1
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Chang L, Li M, Shao S, Li C, Ai S, Xue B, Hou Y, Zhang Y, Li R, Fan X, He A, Li C, Sun Y. Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells. Protein Cell 2022; 13:258-280. [PMID: 33155082 PMCID: PMC8934373 DOI: 10.1007/s13238-020-00794-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.
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Affiliation(s)
- Lei Chang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Mengfan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Shipeng Shao
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Chen Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Shanshan Ai
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Yingping Hou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiwen Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
| | - Ruifeng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoying Fan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510530 China
| | - Aibin He
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Statistical Science, Peking University, Beijing, 100871 China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871 China
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2
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Kim KD. Potential roles of condensin in genome organization and beyond in fission yeast. J Microbiol 2021; 59:449-459. [PMID: 33877578 DOI: 10.1007/s12275-021-1039-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/24/2022]
Abstract
The genome is highly organized hierarchically by the function of structural maintenance of chromosomes (SMC) complex proteins such as condensin and cohesin from bacteria to humans. Although the roles of SMC complex proteins have been well characterized, their specialized roles in nuclear processes remain unclear. Condensin and cohesin have distinct binding sites and mediate long-range and short-range genomic associations, respectively, to form cell cycle-specific genome organization. Condensin can be recruited to highly expressed genes as well as dispersed repeat genetic elements, such as Pol III-transcribed genes, LTR retrotransposon, and rDNA repeat. In particular, mitotic transcription factors Ace2 and Ams2 recruit condensin to their target genes, forming centromeric clustering during mitosis. Condensin is potentially involved in various chromosomal processes such as the mobility of chromosomes, chromosome territories, DNA reannealing, and transcription factories. The current knowledge of condensin in fission yeast summarized in this review can help us understand how condensin mediates genome organization and participates in chromosomal processes in other organisms.
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Affiliation(s)
- Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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3
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Gallardo P, Barrales RR, Daga RR, Salas-Pino S. Nuclear Mechanics in the Fission Yeast. Cells 2019; 8:cells8101285. [PMID: 31635174 PMCID: PMC6829894 DOI: 10.3390/cells8101285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022] Open
Abstract
In eukaryotic cells, the organization of the genome within the nucleus requires the nuclear envelope (NE) and its associated proteins. The nucleus is subjected to mechanical forces produced by the cytoskeleton. The physical properties of the NE and the linkage of chromatin in compacted conformation at sites of cytoskeleton contacts seem to be key for withstanding nuclear mechanical stress. Mechanical perturbations of the nucleus normally occur during nuclear positioning and migration. In addition, cell contraction or expansion occurring for instance during cell migration or upon changes in osmotic conditions also result innuclear mechanical stress. Recent studies in Schizosaccharomyces pombe (fission yeast) have revealed unexpected functions of cytoplasmic microtubules in nuclear architecture and chromosome behavior, and have pointed to NE-chromatin tethers as protective elements during nuclear mechanics. Here, we review and discuss how fission yeast cells can be used to understand principles underlying the dynamic interplay between genome organization and function and the effect of forces applied to the nucleus by the microtubule cytoskeleton.
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Affiliation(s)
- Paola Gallardo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Silvia Salas-Pino
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
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4
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Zhurinsky J, Salas-Pino S, Iglesias-Romero AB, Torres-Mendez A, Knapp B, Flor-Parra I, Wang J, Bao K, Jia S, Chang F, Daga RR. Effects of the microtubule nucleator Mto1 on chromosomal movement, DNA repair, and sister chromatid cohesion in fission yeast. Mol Biol Cell 2019; 30:2695-2708. [PMID: 31483748 PMCID: PMC6761766 DOI: 10.1091/mbc.e19-05-0301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 11/11/2022] Open
Abstract
Although the function of microtubules (MTs) in chromosomal segregation during mitosis is well characterized, much less is known about the role of MTs in chromosomal functions during interphase. In the fission yeast Schizosaccharomyces pombe, dynamic cytoplasmic MT bundles move chromosomes in an oscillatory manner during interphase via linkages through the nuclear envelope (NE) at the spindle pole body (SPB) and other sites. Mto1 is a cytoplasmic factor that mediates the nucleation and attachment of cytoplasmic MTs to the nucleus. Here, we test the function of these cytoplasmic MTs and Mto1 on DNA repair and recombination during interphase. We find that mto1Δ cells exhibit defects in DNA repair and homologous recombination (HR) and abnormal DNA repair factory dynamics. In these cells, sister chromatids are not properly paired, and binding of Rad21 cohesin subunit along chromosomal arms is reduced. Our findings suggest a model in which cytoplasmic MTs and Mto1 facilitate efficient DNA repair and HR by promoting dynamic chromosomal organization and cohesion in the nucleus.
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Affiliation(s)
- Jacob Zhurinsky
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Silvia Salas-Pino
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Ana B. Iglesias-Romero
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Antonio Torres-Mendez
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Benjamin Knapp
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - Ignacio Flor-Parra
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Jiyong Wang
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Kehan Bao
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Songtao Jia
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Fred Chang
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - Rafael R. Daga
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
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5
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Spindle pole body movement is affected by glucose and ammonium chloride in fission yeast. Biochem Biophys Res Commun 2019; 511:820-825. [PMID: 30846209 DOI: 10.1016/j.bbrc.2019.02.128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/23/2019] [Indexed: 02/06/2023]
Abstract
The complexity of chromatin dynamics is orchestrated by several active processes. In fission yeast, the centromeres are clustered around the spindle pole body (SPB) and oscillate in a microtubule- and adenosine triphosphate (ATP)-dependent manner. However, whether and how SPB oscillation are affected by different environmental conditions remain poorly understood. In this study, we quantitated movements of the SPB component, which colocalizes with the centromere in fission yeast. We found that SPB movement was significantly reduced at low glucose concentrations. Movement of the SPB was also affected by the presence of ammonium chloride. Power spectral analysis revealed that periodic movement of the SPB is disrupted by low glucose concentrations. Measurement of ATP levels in living cells by quantitative single-cell imaging suggests that ATP levels are not the only determinant of SPB movement. Our results provide novel insight into how SPB movement is regulated by cellular energy status and additional factors such as the medium nutritional composition.
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6
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Abstract
The three-dimensional (3D) genome structure is highly ordered by a hierarchy of organizing events ranging from enhancer-promoter or gene-gene contacts to chromosomal territorial arrangement. It is becoming clear that the cohesin and condensin complexes are key molecular machines that organize the 3D genome structure. These complexes are highly conserved from simple systems, e.g., yeast cells, to the much more complex human system. Therefore, knowledge from the budding and fission yeast systems illuminates highly conserved molecular mechanisms of how cohesin and condensin establish the functional 3D genome structures. Here I discuss how these complexes are recruited across the yeast genomes, mediate distinct genome-organizing events such as gene contacts and topological domain formation, and participate in important nuclear activities including transcriptional regulation and chromosomal dynamics.
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Affiliation(s)
- Ken-Ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA;
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7
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Tanizawa H, Kim KD, Iwasaki O, Noma KI. Architectural alterations of the fission yeast genome during the cell cycle. Nat Struct Mol Biol 2017; 24:965-976. [PMID: 28991264 PMCID: PMC5724045 DOI: 10.1038/nsmb.3482] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/13/2017] [Indexed: 02/03/2023]
Abstract
Eukaryotic genomes are highly ordered through various mechanisms, including topologically associating domain (TAD) organization. We employed an in situ Hi-C approach to follow the 3D organization of the fission yeast genome during the cell cycle. We demonstrate that during mitosis, large domains of 300 kb-1 Mb are formed by condensin. This mitotic domain organization does not suddenly dissolve, but gradually diminishes until the next mitosis. By contrast, small domains of 30-40 kb that are formed by cohesin are relatively stable across the cell cycle. Condensin and cohesin mediate long- and short-range contacts, respectively, by bridging their binding sites, thereby forming the large and small domains. These domains are inversely regulated during the cell cycle but assemble independently. Our study describes the chromosomal oscillation between the formation and decay phases of the large and small domains, and we predict that the condensin-mediated domains serve as chromosomal compaction units.
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Affiliation(s)
| | | | - Osamu Iwasaki
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Ken-Ichi Noma
- The Wistar Institute, Philadelphia, Pennsylvania, USA
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8
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Rana V, Bosco G. Condensin Regulation of Genome Architecture. J Cell Physiol 2017; 232:1617-1625. [PMID: 27888504 DOI: 10.1002/jcp.25702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
Condensin complexes exist across all domains of life and are central to the structure and organization of chromatin. As architectural proteins, condensins control chromatin compaction during interphase and mitosis. Condensin activity has been well studied in mitosis but have recently emerged as important regulators of genome organization and gene expression during interphase. Here, we focus our discussion on recent findings on the molecular mechanism and how condensins are used to shape chromosomes during interphase. These findings suggest condensin activity during interphase is required for proper chromosome organization. J. Cell. Physiol. 232: 1617-1625, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vibhuti Rana
- Department of Molecular Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Giovanni Bosco
- Department of Molecular Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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9
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Kim KD, Tanizawa H, Iwasaki O, Noma KI. Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. Nat Genet 2016; 48:1242-52. [PMID: 27548313 PMCID: PMC5042855 DOI: 10.1038/ng.3647] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/22/2016] [Indexed: 12/13/2022]
Abstract
It is becoming clear that structural-maintenance-of-chromosomes (SMC) complexes such as condensin and cohesin are involved in three-dimensional genome organization, yet their exact roles in functional organization remain unclear. We used chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) to comprehensively identify genome-wide associations mediated by condensin and cohesin in fission yeast. We found that although cohesin and condensin often bind to the same loci, they direct different association networks and generate small and larger chromatin domains, respectively. Cohesin mediates associations between loci positioned within 100 kb of each other; condensin can drive longer-range associations. Moreover, condensin, but not cohesin, connects cell cycle-regulated genes bound by mitotic transcription factors. This study describes the different functions of condensin and cohesin in genome organization and how specific transcription factors function in condensin loading, cell cycle-dependent genome organization and mitotic chromosome organization to support faithful chromosome segregation.
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10
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Kim KD, Iwasaki O, Noma K. An IF-FISH Approach for Covisualization of Gene Loci and Nuclear Architecture in Fission Yeast. Methods Enzymol 2016; 574:167-180. [PMID: 27423862 DOI: 10.1016/bs.mie.2016.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent genomic studies have revealed that chromosomal structures are formed by a hierarchy of organizing processes ranging from gene associations, including interactions among enhancers and promoters, to topologically associating domain formations. Gene associations identified by these studies can be characterized by microscopic analyses. Fission yeast is a model organism, in which gene associations have been broadly mapped across the genome, although many of those associations have not been further examined by cell biological approaches. To address the technically challenging process of the visualization of associating gene loci in the fission yeast nuclei, we provide, in detail, an IF-FISH procedure that allows for covisualizing both gene loci and nuclear structural markers such as the nuclear membrane and nucleolus.
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Affiliation(s)
- K-D Kim
- The Wistar Institute, Philadelphia, PA, United States
| | - O Iwasaki
- The Wistar Institute, Philadelphia, PA, United States
| | - K Noma
- The Wistar Institute, Philadelphia, PA, United States.
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11
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Iwasaki O, Corcoran CJ, Noma KI. Involvement of condensin-directed gene associations in the organization and regulation of chromosome territories during the cell cycle. Nucleic Acids Res 2016; 44:3618-28. [PMID: 26704981 PMCID: PMC4856965 DOI: 10.1093/nar/gkv1502] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/11/2014] [Accepted: 12/14/2015] [Indexed: 11/14/2022] Open
Abstract
Chromosomes are not randomly disposed in the nucleus but instead occupy discrete sub-nuclear domains, referred to as chromosome territories. The molecular mechanisms that underlie the formation of chromosome territories and how they are regulated during the cell cycle remain largely unknown. Here, we have developed two different chromosome-painting approaches to address how chromosome territories are organized in the fission yeast model organism. We show that condensin frequently associates RNA polymerase III-transcribed genes (tRNA and 5S rRNA) that are present on the same chromosomes, and that the disruption of these associations by condensin mutations significantly compromises the chromosome territory arrangement. We also find that condensin-dependent intra-chromosomal gene associations and chromosome territories are co-regulated during the cell cycle. For example, condensin-directed gene associations occur to the least degree during S phase, with the chromosomal overlap becoming largest. In clear contrast, condensin-directed gene associations become tighter in other cell-cycle phases, especially during mitosis, with the overlap between the different chromosomes being smaller. This study suggests that condensin-driven intra-chromosomal gene associations contribute to the organization and regulation of chromosome territories during the cell cycle.
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12
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Mizuguchi T, Barrowman J, Grewal SIS. Chromosome domain architecture and dynamic organization of the fission yeast genome. FEBS Lett 2015; 589:2975-86. [PMID: 26096785 PMCID: PMC4598268 DOI: 10.1016/j.febslet.2015.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 12/20/2022]
Abstract
Advanced techniques including the chromosome conformation capture (3C) methodology and its derivatives are complementing microscopy approaches to study genome organization, and are revealing new details of three-dimensional (3D) genome architecture at increasing resolution. The fission yeast Schizosaccharomyces pombe (S. pombe) comprises a small genome featuring organizational elements of more complex eukaryotic systems, including conserved heterochromatin assembly machinery. Here we review key insights into genome organization revealed in this model system through a variety of techniques. We discuss the predominant role of Rabl-like configuration for interphase chromosome organization and the dynamic changes that occur during mitosis and meiosis. High resolution Hi-C studies have also revealed the presence of locally crumpled chromatin regions called "globules" along chromosome arms, and implicated a critical role for pericentromeric heterochromatin in imposing fundamental constraints on the genome to maintain chromosome territoriality and stability. These findings have shed new light on the connections between genome organization and function. It is likely that insights gained from the S. pombe system will also broadly apply to higher eukaryotes.
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Affiliation(s)
- Takeshi Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jemima Barrowman
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Awazu A. Nuclear dynamical deformation induced hetero- and euchromatin positioning. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:032709. [PMID: 26465500 DOI: 10.1103/physreve.92.032709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Indexed: 06/05/2023]
Abstract
We studied the role of active deformation dynamics in cell nuclei in chromatin positioning. Model chains containing two types of regions, with high (euchromatic) or low (heterochromatic) mobility, were confined in a pulsating container simulating a nucleus showing dynamic deformations. Brownian dynamic simulations show that the positioning of low mobility regions changes from sites near the periphery to the center if the affinity between these regions and the container periphery disappears. The former and latter positionings are similar to the "conventional" and "inverted" chromatin positionings in nuclei of normal differentiated cells and cells lacking Lamin-related proteins. Additionally, nuclear dynamical deformation played essential roles in "inverted" chromatin positioning.
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Affiliation(s)
- Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima University and Research Center for Mathematics on Chromatin Live Dynamics, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan
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14
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Iwasaki O, Tanizawa H, Kim KD, Yokoyama Y, Corcoran CJ, Tanaka A, Skordalakes E, Showe LC, Noma KI. Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes. Mol Cell 2015; 59:755-67. [PMID: 26257282 DOI: 10.1016/j.molcel.2015.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/16/2015] [Accepted: 07/01/2015] [Indexed: 10/25/2022]
Abstract
Genome/chromosome organization is highly ordered and controls various nuclear events, although the molecular mechanisms underlying the functional organization remain largely unknown. Here, we show that the TATA box-binding protein (TBP) interacts with the Cnd2 kleisin subunit of condensin to mediate interphase and mitotic chromosomal organization in fission yeast. TBP recruits condensin onto RNA polymerase III-transcribed (Pol III) genes and highly transcribed Pol II genes; condensin in turn associates these genes with centromeres. Inhibition of the Cnd2-TBP interaction disrupts condensin localization across the genome and the proper assembly of mitotic chromosomes, leading to severe defects in chromosome segregation and eventually causing cellular lethality. We propose that the Cnd2-TBP interaction coordinates transcription with chromosomal architecture by linking dispersed gene loci with centromeres. This chromosome arrangement can contribute to the efficient transmission of physical force at the kinetochore to chromosomal arms, thereby supporting the fidelity of chromosome segregation.
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15
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Glunčić M, Maghelli N, Krull A, Krstić V, Ramunno-Johnson D, Pavin N, Tolić IM. Kinesin-8 motors improve nuclear centering by promoting microtubule catastrophe. PHYSICAL REVIEW LETTERS 2015; 114:078103. [PMID: 25763975 DOI: 10.1103/physrevlett.114.078103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Indexed: 06/04/2023]
Abstract
In fission yeast, microtubules push against the cell edge, thereby positioning the nucleus in the cell center. Kinesin-8 motors regulate microtubule catastrophe; however, their role in nuclear positioning is not known. Here we develop a physical model that describes how kinesin-8 motors affect nuclear centering by promoting a microtubule catastrophe. Our model predicts the improved centering of the nucleus in the presence of motors, which we confirmed experimentally in living cells. The model also predicts a characteristic time for the recentering of a displaced nucleus, which is supported by our experiments where we displaced the nucleus using optical tweezers.
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Affiliation(s)
- Matko Glunčić
- Department of Physics, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Nicola Maghelli
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Alexander Krull
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Vladimir Krstić
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | | | - Nenad Pavin
- Department of Physics, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Iva M Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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