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Garimberti E, Federico C, Ragusa D, Bruno F, Saccone S, Bridger JM, Tosi S. Alterations in Genome Organization in Lymphoma Cell Nuclei due to the Presence of the t(14;18) Translocation. Int J Mol Sci 2024; 25:2377. [PMID: 38397052 PMCID: PMC10889133 DOI: 10.3390/ijms25042377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/10/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Chromosomal rearrangements have been shown to alter genome organization, consequently having an impact on gene expression. Studies on certain types of leukemia have shown that gene expression can be exacerbated by the altered nuclear positioning of fusion genes arising from chromosomal translocations. However, studies on lymphoma have been, so far, very limited. The scope of this study was to explore genome organization in lymphoma cells carrying the t(14;18)(q32;q21) rearrangement known to results in over-expression of the BCL2 gene. In order to achieve this aim, we used fluorescence in situ hybridization to carefully map the positioning of whole chromosome territories and individual genes involved in translocation in the lymphoma-derived cell line Pfeiffer. Our data show that, although there is no obvious alteration in the positioning of the whole chromosome territories, the translocated genes may take the nuclear positioning of either of the wild-type genes. Furthermore, the BCL2 gene was looping out in a proportion of nuclei with the t(14;18) translocation but not in control nuclei without the translocation, indicating that chromosome looping may be an essential mechanism for BCL2 expression in lymphoma cells.
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Affiliation(s)
- Elisa Garimberti
- Clinical Genomics Laboratory, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK;
| | - Concetta Federico
- Department of Biological, Geological, and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (F.B.); (S.S.)
| | - Denise Ragusa
- Centre for Genome Engineering and Maintenance (CenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (D.R.); (J.M.B.)
| | - Francesca Bruno
- Department of Biological, Geological, and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (F.B.); (S.S.)
| | - Salvatore Saccone
- Department of Biological, Geological, and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (C.F.); (F.B.); (S.S.)
| | - Joanna Mary Bridger
- Centre for Genome Engineering and Maintenance (CenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (D.R.); (J.M.B.)
| | - Sabrina Tosi
- Centre for Genome Engineering and Maintenance (CenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK; (D.R.); (J.M.B.)
- Leukaemia and Chromosome Research Laboratory, College of Health, Medicine and Life Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
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2
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Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation. Mol Biol Cell 2022; 33:ar72. [PMID: 35476603 PMCID: PMC9635277 DOI: 10.1091/mbc.e21-11-0593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Chromosome structure and nuclear organization are important factors in the regulation of gene expression. Transcription of a gene is influenced by local and global chromosome features such as chromatin condensation status. The relationship between the 3D position of a gene in the nucleus and its activity is less clear. Here we used high-throughput imaging to perform a large-scale analysis of the spatial location of nearly 100 hypoxia-responsive genes to determine whether their location and activity state are correlated. Radial distance analysis demonstrated that the majority of Hypoxia-Inducible Factor (HIF)- and CREB-dependent hypoxia-responsive genes are located in the intermediate region of the nucleus, and some of them changed their radial position in hypoxia. Analysis of the relative distances among a subset of HIF target genes revealed that some gene pairs altered their relative location to each other on hypoxic treatment, suggesting higher-order chromatin rearrangements. While these changes in location occurred in response to hypoxic activation of the target genes, they did not correlate with the extent of their activation. These results suggest that induction of the hypoxia-responsive gene expression program is accompanied by spatial alterations of the genome, but that radial and relative gene positions are not directly related to gene activity.
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Affiliation(s)
- Koh Nakayama
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan.,Department of Pharmacology, School of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Sigal Shachar
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Elizabeth H Finn
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Hiroyuki Sato
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akihiro Hirakawa
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Tom Misteli
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
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3
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Chebrout M, Koné MC, Jan HU, Cournut M, Letheule M, Fleurot R, Aguirre-Lavin T, Peynot N, Jouneau A, Beaujean N, Bonnet-Garnier A. Transcription of rRNA in early mouse embryos promotes chromatin reorganization and expression of major satellite repeats. J Cell Sci 2022; 135:274059. [DOI: 10.1242/jcs.258798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/09/2022] [Indexed: 11/20/2022] Open
Abstract
During the first cell cycles of the early development, the chromatin of the embryo is highly reprogrammed alongside that embryonic genome starts its own transcription. The spatial organization of the genome is a major process that contributes to regulating gene transcription in time and space, however, it is poorly studied in the context of early embryos. To study the cause and effect link between transcription and spatial organization in embryos, we focused on the ribosomal genes, that are first silent and begin to transcribe during the 2-cell stage in the mouse. We demonstrated that ribosomal sequences and early unprocessed rRNAs are spatially organized in a very peculiar manner from the 2-cell to the 16-cell. Using drugs interfering with ribosomal DNA transcription, we show that this organization, totally different from somatic cells, depends on an active transcription of ribosomal genes and induces a unique chromatin environment that favors transcription of major satellite sequences after the 4-cell stage.
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Affiliation(s)
- Martine Chebrout
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Maïmouna Coura Koné
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Habib U. Jan
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Marie Cournut
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Martine Letheule
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Renaud Fleurot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Tiphaine Aguirre-Lavin
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Alice Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Beaujean
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Amélie Bonnet-Garnier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
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Genome-wide mapping of genomic DNA damage: methods and implications. Cell Mol Life Sci 2021; 78:6745-6762. [PMID: 34463773 PMCID: PMC8558167 DOI: 10.1007/s00018-021-03923-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022]
Abstract
Exposures from the external and internal environments lead to the modification of genomic DNA, which is implicated in the cause of numerous diseases, including cancer, cardiovascular, pulmonary and neurodegenerative diseases, together with ageing. However, the precise mechanism(s) linking the presence of damage, to impact upon cellular function and pathogenesis, is far from clear. Genomic location of specific forms of damage is likely to be highly informative in understanding this process, as the impact of downstream events (e.g. mutation, microsatellite instability, altered methylation and gene expression) on cellular function will be positional—events at key locations will have the greatest impact. However, until recently, methods for assessing DNA damage determined the totality of damage in the genomic location, with no positional information. The technique of “mapping DNA adductomics” describes the molecular approaches that map a variety of forms of DNA damage, to specific locations across the nuclear and mitochondrial genomes. We propose that integrated comparison of this information with other genome-wide data, such as mutational hotspots for specific genotoxins, tumour-specific mutation patterns and chromatin organisation and transcriptional activity in non-cancerous lesions (such as nevi), pre-cancerous conditions (such as polyps) and tumours, will improve our understanding of how environmental toxins lead to cancer. Adopting an analogous approach for non-cancer diseases, including the development of genome-wide assays for other cellular outcomes of DNA damage, will improve our understanding of the role of DNA damage in pathogenesis more generally.
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5
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Desapogu R, Le Marchand G, Smith R, Ray P, Gillier É, Dutertre S, Alouini M, Tramier M, Huet S, Fade J. Label-free microscopy of mitotic chromosomes using the polarization orthogonality breaking technique. BIOMEDICAL OPTICS EXPRESS 2021; 12:5290-5304. [PMID: 34513257 PMCID: PMC8407833 DOI: 10.1364/boe.426630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 05/31/2023]
Abstract
We report how a recently developed polarization imaging technique, implementing micro-wave photonics and referred to as orthogonality-breaking (OB) imaging, can be adapted on a classical confocal fluorescence microscope, and is able to provide informative polarization images from a single scan of the cell sample. For instance, the comparison of the images of various cell lines at different cell-cycle stages obtained by OB polarization microscopy and fluorescence confocal images shows that an endogenous polarimetric contrast arizes with this instrument on compacted chromosomes during cell division.
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Affiliation(s)
- Rajesh Desapogu
- Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France
- Univ Rennes, CNRS, Institut FOTON-UMR 6082, F-35000 Rennes, France
- These authors contributed equally to this work
| | - Gilles Le Marchand
- Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France
- These authors contributed equally to this work
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France
| | - Paulami Ray
- Univ Rennes, CNRS, Institut FOTON-UMR 6082, F-35000 Rennes, France
| | - Émilie Gillier
- Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France
| | - Stéphanie Dutertre
- Univ Rennes, BIOSIT, UMS CNRS 3480, US INSERM 018, F-35000 Rennes, France
| | - Mehdi Alouini
- Univ Rennes, CNRS, Institut FOTON-UMR 6082, F-35000 Rennes, France
| | - Marc Tramier
- Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France
- Univ Rennes, BIOSIT, UMS CNRS 3480, US INSERM 018, F-35000 Rennes, France
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR, UMR 6290, F-35000 Rennes, France
- Univ Rennes, BIOSIT, UMS CNRS 3480, US INSERM 018, F-35000 Rennes, France
- Institut Universitaire de France, France
| | - Julien Fade
- Univ Rennes, CNRS, Institut FOTON-UMR 6082, F-35000 Rennes, France
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6
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Aboelnour E, Bonev B. Decoding the organization, dynamics, and function of the 4D genome. Dev Cell 2021; 56:1562-1573. [PMID: 33984271 DOI: 10.1016/j.devcel.2021.04.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/15/2021] [Accepted: 04/21/2021] [Indexed: 11/15/2022]
Abstract
Understanding how complex cell-fate decisions emerge at the molecular level is a key challenge in developmental biology. Despite remarkable progress in decoding the contribution of the linear epigenome, how spatial genome architecture functionally informs changes in gene expression remains unclear. In this review, we discuss recent insights in elucidating the molecular landscape of genome folding, emphasizing the multilayered nature of the 3D genome, its importance for gene regulation, and its spatiotemporal dynamics. Finally, we discuss how these new concepts and emergent technologies will enable us to address some of the outstanding questions in development and disease.
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Affiliation(s)
- Erin Aboelnour
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany.
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7
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de Castro IJ, Toner B, Xie SQ, Swingland J, Hodges A, Tabrizi SJ, Turkheimer F, Pombo A, Khalil A. Altered nuclear architecture in blood cells from Huntington's disease patients. Neurol Sci 2021; 43:379-385. [PMID: 33974169 DOI: 10.1007/s10072-021-05289-w] [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: 12/02/2020] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Cell nuclear architecture has been explored in cancer and laminopathies but not in neurodegenerative disorders. Huntington's disease (HD) is a neurodegenerative disorder that leads to neuronal death. Chromosome-wide changes in gene expression have been reported in HD, not only in the brain but also in peripheral blood cells, but whether this translates into nuclear and chromosome architecture alterations has not yet been studied. METHODS We investigate nuclear structure and chromosome organization in HD blood cells using fluorescence in situ hybridization in ultrathin cryosections (cryoFISH), coupled with machine learning image analysis to evaluate size, distribution, and morphology of nuclei and chromosomes. Four chromosomes were analyzed based on up- or downregulation of gene expression in HD. RESULTS We show that blood cells from HD patients display increased nuclear size and filamentary shape, increased size of gene-rich chromosome 19, decreased filamentary shape of gene-rich chromosome 22, and a more radially centralized position for chromosome 19, whereas chromosomes 4 and 5 do not show detectable differences. CONCLUSIONS We identify gross changes in nuclear architecture and chromosome organization associated with HD in blood. This adds a new layer of information onto disrupting mechanisms in HD and increases the potential of using blood to survey HD.
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Affiliation(s)
- Inês J de Castro
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK. .,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany. .,Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, Im Neuenheimer Feld 344, Heidelberg, 69120, Germany.
| | - Brian Toner
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA
| | - Sheila Q Xie
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Chromatin and Development Group, MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - James Swingland
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,GRIP AI, London, EC2A 3AZ, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Angela Hodges
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Sarah J Tabrizi
- UCL Institute of Neurology, Box 104, National Hospital for Neurology and Neurosurgery Queen Square, University College London, London, WC1N 3BG, UK
| | - Federico Turkheimer
- Institute of Psychiatry, King's College London, London, SE5 8AF, UK.,Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK.,Huntington's Disease Centre, Department of Neurodegenerative Disease, University College London (UCL) Queen Square Institute of Neurology and the UK Dementia Research Institute, UCL, London, UK
| | - Ana Pombo
- Genome Function Group, MRC London Institute for Medical Sciences, London, W12 0NN, UK.,Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, 10115, Berlin, Germany
| | - André Khalil
- CompuMAINE Lab, Department of Chemical and Biomedical Engineering, University of Maine, Orono, ME, 04469, USA.
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8
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Bayguinov PO, Fisher MR, Fitzpatrick JAJ. Assaying three-dimensional cellular architecture using X-ray tomographic and correlated imaging approaches. J Biol Chem 2020; 295:15782-15793. [PMID: 32938716 PMCID: PMC7667966 DOI: 10.1074/jbc.rev120.009633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Much of our understanding of the spatial organization of and interactions between cellular organelles and macromolecular complexes has been the result of imaging studies utilizing either light- or electron-based microscopic analyses. These classical approaches, while insightful, are nonetheless limited either by restrictions in resolution or by the sheer complexity of generating multidimensional data. Recent advances in the use and application of X-rays to acquire micro- and nanotomographic data sets offer an alternative methodology to visualize cellular architecture at the nanoscale. These new approaches allow for the subcellular analyses of unstained vitrified cells and three-dimensional localization of specific protein targets and have served as an essential tool in bridging light and electron correlative microscopy experiments. Here, we review the theory, instrumentation details, acquisition principles, and applications of both soft X-ray tomography and X-ray microscopy and how the use of these techniques offers a succinct means of analyzing three-dimensional cellular architecture. We discuss some of the recent work that has taken advantage of these approaches and detail how they have become integral in correlative microscopy workflows.
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Affiliation(s)
- Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Max R Fisher
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA; Departments of Cell Biology and Physiology and Neuroscience, Washington University School of Medicine, Saint Louis, Missouri, USA; Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA.
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9
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Das P, Shen T, McCord RP. Inferring chromosome radial organization from Hi-C data. BMC Bioinformatics 2020; 21:511. [PMID: 33167851 PMCID: PMC7654587 DOI: 10.1186/s12859-020-03841-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being used to characterize the genome structure of many cell types and conditions. Computational methods to extract 3D arrangements of CTs from this type of pairwise contact data will thus increase our ability to analyze CT organization in a wider variety of biological situations. RESULTS A number of full-scale polymer models have successfully reconstructed the 3D structure of chromosome territories from Hi-C. To supplement such methods, we explore alternative, direct, and less computationally intensive approaches to capture radial CT organization from Hi-C data. We show that we can infer relative chromosome ordering using PCA on a thresholded inter-chromosomal contact matrix. We simulate an ensemble of possible CT arrangements using a force-directed network layout algorithm and propose an approach to integrate additional chromosome properties into our predictions. Our CT radial organization predictions have a high correlation with microscopy imaging data for various cell nucleus geometries (lymphoblastoid, skin fibroblast, and breast epithelial cells), and we can capture previously documented changes in senescent and progeria cells. CONCLUSIONS Our analysis approaches provide rapid and modular approaches to screen for alterations in CT organization across widely available Hi-C data. We demonstrate which stages of the approach can extract meaningful information, and also describe limitations of pairwise contacts alone to predict absolute 3D positions.
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Affiliation(s)
- Priyojit Das
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Tongye Shen
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Rachel Patton McCord
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 USA
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10
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Guin K, Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O'Brien CE, Butler G, Sanyal A, Sanyal K. Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres. eLife 2020; 9:e58556. [PMID: 32469306 PMCID: PMC7292649 DOI: 10.7554/elife.58556] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Centromeres of Candida albicans form on unique and different DNA sequences but a closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR)-associated centromeres. To investigate the mechanism of centromere type transition, we improved the fragmented genome assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio sequencing, chromosome conformation capture sequencing (3C-seq), chromoblot, and genetic analysis of engineered aneuploid strains. Further, we analyzed the 3D genome organization using 3C-seq data, which revealed spatial proximity among the centromeres as well as telomeres of seven chromosomes in C. tropicalis. Intriguingly, we observed evidence of inter-centromeric translocations in the common ancestor of C. albicans and C. tropicalis. Identification of putative centromeres in closely related Candida sojae, Candida viswanathii and Candida parapsilosis indicates loss of ancestral HIR-associated centromeres and establishment of evolutionary new centromeres (ENCs) in C. albicans. We propose that spatial proximity of the homologous centromere DNA sequences facilitated karyotype rearrangements and centromere type transitions in human pathogenic yeasts of the CUG-Ser1 clade.
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Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Yao Chen
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Radha Mishra
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | | | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Caoimhe E O'Brien
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Geraldine Butler
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
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11
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Meaburn KJ, Misteli T. Assessment of the Utility of Gene Positioning Biomarkers in the Stratification of Prostate Cancers. Front Genet 2019; 10:1029. [PMID: 31681438 PMCID: PMC6812139 DOI: 10.3389/fgene.2019.01029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/25/2019] [Indexed: 12/24/2022] Open
Abstract
There is a pressing need for additional clinical biomarkers to predict the aggressiveness of individual cancers. Here, we examine the potential usefulness of spatial genome organization as a prognostic tool for prostate cancer. Using fluorescence in situ hybridization on formalin-fixed, paraffin embedded human prostate tissue specimens, we compared the nuclear positions of four genes between clinically relevant subgroups of prostate tissues. We find that directional repositioning of SP100 and TGFB3 gene loci stratifies prostate cancers of differing Gleason scores. A more peripheral position of SP100 and TGFB3 in the nucleus, compared to benign tissues, is associated with low Gleason score cancers, whereas more internal positioning correlates with higher Gleason scores. Conversely, LMNA is more internally positioned in many non-metastatic prostate cancers, while its position is indistinguishable from benign tissue in metastatic cancer. The false positive rates were relatively low, whereas, the false negative rates of single or combinations of genes were high, limiting the clinical utility of this assay in its current form. Nevertheless, our findings of subtype-specific gene positioning patterns in prostate cancer provides proof-of-concept for the potential usefulness of spatial gene positioning for prognostic applications, and encourage further exploration of spatial gene positioning patterns to identify novel clinically relevant molecular biomarkers, which may aid treatment decisions for cancer patients.
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Affiliation(s)
- Karen J Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Tom Misteli
- Cell Biology of Genomes Group, National Cancer Institute, NIH, Bethesda, MD, United States
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12
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Damodaran K, Crestani M, Jokhun DS, Shivashankar GV. Nuclear morphometrics and chromatin condensation patterns as disease biomarkers using a mobile microscope. PLoS One 2019; 14:e0218757. [PMID: 31314779 PMCID: PMC6636717 DOI: 10.1371/journal.pone.0218757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/08/2019] [Indexed: 12/26/2022] Open
Abstract
Current cancer diagnosis involves the use of nuclear morphology and chromatin condensation signatures for accurate advanced stage classification. While such diagnostic approaches rely on high resolution imaging of the cell nucleus using expensive microscopy systems, developing portable mobile microscopes to visualize nuclear and chromatin condensation patterns is desirable at clinical settings with limited infrastructure. In this study, we develop a portable fluorescent mobile microscope capable of acquiring high resolution images of the nucleus and chromatin. Using this we extracted nuclear morphometric and chromatin texture based features and were able to discriminate between normal and cancer cells with similar accuracy as wide-field fluorescence microscopy. We were also able to detect subtle changes in nuclear and chromatin features in cells subjected to compressive forces, cytoskeletal perturbations and cytokine stimulation, thereby highlighting the sensitivity of the portable microscope. Taken together, we present a versatile platform to exploit nuclear morphometrics and chromatin condensation features as physical biomarkers for point-of-care diagnostic solutions.
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Affiliation(s)
- Karthik Damodaran
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Michele Crestani
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Doorgesh Sharma Jokhun
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - G. V. Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular Oncology, Italian Foundation for Cancer Research, Milan, Italy
- * E-mail:
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13
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Genome reorganization in different cancer types: detection of cancer specific breakpoint regions. Mol Cytogenet 2019; 12:25. [PMID: 31249626 PMCID: PMC6585066 DOI: 10.1186/s13039-019-0435-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/15/2019] [Indexed: 01/11/2023] Open
Abstract
Background Tumorigenesis is a multi-step process which is accompanied by substantial changes in genome organization. The development of these changes is not only a random process, but rather comprise specific DNA regions that are prone to the reorganization process. Results We have analyzed previously published SNP arrays from three different cancer types (pancreatic adenocarcinoma, breast cancer and metastatic melanoma) and from non-malignant control samples. We calculated segmental copy number variations as well as breakpoint regions. Some of these regions were not randomly involved in genome reorganization since we detected fifteen of them in at least 20% of all tumor samples and one region on chromosome 9 where 43% of tumors have a breakpoint. Further, the top-15 breakpoint regions show an association to known fragile sites. The relevance of these common breakpoint regions was further confirmed by analyzing SNP arrays from 917 cancer cell lines. Conclusion Our analyses suggest that genome reorganization is common in tumorigenesis and that some breakpoint regions can be found across all cancer types, while others exclusively occur in specific entities.
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14
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Fields BD, Nguyen SC, Nir G, Kennedy S. A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans. eLife 2019; 8:42823. [PMID: 31084706 PMCID: PMC6516958 DOI: 10.7554/elife.42823] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/02/2019] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic DNA is highly organized within nuclei and this organization is important for genome function. Fluorescent in situ hybridization (FISH) approaches allow 3D architectures of genomes to be visualized. Scalable FISH technologies, which can be applied to whole animals, are needed to help unravel how genomic architecture regulates, or is regulated by, gene expression during development, growth, reproduction, and aging. Here, we describe a multiplexed DNA FISH Oligopaint library that targets the entire Caenorhabditis elegans genome at chromosome, three megabase, and 500 kb scales. We describe a hybridization strategy that provides flexibility to DNA FISH experiments by coupling a single primary probe synthesis reaction to dye conjugated detection oligos via bridge oligos, eliminating the time and cost typically associated with labeling probe sets for individual experiments. The approach allows visualization of genome organization at varying scales in all/most cells across all stages of development in an intact animal model system. DNA contains the instructions needed to build and maintain a living organism. How DNA is physically arranged inside a cell is not random, and DNA organization is important because it can affect, for example, which genes are active, and which are not. Researchers often use a technique called “fluorescence in situ hybridization” (or FISH for short) to study how DNA is organized in cells. FISH tethers fluorescent molecules to defined sections of DNA, making those sections glow under the right wavelength of light. It is possible to collect images of the fluorescent DNA regions under a microscope to see where they are in relation to each other and to the rest of the cell. Fields, Nguyen et al. have now created a new library of FISH molecules that can be used to analyze the DNA of a microscopic worm known as Caenorhabditis elegans – a model organism that is widely used to study genetics, animal development, and cell biology. The library can be used to visualize the worm’s whole genome at different scales. The library enables accurate and reliable investigations of how DNA is organized inside C. elegans, including in intact worms, meaning it also offers the first chance to study DNA organization in a whole organism through all stages of its life cycle. This new resource could help to reveal the relationships between DNA organization, cell specialization and gene activity in different cells at different stages of development. This could help to clarify the relationships between physical DNA organization and biological change. This design strategy behind this whole genome library should also be adaptable for similar studies in other animal species.
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Affiliation(s)
- Brandon D Fields
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Son C Nguyen
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Guy Nir
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Scott Kennedy
- Department of Genetics, Harvard Medical School, Boston, United States
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15
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See YX, Wang BZ, Fullwood MJ. Chromatin Interactions and Regulatory Elements in Cancer: From Bench to Bedside. Trends Genet 2019; 35:145-158. [DOI: 10.1016/j.tig.2018.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/14/2018] [Accepted: 11/27/2018] [Indexed: 12/16/2022]
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16
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Mai S. The three-dimensional cancer nucleus. Genes Chromosomes Cancer 2019; 58:462-473. [PMID: 30536826 DOI: 10.1002/gcc.22720] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
Research into the three-dimensional (3D) organization of the cancer cell genome started over 100 years ago. We follow an exciting avenue of research in this field, from Hansemann's early observations of aberrant mitoses and nuclei in cancer cells in the late 19th century to Boveri's theory of the cancer cell in the early 20th century, to current views of nuclear organization and its changes in cancer. Molecular and imaging methods go hand in hand with providing us with a better understanding of the spatial nature of the cancer cell genome. This has led to the concept that the structural order of the nucleus can be used as cancer cell biomarker.
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Affiliation(s)
- Sabine Mai
- Cell Biology, Research Institute for Oncology and Hematology, CancerCare Manitoba, The University of Manitoba, Winnipeg, Manitoba, Canada
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17
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Stachecka J, Nowacka-Woszuk J, Kolodziejski PA, Szczerbal I. The importance of the nuclear positioning of the PPARG gene for its expression during porcine in vitro adipogenesis. Chromosome Res 2019; 27:271-284. [PMID: 30656515 PMCID: PMC6733831 DOI: 10.1007/s10577-019-09604-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 01/27/2023]
Abstract
Proper expression of the PPARG gene, which encodes a key transcription factor of adipogenesis, is indispensable in the formation of mature adipocytes. The positioning of a gene within the nuclear space has been implicated in gene regulation. We here report on the significance of the PPARG gene’s nuclear positioning for its activity during in vitro adipogenesis in the pig. We used an established system of differentiation of mesenchymal stem cells derived from bone marrow and adipose tissue into adipocytes. The differentiation process was carried out for 7 days, and the cells were examined using the 3D DNA/immuno-FISH and RNA/DNA-FISH approaches. PPARG transcript level was measured using real-time PCR, and PPARγ activity was detected with colorimetric assay. Changes in the nuclear location of the PPARG gene were observed when we compared undifferentiated mesenchymal stem cells with mature adipocytes. The gene moved from the nuclear periphery to the nuclear center as its transcriptional activity increased. The RNA/DNA-FISH approach shows that differences in primary transcript production correlated with the allele’s nuclear positioning. Transcriptionally active alleles preferentially occupy the central part of the nucleus, while inactive alleles are found on the nuclear periphery. We also show that transcription of PPARG begins with one allele, but that both alleles are active in later stages of differentiation. Our results provide evidence that functionally distinct alleles of the PPARG gene are positioned in different parts of the cell nucleus. This confirms the importance of nuclear architecture to the regulation of PPARG gene transcription, and thus to the fate of the adipose cell.
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Affiliation(s)
- Joanna Stachecka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Pawel A Kolodziejski
- Department of Animal Physiology and Biochemistry, Poznan University of Life Sciences, Wolynska 35, 60-637, Poznan, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland.
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18
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Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol 2018; 150:579-592. [PMID: 30238154 DOI: 10.1007/s00418-018-1726-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.
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19
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Kalinin AA, Allyn-Feuer A, Ade A, Fon GV, Meixner W, Dilworth D, Husain SS, de Wet JR, Higgins GA, Zheng G, Creekmore A, Wiley JW, Verdone JE, Veltri RW, Pienta KJ, Coffey DS, Athey BD, Dinov ID. 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification. Sci Rep 2018; 8:13658. [PMID: 30209281 PMCID: PMC6135819 DOI: 10.1038/s41598-018-31924-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/29/2018] [Indexed: 02/08/2023] Open
Abstract
Quantitative analysis of morphological changes in a cell nucleus is important for the understanding of nuclear architecture and its relationship with pathological conditions such as cancer. However, dimensionality of imaging data, together with a great variability of nuclear shapes, presents challenges for 3D morphological analysis. Thus, there is a compelling need for robust 3D nuclear morphometric techniques to carry out population-wide analysis. We propose a new approach that combines modeling, analysis, and interpretation of morphometric characteristics of cell nuclei and nucleoli in 3D. We used robust surface reconstruction that allows accurate approximation of 3D object boundary. Then, we computed geometric morphological measures characterizing the form of cell nuclei and nucleoli. Using these features, we compared over 450 nuclei with about 1,000 nucleoli of epithelial and mesenchymal prostate cancer cells, as well as 1,000 nuclei with over 2,000 nucleoli from serum-starved and proliferating fibroblast cells. Classification of sets of 9 and 15 cells achieved accuracy of 95.4% and 98%, respectively, for prostate cancer cells, and 95% and 98% for fibroblast cells. To our knowledge, this is the first attempt to combine these methods for 3D nuclear shape modeling and morphometry into a highly parallel pipeline workflow for morphometric analysis of thousands of nuclei and nucleoli in 3D.
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Affiliation(s)
- Alexandr A Kalinin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.,Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan School of Nursing, Ann Arbor, MI, USA
| | - Ari Allyn-Feuer
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alex Ade
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gordon-Victor Fon
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Walter Meixner
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David Dilworth
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Syed S Husain
- Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan School of Nursing, Ann Arbor, MI, USA
| | - Jeffrey R de Wet
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gerald A Higgins
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gen Zheng
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Amy Creekmore
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John W Wiley
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James E Verdone
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert W Veltri
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth J Pienta
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donald S Coffey
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian D Athey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. .,Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, MI, USA.
| | - Ivo D Dinov
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. .,Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan School of Nursing, Ann Arbor, MI, USA. .,Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, MI, USA.
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20
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Bridger JM, Brindley PJ, Knight M. The snail Biomphalaria glabrata as a model to interrogate the molecular basis of complex human diseases. PLoS Negl Trop Dis 2018; 12:e0006552. [PMID: 30091971 PMCID: PMC6084811 DOI: 10.1371/journal.pntd.0006552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Joanna M. Bridger
- Institute of Environment, Health, and Societies, Brunel University London, Uxbridge, United Kingdom
| | - Paul J. Brindley
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
| | - Matty Knight
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington DC, United States of America
- Division of Science and Mathematics, University of the District of Columbia, Washington DC, United States of America
- * E-mail: ,
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21
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The three-dimensional organization of the genome in cellular senescence and age-associated diseases. Semin Cell Dev Biol 2018; 90:154-160. [PMID: 30031215 DOI: 10.1016/j.semcdb.2018.07.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 07/17/2018] [Indexed: 01/18/2023]
Abstract
Recent advances in genomics and imaging technologies have increased our ability to interrogate the 3D conformation of chromosomes and to better understand principles of organization and dynamics, as well as how their alteration can lead to disease. In this review we describe how these technologies have shed new light into the role of the 3D organization of the genome in defining cellular states in aging and age-associated diseases. We compare the genomic organization in cellular senescence and cancer, discuss the role of the lamina in maintaining the structural and functional integrity of the genome, and we highlight the recent findings on how this organization breaks down in disease states.
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22
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Ioannou D, Tempest HG. Does genome organization matter in spermatozoa? A refined hypothesis to awaken the silent vessel. Syst Biol Reprod Med 2018; 64:518-534. [DOI: 10.1080/19396368.2017.1421278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- IVF Florida Reproductive Associates, Margate, FL, USA
| | - Helen G. Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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23
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Stachecka J, Walczak A, Kociucka B, Ruszczycki B, Wilczyński G, Szczerbal I. Nuclear organization during in vitro differentiation of porcine mesenchymal stem cells (MSCs) into adipocytes. Histochem Cell Biol 2017; 149:113-126. [PMID: 29134302 DOI: 10.1007/s00418-017-1618-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2017] [Indexed: 12/19/2022]
Abstract
Differentiation of progenitor cells into adipocytes is accompanied by remarkable changes in cell morphology, cytoskeletal organization, and gene expression profile. Mature adipocytes are filled with a large lipid droplet and the nucleus tends to move to the cell periphery. It was hypothesized that the differentiation process is also associated with changes of nuclear organization. The aim of this study was to determine the number and distribution of selected components of nuclear architecture during porcine in vitro adipogenesis. The pig is an important animal model sharing many similarities to humans at the anatomical, physiological, and genetic levels and has been recognized as a good model for human obesity. Thus, understanding how cellular structures important for fundamental nuclear processes may be altered during adipocyte differentiation is of great importance. Mesenchymal stem cells (MSCs) were derived from bone marrow (BM-MSCs) and adipose tissue (AD-MSCs) and were cultured for 7 days in the adipogenic medium. A variable differentiation potential of these cell populations towards adipogenic lineage was observed, and for further study, a comparative characteristic of the nuclear organization in BM-MSCs and AD-MSCs was performed. Nuclear substructures were visualized by indirect immunofluorescence (nucleoli, nuclear speckles, PML bodies, lamins, and HP1α) or fluorescence in situ hybridization (telomeres) on fixed cells at 0, 3, 5, and 7 days of differentiation. Comprehensive characterization of these structures, in terms of their number, size, dynamics, and arrangement in three-dimensional space of the nucleus, was performed. It was found that during differentiation of porcine MSCs into adipocytes, changes of nuclear organization occurred and concerned: (1) the nuclear size and shape; (2) reduced lamin A/C expression; and (3) reorganization of chromocenters. Other elements of nuclear architecture such as nucleoli, SC-35 nuclear speckles, and telomeres showed no significant changes when compared to undifferentiated and mature fat cells. In addition, the presence of a low number of PML bodies was characteristic of the studied porcine mesenchymal stem cell adipogenesis system. It has been shown that the arrangement of selected components of nuclear architecture was very similar in MSCs derived from different sources, whereas adipocyte differentiation involves nuclear reorganization. This study adds new data on nuclear organization during adipogenesis using the pig as a model organism.
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Affiliation(s)
- Joanna Stachecka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Agnieszka Walczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Beata Kociucka
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland
| | - Błażej Ruszczycki
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093, Warsaw, Poland
| | - Grzegorz Wilczyński
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093, Warsaw, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637, Poznan, Poland.
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24
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Serebryannyy L, Misteli T. Protein sequestration at the nuclear periphery as a potential regulatory mechanism in premature aging. J Cell Biol 2017; 217:21-37. [PMID: 29051264 PMCID: PMC5748986 DOI: 10.1083/jcb.201706061] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/10/2017] [Accepted: 08/17/2017] [Indexed: 12/19/2022] Open
Abstract
Serebryannyy and Misteli provide a perspective on how protein sequestration at the inner nuclear membrane and nuclear lamina might influence aging. Despite the extensive description of numerous molecular changes associated with aging, insights into the driver mechanisms of this fundamental biological process are limited. Based on observations in the premature aging syndrome Hutchinson–Gilford progeria, we explore the possibility that protein regulation at the inner nuclear membrane and the nuclear lamina contributes to the aging process. In support, sequestration of nucleoplasmic proteins to the periphery impacts cell stemness, the response to cytotoxicity, proliferation, changes in chromatin state, and telomere stability. These observations point to the nuclear periphery as a central regulator of the aging phenotype.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD
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25
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Garcia A, Huang D, Righolt A, Righolt C, Kalaw MC, Mathur S, McAvoy E, Anderson J, Luedke A, Itorralba J, Mai S. Super-resolution structure of DNA significantly differs in buccal cells of controls and Alzheimer's patients. J Cell Physiol 2017; 232:2387-2395. [PMID: 27996096 PMCID: PMC5485033 DOI: 10.1002/jcp.25751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/01/2023]
Abstract
The advent of super-resolution microscopy allowed for new insights into cellular and physiological processes of normal and diseased cells. In this study, we report for the first time on the super-resolved DNA structure of buccal cells from patients with Alzheimer's disease (AD) versus age- and gender-matched healthy, non-caregiver controls. In this super-resolution study cohort of 74 participants, buccal cells were collected and their spatial DNA organization in the nucleus examined by 3D Structured Illumination Microscopy (3D-SIM). Quantitation of the super-resolution DNA structure revealed that the nuclear super-resolution DNA structure of individuals with AD significantly differs from that of their controls (p < 0.05) with an overall increase in the measured DNA-free/poor spaces. This represents a significant increase in the interchromatin compartment. We also find that the DNA structure of AD significantly differs in mild, moderate, and severe disease with respect to the DNA-containing and DNA-free/poor spaces. We conclude that whole genome remodeling is a feature of buccal cells in AD.
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Affiliation(s)
- Angeles Garcia
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - David Huang
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Amanda Righolt
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Christiaan Righolt
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Maria Carmela Kalaw
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Shubha Mathur
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
| | - Elizabeth McAvoy
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - James Anderson
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Angela Luedke
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Justine Itorralba
- Department of Medicine (Geriatrics) and Neuroscience CenterQueen's UniversitySMOLKingstonOntarioCanada
| | - Sabine Mai
- Department of Physiology and PathophysiologyManitoba Institute of Cell BiologyUniversity of ManitobaCancerCare ManitobaWinnipegManitobaCanada
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26
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Sawyer IA, Dundr M. Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture. Chromosoma 2017; 126:541-557. [PMID: 28593374 DOI: 10.1007/s00412-017-0632-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 01/18/2023]
Abstract
An intrinsic and essential trait exhibited by cells is the properly coordinated and integrated regulation of an astoundingly large number of simultaneous molecular decisions and reactions to maintain biochemical homeostasis. This is especially true inside the cell nucleus, where the recognition of DNA and RNA by a vast range of nucleic acid-interacting proteins organizes gene expression patterns. However, this dynamic system is not regulated by simple "on" or "off" signals. Instead, transcription factor and RNA polymerase recruitment to DNA are influenced by the local chromatin and epigenetic environment, a gene's relative position within the nucleus and the action of noncoding RNAs. In addition, major phase-separated structural features of the nucleus, such as nucleoli and paraspeckles, assemble in direct response to specific transcriptional activities and, in turn, influence global genomic function. Currently, the interpretation of these data is trapped in a causality dilemma reminiscent of the "chicken and the egg" paradox as it is unclear whether changes in nuclear architecture promote RNA function or vice versa. Here, we review recent advances that suggest a complex and interdependent interaction network between gene expression, chromatin topology, and noncoding RNA function. We also discuss the functional links between these essential nuclear processes from the nanoscale (gene looping) to the macroscale (sub-nuclear gene positioning and nuclear body function) and briefly highlight some of the challenges that researchers may encounter when studying these phenomena.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.
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Abstract
The eukaryotic genome is organized in a manner that allows folding of the genetic material in the confined space of the cell nucleus, while at the same time enabling its physiological function. A major principle of spatial genome organization is the non-random position of genomic loci relative to other loci and to nuclear bodies. The mechanisms that determine the spatial position of a locus, and how position affects function, are just beginning to be characterized. Initial results suggest that there are multiple, gene-specific mechanisms and the involvement of a wide range of cellular machineries. In this Commentary, we review recent findings from candidate approaches and unbiased screening methods that provide initial insight into the cellular mechanisms of positioning and their functional consequences. We highlight several specific mechanisms, including tethering of genome regions to the nuclear periphery, passage through S-phase and histone modifications, that contribute to gene positioning in yeast, plants and mammals.
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Affiliation(s)
- Sigal Shachar
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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