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Keller D, Stinus S, Umlauf D, Gourbeyre E, Biot E, Olivier N, Mahou P, Beaurepaire E, Andrey P, Crabbe L. Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF. iScience 2024; 27:109343. [PMID: 38510147 PMCID: PMC10951912 DOI: 10.1016/j.isci.2024.109343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Spatial genome organization within the nucleus influences major biological processes and is impacted by the configuration of linear chromosomes. Here, we applied 3D spatial statistics and modeling on high-resolution telomere and centromere 3D-structured illumination microscopy images in cancer cells. We found a multi-scale organization of telomeres that dynamically evolved from a mixed clustered-and-regular distribution in early G1 to a purely regular distribution as cells progressed through the cell cycle. In parallel, our analysis revealed two pools of peripheral and internal telomeres, the proportions of which were inverted during the cell cycle. We then conducted a targeted screen using MadID to identify the molecular pathways driving or maintaining telomere anchoring to the nuclear envelope observed in early G1. Lamina-associated polypeptide (LAP) proteins were found transiently localized to telomeres in anaphase, a stage where LAP2α initiates the reformation of the nuclear envelope, and impacted telomere redistribution in the next interphase together with their partner barrier-to-autointegration factor (BAF).
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Affiliation(s)
- Debora Keller
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Sonia Stinus
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - David Umlauf
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Edith Gourbeyre
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Eric Biot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Nicolas Olivier
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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2
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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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Fatakia SN, Mehta IS, Rao BJ. Systems-level chromosomal parameters represent a suprachromosomal basis for the non-random chromosomal arrangement in human interphase nuclei. Sci Rep 2016; 6:36819. [PMID: 27845379 PMCID: PMC5109186 DOI: 10.1038/srep36819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/18/2016] [Indexed: 02/07/2023] Open
Abstract
Forty-six chromosome territories (CTs) are positioned uniquely in human interphase nuclei, wherein each of their positions can range from the centre of the nucleus to its periphery. A non-empirical basis for their non-random arrangement remains unreported. Here, we derive a suprachromosomal basis of that overall arrangement (which we refer to as a CT constellation), and report a hierarchical nature of the same. Using matrix algebra, we unify intrinsic chromosomal parameters (e.g., chromosomal length, gene density, the number of genes per chromosome), to derive an extrinsic effective gene density matrix, the hierarchy of which is dominated largely by extrinsic mathematical coupling of HSA19, followed by HSA17 (human chromosome 19 and 17, both preferentially interior CTs) with all CTs. We corroborate predicted constellations and effective gene density hierarchy with published reports from fluorescent in situ hybridization based microscopy and Hi-C techniques, and delineate analogous hierarchy in disparate vertebrates. Our theory accurately predicts CTs localised to the nuclear interior, which interestingly share conserved synteny with HSA19 and/or HSA17. Finally, the effective gene density hierarchy dictates how permutations among CT position represents the plasticity within its constellations, based on which we suggest that a differential mix of coding with noncoding genome modulates the same.
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Affiliation(s)
- Sarosh N Fatakia
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Ishita S Mehta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.,UM-DAE Centre for Excellence in Basic Sciences, Biological Sciences, Kalina campus, Santacruz (E), Mumbai, Maharashtra 400098, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
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4
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Sehgal N, Fritz AJ, Vecerova J, Ding H, Chen Z, Stojkovic B, Bhattacharya S, Xu J, Berezney R. Large-scale probabilistic 3D organization of human chromosome territories. Hum Mol Genet 2016; 25:419-36. [PMID: 26604142 PMCID: PMC4731017 DOI: 10.1093/hmg/ddv479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 11/07/2015] [Accepted: 11/16/2015] [Indexed: 01/13/2023] Open
Abstract
There is growing evidence that chromosome territories (CT) have a probabilistic non-random arrangement within the cell nucleus of mammalian cells including radial positioning and preferred patterns of interchromosomal interactions that are cell-type specific. While it is generally assumed that the three-dimensional (3D) arrangement of genes within the CT is linked to genomic regulation, the degree of non-random organization of individual CT remains unclear. As a first step to elucidating the global 3D organization (topology) of individual CT, we performed multi-color fluorescence in situ hybridization using six probes extending across each chromosome in human WI38 lung fibroblasts. Six CT were selected ranging in size and gene density (1, 4, 12, 17, 18 and X). In-house computational geometric algorithms were applied to measure the 3D distances between every combination of probes and to elucidate data-mined structural patterns. Our findings demonstrate a high degree of non-random arrangement of individual CT that vary from chromosome to chromosome and display distinct changes during the cell cycle. Application of a classic, well-defined data mining and pattern recognition approach termed the 'k-means' generated 3D models for the best fit arrangement of each chromosome. These predicted models correlated well with the detailed distance measurements and analysis. We propose that the unique 3D topology of each CT and characteristic changes during the cell cycle provide the structural framework for the global gene expression programs of the individual chromosomes.
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Affiliation(s)
| | | | | | - Hu Ding
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Zihe Chen
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Branislav Stojkovic
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Sambit Bhattacharya
- Department of Mathematics and Computer Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
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Schmälter AK, Righolt CH, Kuzyk A, Mai S. Changes in Nuclear Orientation Patterns of Chromosome 11 during Mouse Plasmacytoma Development. Transl Oncol 2015; 8:417-423. [PMID: 26500032 PMCID: PMC4631097 DOI: 10.1016/j.tranon.2015.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022] Open
Abstract
Studying changes in nuclear architecture is a unique approach toward the understanding of nuclear remodeling during tumor development. One aspect of nuclear architecture is the orientation of chromosomes in the three-dimensional nuclear space. We studied mouse chromosome 11 in lymphocytes of [T38HxBALB/c]N mice with a reciprocal translocation between chromosome X and 11 (T38HT(X;11)) exhibiting a long chromosome T(11;X) and a short chromosome T(X;11) and in fast-onset plasmacytomas (PCTs) induced in the same strain. We determined the three-dimensional orientation of chromosome 11 using a mouse chromosome 11 specific multicolor banding probe. We also examined the nuclear position of the small translocation chromosome T(X;11) which contains cytoband 11E2 and parts of E1. Chromosomes can point either with their centromeric or with their telomeric end toward the nuclear center or periphery, or their position is found in parallel to the nuclear border. In T38HT(X;11) nuclei, the most frequently observed orientation pattern was with both chromosomes 11 in parallel to the nuclear border ("PP"). PCT cells showed nuclei with two or more copies of chromosome 11. In PCTs, the most frequent orientation pattern was with one chromosome in parallel and the other pointing with its centromeric end toward the nuclear periphery ("CP"). There is a significant difference between the orientation patterns observed in T38HT(X;11) and in PCT nuclei (P < .0001).
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Affiliation(s)
- Ann-Kristin Schmälter
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Christiaan H Righolt
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada; Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Alexandra Kuzyk
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Sabine Mai
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada.
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Righolt CH, Schmälter AK, Kuzyk A, Young IT, van Vliet LJ, Mai S. Measuring murine chromosome orientation in interphase nuclei. Cytometry A 2015; 87:733-40. [PMID: 25891972 DOI: 10.1002/cyto.a.22674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/25/2015] [Accepted: 03/31/2015] [Indexed: 11/08/2022]
Abstract
The nuclear architecture of a cell may change as a result of various diseases, including cancer. A variety of nuclear features are, therefore, of interest to cell biologists. Recently, several studies have investigated the orientation of chromosomes in the interphase nucleus either visually or semi-automatically. In this article an automated method to measure this orientation is presented. The theoretical difference between performing these measurements in two and three dimensions is discussed and experimentally verified. The results computed from measurements of murine nuclei correspond with results from visual inspection. We found significant differences in the orientation of chromosome 11 between nuclei from a PreB cell line of BALB/c origin and primary B nuclei from congenic [T38HxBALB/c]N wild-type mice. Since our new automatic method concurs with both the visual and semi-automatic methods, we conclude that the automatic method can replace these methods in assessing chromosome orientation.
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Affiliation(s)
- Christiaan H Righolt
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Ann-Kristin Schmälter
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada.,Institute for Human Genetics, Ludwig Maximilian University, Munich, Germany
| | - Alexandra Kuzyk
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ian T Young
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Lucas J van Vliet
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Sabine Mai
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
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