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Jiménez-Martín A, Pineda-Santaella A, Pinto-Cruz J, León-Periñán D, García-Sánchez S, Delgado-Gestoso D, Marín-Toral L, Fernández-Álvarez A. The Rabl chromosome configuration masks a kinetochore reassembly mechanism in yeast mitosis. Mol Biol Cell 2022; 33:br8. [PMID: 35274979 PMCID: PMC9282007 DOI: 10.1091/mbc.e20-09-0600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 11/21/2022] Open
Abstract
During cell cycle progression in metazoans, the kinetochore is assembled at mitotic onset and disassembled during mitotic exit. Once assembled, the kinetochore complex attached to centromeres interacts directly with the spindle microtubules, the vehicle of chromosome segregation. This reassembly program is assumed to be absent in budding and fission yeast, because most kinetochore proteins are stably maintained at the centromeres throughout the entire cell cycle. Here, we show that the reassembly program of the outer kinetochore at mitotic onset is unexpectedly conserved in the fission yeast Schizosaccharomyces pombe. We identified this behavior by removing the Rabl chromosome configuration, in which centromeres are permanently associated with the nuclear envelope beneath the spindle pole body during interphase. In addition to having evolutionary implications for kinetochore reassembly, our results aid the understanding of the molecular processes responsible for kinetochore disassembly and assembly during mitotic entry.
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Affiliation(s)
- Alberto Jiménez-Martín
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
- Instituto de Biología Funcional y Genómica (IBFG); Consejo Superior de Investigaciones Científicas and Universidad de Salamanca, 37007 Salamanca, Spain
| | - Alberto Pineda-Santaella
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
| | - Jesús Pinto-Cruz
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
| | - Daniel León-Periñán
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
| | - Sabas García-Sánchez
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
| | - David Delgado-Gestoso
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
| | - Laura Marín-Toral
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
| | - Alfonso Fernández-Álvarez
- Andalusian Center for Developmental Biology (CABD); Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide and Junta de Andalucía, 41013 Seville, Spain
- Instituto de Biología Funcional y Genómica (IBFG); Consejo Superior de Investigaciones Científicas and Universidad de Salamanca, 37007 Salamanca, Spain
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2
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Ito K, Takizawa T. Nuclear Architecture in the Nervous System. Results Probl Cell Differ 2022; 70:419-442. [PMID: 36348117 DOI: 10.1007/978-3-031-06573-6_15] [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] [Indexed: 06/16/2023]
Abstract
Neurons and glial cells in the nervous system exhibit different gene expression programs for neural development and function. These programs are controlled by the epigenetic regulatory layers in the nucleus. The nucleus is a well-organized subcellular organelle that includes chromatin, the nuclear lamina, and nuclear bodies. These subnuclear components operate together as epigenetic regulators of neural development and function and are collectively called the nuclear architecture. In the nervous system, dynamic rearrangement of the nuclear architecture has been observed in each cell type, especially in neurons, allowing for their specialized functions, including learning and memory formation. Although the importance of nuclear architecture has been debated for decades, the paradigm has been changing rapidly, owing to the development of new technologies. Here, we reviewed the latest studies on nuclear geometry, nuclear bodies, and heterochromatin compartments, as well as summarized recent novel insights regarding radial positioning, chromatin condensation, and chromatin interaction between genes and cis-regulatory elements.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, Pennsylvania, USA
| | - Takumi Takizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan.
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3
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Single-cell approaches to understand genome organisation throughout the cell cycle. Essays Biochem 2019; 63:209-216. [PMID: 31092688 DOI: 10.1042/ebc20180043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 01/05/2023]
Abstract
Mammalian genomes are ordered at several scales, ranging from nucleosomes (beads on a string), to topologically associated domains (TADs), laminar associated domains (LADs), and chromosome territories. These are described briefly below and we refer the reader to some recent comprehensive reviews on genome architecture summarising the current state of knowledge of the organisational principles of the nucleus [1,2]. Biological observations from populations of millions of individual cells can reveal consensus behaviour. New methods to study and interpret biological data at the single-cell level have recently been instrumental in revealing new understanding of cell-to-cell variation and novel biology. Here we will summarise the recent advances in single-cell technology that have provided insights into the behaviour of the mammalian genome during a cell cycle. We will focus on the interphase domain structure of chromosomes, including TADs and LADs, and how chromosome architecture changes during the cell cycle. The role of genome architecture relating to gene expression has been reviewed elsewhere [3].
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4
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Chakraborty D, Paszkowski-Rogacz M, Berger N, Ding L, Mircetic J, Fu J, Iesmantavicius V, Choudhary C, Anastassiadis K, Stewart AF, Buchholz F. lncRNA Panct1 Maintains Mouse Embryonic Stem Cell Identity by Regulating TOBF1 Recruitment to Oct-Sox Sequences in Early G1. Cell Rep 2018; 21:3012-3021. [PMID: 29241531 DOI: 10.1016/j.celrep.2017.11.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 11/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in diverse biological processes, including embryonic stem cell (ESC) maintenance. However, their functional mechanisms remain largely undefined. Here, we show that the lncRNA Panct1 regulates the transient recruitment of a putative X-chromosome-encoded protein A830080D01Rik, hereafter referred to as transient octamer binding factor 1 (TOBF1), to genomic sites resembling the canonical Oct-Sox motif. TOBF1 physically interacts with Panct1 and exhibits a cell-cycle-specific punctate localization in ESCs. At the chromatin level, this correlates with its recruitment to promoters of pluripotency genes. Strikingly, mutating an octamer-like motif in Panct1 RNA abrogates the strength of TOBF1 localization and recruitment to its targets. Taken together, our data reveal a tightly controlled spatial and temporal pattern of lncRNA-mediated gene regulation in a cell-cycle-dependent manner and suggest that lncRNAs might function as barcodes for identifying genomic addresses for maintaining cellular states.
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Affiliation(s)
- Debojyoti Chakraborty
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Nicolas Berger
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Jovan Mircetic
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - Vytautas Iesmantavicius
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) partner site Dresden, 01307 Dresden, Germany; National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany.
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5
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Iashina EG, Velichko EV, Filatov MV, Bouwman WG, Duif CP, Brulet A, Grigoriev SV. Additive scaling law for structural organization of chromatin in chicken erythrocyte nuclei. Phys Rev E 2017; 96:012411. [PMID: 29347273 DOI: 10.1103/physreve.96.012411] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Indexed: 11/07/2022]
Abstract
Small-angle neutron scattering (SANS) on nuclei of chicken erythrocytes demonstrates the cubic dependence of the scattering intensity Q^{-3} in the range of momentum transfer Q∈10^{-3}-10^{-2}nm^{-1}. Independent spin-echo SANS measurements give the spin-echo function, which is well described by the exponential law in a range of sizes (3×10^{2})-(3×10^{4}) nm. Both experimental dependences reflect the nature of the structural organization of chromatin in the nucleus of a living cell, which corresponds to the correlation function γ(r)=ln(ξ/r) for r<ξ, where ξ=(3.69±0.07)×10^{3} nm, the size of the nucleus. It has the specific scaling property of the logarithmic fractal γ(r/a)=γ(r)+ln(a), i.e., the scaling down by a gives an additive constant to the correlation function, which distinguishes it from the mass fractal, which is characterized by multiplicative constant.
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Affiliation(s)
- E G Iashina
- Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg 188300, Russia.,Saint Petersburg State University, Ulyanovskaya 1, St. Petersburg 198504, Russia
| | - E V Velichko
- Delft University of Technology, Mekelweg 15, 2629 JB Delft, Netherlands
| | - M V Filatov
- Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg 188300, Russia
| | - W G Bouwman
- Delft University of Technology, Mekelweg 15, 2629 JB Delft, Netherlands
| | - C P Duif
- Delft University of Technology, Mekelweg 15, 2629 JB Delft, Netherlands
| | - A Brulet
- Leon Brillouin Laboratory, CEA Saclay, 91191 Gif sur Yvette Cedex, France
| | - S V Grigoriev
- Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg 188300, Russia.,Saint Petersburg State University, Ulyanovskaya 1, St. Petersburg 198504, Russia
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Spichal M, Fabre E. The Emerging Role of the Cytoskeleton in Chromosome Dynamics. Front Genet 2017; 8:60. [PMID: 28580009 PMCID: PMC5437106 DOI: 10.3389/fgene.2017.00060] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/28/2017] [Indexed: 01/15/2023] Open
Abstract
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus. Monomers of these cytoplasmic polymers and related proteins can also enter the nucleus and play different roles in the interior of the nucleus than they do in the cytoplasm. Nuclear cytoskeletal proteins can act as chromatin remodelers alone or in complexes with other nuclear proteins. They can also act as transcription factors. Many of these mechanisms have been conserved during evolution, indicating that the cytoskeletal regulation of chromosome dynamics is an essential process. In this review, we discuss the different influences of cytoskeletal proteins on chromosome dynamics by focusing on the well-studied model organism budding yeast.
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Affiliation(s)
- Maya Spichal
- Department of Genetics, University of North Carolina, Chapel HillNC, United States
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, CNRS UMR 7212, INSERM U944, Hôpital St. Louis 1Paris, France
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7
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Billmann M, Boutros M. Systematic epistatic mapping of cellular processes. Cell Div 2017; 12:2. [PMID: 28077953 PMCID: PMC5223360 DOI: 10.1186/s13008-016-0028-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/26/2016] [Indexed: 12/12/2022] Open
Abstract
Genetic screens have identified many novel components of various biological processes, such as components required for cell cycle and cell division. While forward genetic screens typically generate unstructured ‘hit’ lists, genetic interaction mapping approaches can identify functional relations in a systematic fashion. Here, we discuss a recent study by our group demonstrating a two-step approach to first screen for regulators of the mitotic cell cycle, and subsequently guide hypothesis generation by using genetic interaction analysis. The screen used a high-content microscopy assay and automated image analysis to capture defects during mitotic progression and cytokinesis. Genetic interaction networks derived from process-specific features generate a snapshot of functional gene relations in those processes, which follow a temporal order during the cell cycle. This complements a recently published approach, which inferred directional genetic interactions reconstructing hierarchical relationships between genes across different phases during mitotic progression. In conclusion, this strategy leverages unbiased, genome-wide, yet highly sensitive and process-focused functional screening in cells.
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Affiliation(s)
- Maximilian Billmann
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany ; Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union St SE, Minneapolis, MN 55455 USA
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany ; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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8
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Altered bivalent positioning in metaphase I human spermatocytes from Robertsonian translocation carriers. J Assist Reprod Genet 2016; 34:131-138. [PMID: 27655390 DOI: 10.1007/s10815-016-0809-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/05/2016] [Indexed: 10/21/2022] Open
Abstract
PURPOSE The study aims to determine whether there is an altered bivalent positioning in metaphase I human spermatocytes from Robertsonian translocation carriers. METHODS Metaphase I human spermatocytes from three 45,XY,der(13;14)(q10;q10) individuals and a 45,XY,der(14;15)(q10;q10) individual were analyzed. Proximity relationships of bivalents were established by analyzing meiotic preparations combining Leishman staining and multiplex-FISH procedures. Poisson regression model was used to determine proximity frequencies between bivalents and to assess associations with chromosome size, gene density, acrocentric morphology, and chromosomes with heterochromatic blocks. The hierarchical cluster Ward method was used to characterize the groups of bivalents with preferred proximities in a cluster analysis. Bivalent groups obtained were individually compared with those obtained in normal karyotype individuals evaluated in a previous study. RESULTS A total of 1288 bivalents were examined, giving a total of 2289 proximity data. Only four positive significant proximities were detected for each type of Robertsonian translocation. Significant bivalent associations were only observed by small-size chromosomes for MI,22,XY,III(13q14q). These results were clearly divergent from 46,XY individuals. Moreover, cluster analysis revealed that about 30 % of the bivalents showed changes in their proximity relationships in metaphase I. CONCLUSIONS The territorial organization of bivalents in metaphase I human spermatocytes changes in the presence of a Robertsonian translocation.
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9
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Strickfaden H, Zunhammer A, van Koningsbruggen S, Köhler D, Cremer T. 4D Chromatin dynamics in cycling cells. Nucleus 2014. [DOI: 10.4161/nucl.11969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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10
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Abstract
The LINC (linker of nucleoskeleton and cytoskeleton) complex forms a transcisternal bridge across the NE (nuclear envelope) that connects the cytoskeleton with the nuclear interior. This enables some proteins of the NE to communicate with the centrosome and the microtubule cytoskeleton. The position of the centrosome relative to the NE is of vital importance for many cell functions, such as cell migration and division, and centrosomal dislocation is a frequent phenotype in laminopathic disorders. Also in mitosis, a small group of transmembrane NE proteins associate with microtubules when they concentrate in a specific membrane domain associated with the mitotic spindle. The present review discusses structural and functional aspects of microtubule association with NE proteins and how this association may be maintained over the cell cycle.
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11
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van Koningsbruggen S, Gierlinski M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol Biol Cell 2010; 21:3735-48. [PMID: 20826608 PMCID: PMC2965689 DOI: 10.1091/mbc.e10-06-0508] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.
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Affiliation(s)
- Silvana van Koningsbruggen
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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12
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Strickfaden H, Zunhammer A, van Koningsbruggen S, Köhler D, Cremer T. 4D chromatin dynamics in cycling cells: Theodor Boveri's hypotheses revisited. Nucleus 2010; 1:284-97. [PMID: 21327076 DOI: 10.4161/nucl.1.3.11969] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 04/02/2010] [Accepted: 04/06/2010] [Indexed: 01/14/2023] Open
Abstract
This live cell study of chromatin dynamics in four dimensions (space and time) in cycling human cells provides direct evidence for three hypotheses first proposed by Theodor Boveri in seminal studies of fixed blastomeres from Parascaris equorum embryos: (I) Chromosome territory (CT) arrangements are stably maintained during interphase. (II) Chromosome proximity patterns change profoundly during prometaphase. (III) Similar CT proximity patterns in pairs of daughter nuclei reflect symmetrical chromosomal movements during anaphase and telophase, but differ substantially from the arrangement in mother cell nucleus. Hypothesis I could be confirmed for the majority of interphase cells. A minority, however, showed complex, rotational movements of CT assemblies with large-scale changes of CT proximity patterns, while radial nuclear arrangements were maintained. A new model of chromatin dynamics is proposed. It suggests that long-range DNA-DNA interactions in cell nuclei may depend on a combination of rotational CT movements and locally constrained chromatin movements.
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Affiliation(s)
- Hilmar Strickfaden
- Department Biology II (Anthropology and Human Genetics), LMU Biozentrum, Martinsried, Germany
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13
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Sabbbia V, Romero H, Musto H, Naya H. Composition Profile of the Human Genome at the Chromosome Level. J Biomol Struct Dyn 2009; 27:361-70. [DOI: 10.1080/07391102.2009.10507322] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Marella NV, Bhattacharya S, Mukherjee L, Xu J, Berezney R. Cell type specific chromosome territory organization in the interphase nucleus of normal and cancer cells. J Cell Physiol 2009; 221:130-8. [PMID: 19496171 DOI: 10.1002/jcp.21836] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Numerous studies indicate that the genome of higher eukaryotes is organized into distinct chromosome territories and that the 3-D arrangement of these territories may be closely connected to genomic function and the global regulation of gene expression. Despite this progress, the degree of non-random arrangement remains unclear and no overall model has been proposed for chromosome territory associations. To address this issue, a re-FISH approach was combined with computational analysis to analysis the pair-wise associations for six pairs of human chromosomes (chr #1, 4, 11, 12, 16, 18) in the G(0) state of normal human WI38 lung fibroblast and MCF10A epithelial breast cells. Similar levels of associations were found in WI38 and MCF10A for several of the chromosomes whereas others showed striking differences. A novel computational geometric approach, the generalized median graph (GMG), revealed a preferred probabilistic arrangement distinct for each cell line. Statistical analysis demonstrated that approximately 50% of the associations depicted in the GMG models are present in each individual nucleus. A nearly twofold increase of chromosome 4/16 associations in a malignant breast cancer cell line (MCFCA1a) compared to the related normal epithelial cell line (MCF10A) further demonstrates cancer related changes in chromosome arrangements. Our findings of highly preferred chromosome association profiles that are cell type specific and undergo alterations in cancer cells, lead us to propose a probabilistic chromosome code whereby the 3-D association profile of chromosomes contributes to the functional landscape of the cell nucleus, the global regulation of gene expression and the epigenetic state of chromatin.
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Affiliation(s)
- Narasimharao V Marella
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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Cvačková Z, Mašata M, Staněk D, Fidlerová H, Raška I. Chromatin position in human HepG2 cells: although being non-random, significantly changed in daughter cells. J Struct Biol 2009; 165:107-17. [PMID: 19056497 PMCID: PMC2658736 DOI: 10.1016/j.jsb.2008.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 10/24/2008] [Accepted: 10/27/2008] [Indexed: 12/22/2022]
Abstract
Mammalian chromosomes occupy chromosome territories within nuclear space the positions of which are generally accepted as non-random. However, it is still controversial whether position of chromosome territories/chromatin is maintained in daughter cells. We addressed this issue and investigated maintenance of various chromatin regions of unknown composition as well as nucleolus-associated chromatin, a significant part of which is composed of nucleolus organizer region-bearing chromosomes. The photoconvertible histone H4-Dendra2 was used to label such regions in transfected HepG2 cells, and its position was followed up to next interphase. The distribution of labeled chromatin in daughter cells exhibited a non-random character. However, its distribution in a vast majority of daughter cells extensively differed from the original ones and the labeled nucleolus-associated chromatin differently located into the vicinity of different nucleoli. Therefore, our results were not consistent with a concept of preservation chromatin position. This conclusion was supported by the finding that the numbers of nucleoli significantly differed between the two daughter cells. Our results support a view that while the transfected daughter HepG2 cells maintain some features of the parental cell chromosome organization, there is also a significant stochastic component associated with reassortment of chromosome territories/chromatin that results in their positional rearrangements.
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Affiliation(s)
| | | | | | | | - Ivan Raška
- Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, and Department of Cell Biology, Institute of Physiology, Academy of Sciences of the Czech Republic, v.v.i., Albertov 4, 128 00 Prague 2, Czech Republic
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16
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Zwerger M, Herrmann H, Gaines P, Olins AL, Olins DE. Granulocytic nuclear differentiation of lamin B receptor-deficient mouse EPRO cells. Exp Hematol 2008; 36:977-87. [PMID: 18495328 PMCID: PMC2547467 DOI: 10.1016/j.exphem.2008.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 03/06/2008] [Accepted: 03/07/2008] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Lamin B receptor (LBR) is an integral protein of the inner nuclear membrane. Recent studies have demonstrated that genetic deficiency of LBR during granulopoiesis results in hypolobulation of the mature neutrophil nucleus, as observed in human Pelger-Huët anomaly and mouse ichthyosis (ic). In this study, we utilized differentiated early promyelocytes (EPRO cells) that were derived from the bone marrow of homozygous and heterozygous ichthyosis mice to examine changes to the expression of nuclear envelope proteins and heterochromatin structure that result from deficient LBR expression. MATERIALS AND METHODS Wild-type (+/+), heterozygous (+/ic), and homozygous (ic/ic) granulocytic forms of EPRO cells were analyzed for the expression of multiple lamins and inner nuclear envelope proteins by immunostaining and immunoblotting techniques. The heterochromatin architecture was also examined by immunostaining for histone lysine methylation. RESULTS Wild-type (+/+) and heterozygous (+/ic) granulocytic forms revealed ring-shaped nuclei and contained LBR within the nuclear envelope; ic/ic granulocytes exhibited smaller ovoid nuclei devoid of LBR. The pericentric heterochromatin of undifferentiated and granulocytic ic/ic cells was condensed into larger spots and shifted away from the nuclear envelope, compared to +/+ and +/ic cell forms. Lamin A/C, which is normally not present in mature granulocytes, was significantly elevated in LBR-deficient EPRO cells. CONCLUSIONS Our observations suggest roles for LBR during granulopoiesis, which can involve augmenting nuclear membrane growth, facilitating compartmentalization of heterochromatin, and promoting downregulation of lamin A/C expression.
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Affiliation(s)
- Monika Zwerger
- B065, German Cancer Research Center, Heidelberg, D-69120, Germany
| | - Harald Herrmann
- B065, German Cancer Research Center, Heidelberg, D-69120, Germany
| | - Peter Gaines
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA 01854
| | - Ada L. Olins
- Department of Biology, Bowdoin College, Brunswick, ME 04101
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17
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Lebedev DV, Filatov MV, Kuklin AI, Islamov AK, Stellbrink J, Pantina RA, Denisov YY, Toperverg BP, Isaev-Ivanov VV. Structural hierarchy of chromatin in chicken erythrocyte nuclei based on small-angle neutron scattering: Fractal nature of the large-scale chromatin organization. CRYSTALLOGR REP+ 2008. [DOI: 10.1134/s1063774508010136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Gotoh E. Visualizing the dynamics of chromosome structure formation coupled with DNA replication. Chromosoma 2007; 116:453-62. [PMID: 17503067 DOI: 10.1007/s00412-007-0109-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 04/02/2007] [Accepted: 04/18/2007] [Indexed: 11/25/2022]
Abstract
A basic question of cell biology is how DNA folds to chromosome. Numbers of examples have suggested the involvement of DNA replication in chromosome structure formation. To visualize and identify the dynamics of chromosome structure formation and to elucidate the involvement of DNA replication in chromosome construction, Cy3-2'-deoxyuridine-5'-triphosphate direct-labeled active replicating DNA was observed in prematurely condensed chromosomes (PCCs) under a confocal scanning microscope utilized with drug-induced premature chromosome condensation (PCC) technique that facilitates the visualization of interphase chromatin as condensed chromosome form. S-phase PCCs revealed clearly the drastic dynamics of chromosome formation that transits during S-phase from a 'cloudy nebula' to numerous numbers of 'beads on a string' and finally to 'striped arrays of banding structured chromosome' along with the progress of DNA replication. The number, distribution, and shape of replication foci were also measured in individual subphases of S-phase more precisely than reported previously; maximally, approximately 1,400 foci of 0.35 microm average radius size were scored at the beginning of the S-phase, and the number reduced to approximately 100 at the end of the S-phase. Drug-induced PCC clearly provided the new insight that eukaryote DNA replication is tightly coupled with the chromosome condensation/compaction for the construction of the higher-ordered structure of the eukaryote chromosome.
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Affiliation(s)
- Eisuke Gotoh
- Division of Genetic Resources, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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19
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Meaburn KJ, Misteli T, Soutoglou E. Spatial genome organization in the formation of chromosomal translocations. Semin Cancer Biol 2007; 17:80-90. [PMID: 17137790 PMCID: PMC1805052 DOI: 10.1016/j.semcancer.2006.10.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 10/17/2006] [Indexed: 10/24/2022]
Abstract
Chromosomal translocations and genomic instability are universal hallmarks of tumor cells. While the molecular mechanisms leading to the formation of translocations are rapidly being elucidated, a cell biological understanding of how chromosomes undergo translocations in the context of the cell nucleus in vivo is largely lacking. The recent realization that genomes are non-randomly arranged within the nuclear space has profound consequences for mechanisms of chromosome translocations. We review here the emerging principles of spatial genome organization and discuss the implications of non-random spatial genome organization for the genesis and specificity of cancerous chromosomal translocations.
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Affiliation(s)
- Karen J Meaburn
- National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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20
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Olins AL, Olins DE. The mechanism of granulocyte nuclear shape determination: possible involvement of the centrosome. Eur J Cell Biol 2005; 84:181-8. [PMID: 15819399 DOI: 10.1016/j.ejcb.2004.12.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mature blood neutrophils (polymorphonuclear granulocytes) have characteristically complex nuclear shapes. The human neutrophil nucleus generally possesses 3-4 lobes; the mouse neutrophil nucleus frequently resembles a twisted toroid with a central hole. Myeloid tissue culture systems (e.g., human HL-60 and murine MPRO) can be induced to differentiate in vitro towards neutrophils by addition of retinoic acid, exhibiting the characteristic nuclear shape changes. Confocal immunostaining and thin-section transmission electron microscopic image data from differentiated HL-60 and MPRO cells clearly demonstrate proximity of the centrosomal region (containing dynein, gamma-tubulin and C-Nap1) to regions of granulocytic nuclear indentations. In addition, the centrosomal region, flanked by the Golgi apparatus, is shown to be present within the central hole of the toroidal mouse granulocyte nucleus. A role for the centrosomal region and associated microtubules in molding granulocytic nuclear shape is suggested.
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Affiliation(s)
- Ada L Olins
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04101, USA
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21
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Lebedev DV, Filatov MV, Kuklin AI, Islamov AK, Kentzinger E, Pantina R, Toperverg BP, Isaev-Ivanov VV. Fractal nature of chromatin organization in interphase chicken erythrocyte nuclei: DNA structure exhibits biphasic fractal properties. FEBS Lett 2005; 579:1465-8. [PMID: 15733858 DOI: 10.1016/j.febslet.2005.01.052] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 12/29/2004] [Accepted: 01/14/2005] [Indexed: 10/25/2022]
Abstract
Arrangement of chromatin in intact chicken erythrocyte nuclei was investigated by small angle neutron scattering. The scattering spectra have revealed that on the scales between 15 nm and 1.5 microm the interior of the nucleus exhibited properties of a mass fractal. The fractal dimension of the protein component of cell nucleus held constant at approximately 2.5, while the DNA organization was biphasic, with the fractal dimension slightly higher than 2 on the scales smaller than 300 nm and approaching 3 on the larger scales.
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Affiliation(s)
- D V Lebedev
- Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Russia
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22
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Essers J, van Cappellen WA, Theil AF, van Drunen E, Jaspers NGJ, Hoeijmakers JHJ, Wyman C, Vermeulen W, Kanaar R. Dynamics of relative chromosome position during the cell cycle. Mol Biol Cell 2004; 16:769-75. [PMID: 15574874 PMCID: PMC545910 DOI: 10.1091/mbc.e04-10-0876] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The position of chromosomal neighborhoods in living cells was followed using three different methods for marking chromosomal domains occupying arbitrary locations in the nucleus; photobleaching of GFP-labeled histone H2B, local UV-marked DNA, and photobleaching of fluorescently labeled DNA. All methods revealed that global chromosomal organization can be reestablished through one cell division from mother to daughters. By simultaneously monitoring cell cycle stage in the cells in which relative chromosomal domain positions were tracked, we observed that chromosomal neighborhood organization is apparently lost in the early G1 phase of the cell cycle. However, the daughter cells eventually regain the general chromosomal organization pattern of their mothers, suggesting an active mechanism could be at play to reestablish chromosomal neighborhoods.
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Affiliation(s)
- Jeroen Essers
- Department of Cell Biology and Genetics, Erasmus Medical Center, 3000 DR Rotterdam, The Netherlands
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23
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4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin - poor tracks. BMC Cell Biol 2004; 5:45. [PMID: 15560848 PMCID: PMC535927 DOI: 10.1186/1471-2121-5-45] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Accepted: 11/23/2004] [Indexed: 11/25/2022] Open
Abstract
Background The dynamics of nuclear organization, nuclear bodies and RNPs in particular has been the focus of many studies. To understand their function, knowledge of their spatial nuclear position and temporal translocation is essential. Typically, such studies generate a wealth of data that require novel methods in image analysis and computational tools to quantitatively track particle movement on the background of moving cells and shape changing nuclei. Results We developed a novel 4-D image processing platform (TIKAL) for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software. With this new tool, we studied the dynamics of two different types of nuclear particles, namely nuclear bodies made from GFP-NLS-vimentin and microinjected 0.1 μm – wide polystyrene beads, by live cell time-lapse microscopy combined with single particle tracking and mobility analysis. We now provide a tool for the automatic 3-D analysis of particle movement in parallel with the acquisition of chromatin density data. Conclusions Kinetic analysis revealed 4 modes of movement: confined obstructed, normal diffusion and directed motion. Particle tracking on the background of stained chromatin revealed that particle movement is directly related to local reorganization of chromatin. Further a direct comparison of particle movement in the nucleoplasm and the cytoplasm exhibited an entirely different kinetic behaviour of vimentin particles in both compartments. The kinetics of nuclear particles were slightly affected by depletion of ATP and significantly disturbed by disruption of actin and microtubule networks. Moreover, the hydration state of the nucleus had a strong impact on the mobility of nuclear bodies since both normal diffusion and directed motion were entirely abolished when cells were challenged with 0.6 M sorbitol. This effect correlated with the compaction of chromatin. We conclude that alteration in chromatin density directly influences the mobility of protein assemblies within the nucleus.
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24
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Leung AKL, Gerlich D, Miller G, Lyon C, Lam YW, Lleres D, Daigle N, Zomerdijk J, Ellenberg J, Lamond AI. Quantitative kinetic analysis of nucleolar breakdown and reassembly during mitosis in live human cells. ACTA ACUST UNITED AC 2004; 166:787-800. [PMID: 15353547 PMCID: PMC2172103 DOI: 10.1083/jcb.200405013] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
One of the great mysteries of the nucleolus surrounds its disappearance during mitosis and subsequent reassembly at late mitosis. Here, the relative dynamics of nucleolar disassembly and reformation were dissected using quantitative 4D microscopy with fluorescent protein-tagged proteins in human stable cell lines. The data provide a novel insight into the fates of the three distinct nucleolar subcompartments and their associated protein machineries in a single dividing cell. Before the onset of nuclear envelope (NE) breakdown, nucleolar disassembly started with the loss of RNA polymerase I subunits from the fibrillar centers. Dissociation of proteins from the other subcompartments occurred with faster kinetics but commenced later, coincident with the process of NE breakdown. The reformation pathway also follows a reproducible and defined temporal sequence but the order of reassembly is shown not to be dictated by the order in which individual nucleolar components reaccumulate within the nucleus after mitosis.
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Affiliation(s)
- Anthony Kar Lun Leung
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, UK
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