings suggest a highly cross-linked and interdependent regulation of these different functions, particularly in mechanosignaling. In this newly emerging concept, lamins act as a “mechanostat” that senses forces from outside and responds to tension by reinforcing the cytoskeleton and the extracellular matrix. A-type lamins, emerin, and the linker of the nucleoskeleton and cytoskeleton (LINC) complex directly transmit forces from the extracellular matrix into the nucleus. These mechanical forces lead to changes in the molecular structure, modification, and assembly state of A-type lamins. This in turn activates a tension-induced “inside-out signaling” through which the nucleus feeds back to the cytoskeleton and the extracellular matrix to balance outside and inside forces. These functions regulate differentiation and may be impaired in lamin-linked diseases, leading to cellular phenotypes, particularly in mechanical load-bearing tissues.
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29
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Hänzelmann S, Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Brümmendorf TH, Reid G, Costa IG, Wagner W. Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites. Clin Epigenetics 2015; 7:19. [PMID: 25763115 PMCID: PMC4356053 DOI: 10.1186/s13148-015-0057-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/10/2015] [Indexed: 02/08/2023] Open
Abstract
Background Primary cells enter replicative senescence after a limited number of cell divisions. This process needs to be considered in cell culture experiments, and it is particularly important for regenerative medicine. Replicative senescence is associated with reproducible changes in DNA methylation (DNAm) at specific sites in the genome. The mechanism that drives senescence-associated DNAm changes remains unknown - it may involve stochastic DNAm drift due to imperfect maintenance of epigenetic marks or it is directly regulated at specific sites in the genome. Results In this study, we analyzed the reorganization of nuclear architecture and DNAm changes during long-term culture of human fibroblasts and mesenchymal stromal cells (MSCs). We demonstrate that telomeres shorten and shift towards the nuclear center at later passages. In addition, DNAm profiles, either analyzed by MethylCap-seq or by 450k IlluminaBeadChip technology, revealed consistent senescence-associated hypermethylation in regions associated with H3K27me3, H3K4me3, and H3K4me1 histone marks, whereas hypomethylation was associated with chromatin containing H3K9me3 and lamina-associated domains (LADs). DNA hypermethylation was significantly enriched in the vicinity of genes that are either up- or downregulated at later passages. Furthermore, specific transcription factor binding motifs (e.g. EGR1, TFAP2A, and ETS1) were significantly enriched in differentially methylated regions and in the promoters of differentially expressed genes. Conclusions Senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence. These results indicate that tightly regulated epigenetic modifications during long-term culture contribute to changes in nuclear organization and gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0057-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonja Hänzelmann
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Eduardo G Gusmao
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Carmen M Koch
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
| | - Sebastian Hummel
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | | | - Sylvia Joussen
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - George Reid
- Institute for Molecular Biology, Mainz, Germany
| | - Ivan G Costa
- Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany ; Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany ; Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany
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30
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Bianchi A, Lanzuolo C. Into the chromatin world: Role of nuclear architecture in epigenome regulation. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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31
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Lye CM, Naylor HW, Sanson B. Subcellular localisations of the CPTI collection of YFP-tagged proteins in Drosophila embryos. Development 2014; 141:4006-17. [PMID: 25294944 PMCID: PMC4197698 DOI: 10.1242/dev.111310] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A key challenge in the post-genomic area is to identify the function of the genes discovered, with many still uncharacterised in all metazoans. A first step is transcription pattern characterisation, for which we now have near whole-genome coverage in Drosophila. However, we have much more limited information about the expression and subcellular localisation of the corresponding proteins. The Cambridge Protein Trap Consortium generated, via piggyBac transposition, over 600 novel YFP-trap proteins tagging just under 400 Drosophila loci. Here, we characterise the subcellular localisations and expression patterns of these insertions, called the CPTI lines, in Drosophila embryos. We have systematically analysed subcellular localisations at cellularisation (stage 5) and recorded expression patterns at stage 5, at mid-embryogenesis (stage 11) and at late embryogenesis (stages 15-17). At stage 5, 31% of the nuclear lines (41) and 26% of the cytoplasmic lines (67) show discrete localisations that provide clues on the function of the protein and markers for organelles or regions, including nucleoli, the nuclear envelope, nuclear speckles, centrosomes, mitochondria, the endoplasmic reticulum, Golgi, lysosomes and peroxisomes. We characterised the membranous/cortical lines (102) throughout stage 5 to 10 during epithelial morphogenesis, documenting their apico-basal position and identifying those secreted in the extracellular space. We identified the tricellular vertices as a specialized membrane domain marked by the integral membrane protein Sidekick. Finally, we categorised the localisation of the membranous/cortical proteins during cytokinesis.
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Affiliation(s)
- Claire M Lye
- The Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Huw W Naylor
- The Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Bénédicte Sanson
- The Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
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32
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Bryant JA, Sellars LE, Busby SJW, Lee DJ. Chromosome position effects on gene expression in Escherichia coli K-12. Nucleic Acids Res 2014; 42:11383-92. [PMID: 25209233 PMCID: PMC4191405 DOI: 10.1093/nar/gku828] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In eukaryotes, the location of a gene on the chromosome is known to affect its expression, but such position effects are poorly understood in bacteria. Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. At some positions, expression was more than 3-fold higher than at the natural lac promoter locus, whereas at several other locations, the reporter cassette was completely silenced: effectively overriding local lac promoter control. These effects were not due to differences in gene copy number, caused by partially replicated genomes. Rather, the differences in gene expression occur predominantly at the level of transcription and are mediated by several different features that are involved in chromosome organization. Taken together, our findings identify a tier of gene regulation above local promoter control and highlight the importance of chromosome position effects on gene expression profiles in bacteria.
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Affiliation(s)
- Jack A Bryant
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Laura E Sellars
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen J W Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - David J Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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33
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Poleshko A, Kossenkov AV, Shalginskikh N, Pecherskaya A, Einarson MB, Marie Skalka A, Katz RA. Human factors and pathways essential for mediating epigenetic gene silencing. Epigenetics 2014; 9:1280-9. [PMID: 25147916 PMCID: PMC4169020 DOI: 10.4161/epi.32088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cellular identity in both normal and disease processes is determined by programmed epigenetic activation or silencing of specific gene subsets. Here, we have used human cells harboring epigenetically silent GFP-reporter genes to perform a genome-wide siRNA knockdown screen for the identification of cellular factors that are required to maintain epigenetic gene silencing. This unbiased screen interrogated 21,121 genes, and we identified and validated a set of 128 protein factors. This set showed enrichment for functional categories, and protein-protein interactions. Among this set were known epigenetic silencing factors, factors with no previously identified role in epigenetic gene silencing, as well as unstudied factors. The set included non-nuclear factors, for example, components of the integrin-adhesome. A key finding was that the E1 and E2 enzymes of the small ubiquitin-like modifier (SUMO) pathway (SAE1, SAE2/UBA2, UBC9/UBE2I) are essential for maintenance of epigenetic silencing. This work provides the first genome-wide functional view of human factors that mediate epigenetic gene silencing. The screen output identifies novel epigenetic factors, networks, and mechanisms, and provides a set of candidate targets for epigenetic therapy and cellular reprogramming.
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Affiliation(s)
| | - Andrew V Kossenkov
- Center for Systems and Computational Biology; The Wistar Institute; Philadelphia, PA USA
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34
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Lund E, Oldenburg AR, Collas P. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 2014; 42:e92. [PMID: 24782521 PMCID: PMC4066758 DOI: 10.1093/nar/gku324] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 12/31/2022] Open
Abstract
Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations.
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Affiliation(s)
- Eivind Lund
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Anja R Oldenburg
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
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35
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Abstract
A conserved organizational feature of eukaryotic nuclei is the peripheral heterochromatin compartment, which provides a protected area for epigenetically silent genes and gene-poor DNA. In metazoan cells this compartment is associated with the nuclear lamina, the protein meshwork at the inner edge of the nucleus. Heterochromatin-nuclear lamina interactions promote epigenetic gene silencing, which may drive many normal and diseased biological processes. We recently obtained evidence that a previously unstudied human protein, PRR14, participates in the tethering of heterochromatin to the inner nuclear periphery. PRR14 associates with the nuclear lamina and attaches to heterochromatin through its binding partner, heterochromatin protein 1 (HP1). After disassembly early in mitosis, PRR14 reassembles in two steps, first binding to anaphase chromosomes through HP1, followed by association with the nuclear lamina in telophase. PRR14 may thereby play a role in specifying HP1-bound heterochromatin for reattachment to the nuclear lamina at mitotic exit. Here we review the relevant literature, summarize our initial work, and provide additional comments and findings.
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Affiliation(s)
- Andrey Poleshko
- Fox Chase Cancer Center; Institute for Cancer Research; Philadelphia, PA USA
| | - Richard A Katz
- Fox Chase Cancer Center; Institute for Cancer Research; Philadelphia, PA USA
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36
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Abstract
The nuclear lamina guards the genome and in many ways contributes to regulating nuclear function. Increasing evidence indicates that the lamina dynamically interacts with chromatin mainly through large repressive domains, and recent data suggest that at least some of the lamin-genome contacts may be developmentally significant. In an attempt to provide an additional meaning to lamin-genome contacts, a recent study characterized the association of gene promoters with A-type lamins in progenitor and differentiated cells. Here, we discuss how A-type lamins interact with spatially defined promoter regions, and the relationship between these interactions, associated chromatin marks and gene expression outputs. We discuss the impact of A-type lamins on nucleus-wide and local chromatin organization. We also address how lamin-promoter interactions are redistributed during differentiation of adipocyte progenitors into adipocytes. Finally, we propose a model of lineage-specific "unlocking" of developmentally regulated loci and its significance in cellular differentiation.
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Affiliation(s)
- Eivind Lund
- Stem Cell Epigenetics Laboratory; Institute of Basic Medical Sciences; Faculty of Medicine; University of Oslo, and Norwegian Center for Stem Cell Research; Oslo, Norway
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory; Institute of Basic Medical Sciences; Faculty of Medicine; University of Oslo, and Norwegian Center for Stem Cell Research; Oslo, Norway
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