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Arifulin EA, Musinova YR, Vassetzky YS, Sheval EV. Mobility of Nuclear Components and Genome Functioning. BIOCHEMISTRY (MOSCOW) 2018; 83:690-700. [PMID: 30195325 DOI: 10.1134/s0006297918060068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell nucleus is characterized by strong compartmentalization of structural components in its three-dimensional space. Certain genomic functions are accompanied by changes in the localization of chromatin loci and nuclear bodies. Here we review recent data on the mobility of nuclear components and the role of this mobility in genome functioning.
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Affiliation(s)
- E A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Y R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Y S Vassetzky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.,UMR8126, CNRS, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, 94805, France
| | - E V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France
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2
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Fujita Y, Yamashita T. Spatial organization of genome architecture in neuronal development and disease. Neurochem Int 2017; 119:49-56. [PMID: 28757389 DOI: 10.1016/j.neuint.2017.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/19/2017] [Accepted: 06/26/2017] [Indexed: 01/19/2023]
Abstract
Although mammalian genomes encode genetic information in their linear sequences, their fundamental function with regard to gene expression depends on the higher-order structure of chromosomes. Current techniques for the evaluation of chromosomal structure have revealed that genomes are arranged at several hierarchical levels in three-dimensional space. The spatial organization of genomes involves the formation of chromatin loops that bypass a wide range of genomic distances, providing a connection between enhancers and chromosomal domains. Furthermore, they form chromatin domains that are arranged into chromosome territories in the three-dimensional space of the cell nucleus. Recent studies have shown that the spatial organization of the genome is essential for normal brain development and function. Activity-dependent alterations in the spatial organization of the genome can regulate transcriptional activity related to neuronal plasticity. Disruptions in the higher-order chromatin architecture have been implicated in neuropsychiatric disorders, such as cognitive dysfunction and anxiety. Here, we discuss the growing interest in the role of genome organization in brain development and neurological disorders.
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Affiliation(s)
- Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Franek M, Suchánková J, Sehnalová P, Krejčí J, Legartová S, Kozubek S, Večeřa J, Sorokin DV, Bártová E. Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:326-341. [PMID: 26903193 DOI: 10.1017/s1431927616000052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Studies on fixed samples or genome-wide analyses of nuclear processes are useful for generating snapshots of a cell population at a particular time point. However, these experimental approaches do not provide information at the single-cell level. Genome-wide studies cannot assess variability between individual cells that are cultured in vitro or originate from different pathological stages. Immunohistochemistry and immunofluorescence are fundamental experimental approaches in clinical laboratories and are also widely used in basic research. However, the fixation procedure may generate artifacts and prevents monitoring of the dynamics of nuclear processes. Therefore, live-cell imaging is critical for studying the kinetics of basic nuclear events, such as DNA replication, transcription, splicing, and DNA repair. This review is focused on the advanced microscopy analyses of the cells, with a particular focus on live cells. We note some methodological innovations and new options for microscope systems that can also be used to study tissue sections. Cornerstone methods for the biophysical research of living cells, such as fluorescence recovery after photobleaching and fluorescence resonance energy transfer, are also discussed, as are studies on the effects of radiation at the individual cellular level.
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Affiliation(s)
- Michal Franek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Suchánková
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Krejčí
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Soňa Legartová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | | | | | - Eva Bártová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
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de Castro IJ, Gokhan E, Vagnarelli P. Resetting a functional G1 nucleus after mitosis. Chromosoma 2016; 125:607-19. [PMID: 26728621 PMCID: PMC5023730 DOI: 10.1007/s00412-015-0561-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/13/2015] [Indexed: 12/21/2022]
Abstract
The maintenance of the correct cellular information goes beyond the simple transmission of an intact genetic code from one generation to the next. Epigenetic changes, topological cues and correct protein-protein interactions need to be re-established after each cell division to allow the next cell cycle to resume in the correct regulated manner. This process begins with mitotic exit and re-sets all the changes that occurred during mitosis thus restoring a functional G1 nucleus in preparation for the next cell cycle. Mitotic exit is triggered by inactivation of mitotic kinases and the reversal of their phosphorylation activities on many cellular components, from nuclear lamina to transcription factors and chromatin itself. To reverse all these phosphorylations, phosphatases act during mitotic exit in a timely and spatially controlled manner directing the events that lead to a functional G1 nucleus. In this review, we will summarise the recent developments on the control of phosphatases and their known substrates during mitotic exit, and the key steps that control the restoration of chromatin status, nuclear envelope reassembly and nuclear body re-organisation. Although pivotal work has been conducted in this area in yeast, due to differences between the mitotic exit network between yeast and vertebrates, we will mainly concentrate on the vertebrate system.
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Affiliation(s)
- Ines J de Castro
- College of Health and Life Science, Research Institute of Environment Health and Society, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Ezgi Gokhan
- College of Health and Life Science, Research Institute of Environment Health and Society, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute of Environment Health and Society, Brunel University London, Uxbridge, UB8 3PH, UK.
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5
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Suchánková J, Legartová S, Sehnalová P, Kozubek S, Valente S, Labella D, Mai A, Eckerich C, Fackelmayer FO, Sorokin DV, Bartova E. PRMT1 arginine methyltransferase accumulates in cytoplasmic bodies that respond to selective inhibition and DNA damage. Eur J Histochem 2014; 58:2389. [PMID: 24998928 PMCID: PMC4083328 DOI: 10.4081/ejh.2014.2389] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 12/18/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) are responsible for symmetric and asymmetric methylation of arginine residues of nuclear and cytoplasmic proteins. In the nucleus, PRMTs belong to important chromatin modifying enzymes of immense functional significance that affect gene expression, splicing and DNA repair. By time-lapse microscopy we have studied the sub-cellular localization and kinetics of PRMT1 after inhibition of PRMT1 and after irradiation. Both transiently expressed and endogenous PRMT1 accumulated in cytoplasmic bodies that were located in the proximity of the cell nucleus. The shape and number of these bodies were stable in untreated cells. However, when cell nuclei were microirradiated by UV-A, the mobility of PRMT1 cytoplasmic bodies increased their, size was reduced, and they disappeared within approximately 20 min. The same response occurred after γ-irradiation of the whole cell population, but with delayed kinetics. Treatment with PRMT1 inhibitors induced disintegration of these PRMT1 cytoplasmic bodies and prevented formation of 53BP1 nuclear bodies (NBs) that play a role during DNA damage repair. The formation of 53BP1 NBs was not influenced by PRMT1 over-expression. Taken together, we show that PRMT1 concentrates in cytoplasmic bodies, which respond to DNA injury in the cell nucleus, and to treatment with various PRMT1 inhibitors.
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Legartová S, Stixová L, Laur O, Kozubek S, Sehnalová P, Bártová E. Nuclear Structures Surrounding Internal Lamin Invaginations. J Cell Biochem 2014; 115:476-87. [DOI: 10.1002/jcb.24681] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/23/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Soňa Legartová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Lenka Stixová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Oskar Laur
- Emory University School of Medicine; Emory University; Atlanta Georgia 30322
| | - Stanislav Kozubek
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Eva Bártová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
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Relevance and limitations of crowding, fractal, and polymer models to describe nuclear architecture. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:443-79. [PMID: 24380602 DOI: 10.1016/b978-0-12-800046-5.00013-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chromosome architecture plays an essential role for all nuclear functions, and its physical description has attracted considerable interest over the last few years among the biophysics community. These researches at the frontiers of physics and biology have been stimulated by the demand for quantitative analysis of molecular biology experiments, which provide comprehensive data on chromosome folding, or of live cell imaging experiments that enable researchers to visualize selected chromosome loci in living or fixed cells. In this review our goal is to survey several nonmutually exclusive models that have emerged to describe the folding of DNA in the nucleus, the dynamics of proteins in the nucleoplasm, or the movements of chromosome loci. We focus on three classes of models, namely molecular crowding, fractal, and polymer models, draw comparisons, and discuss their merits and limitations in the context of chromosome structure and dynamics, or nuclear protein navigation in the nucleoplasm. Finally, we identify future challenges in the roadmap to a unified model of the nuclear environment.
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8
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Chromosomal contact permits transcription between coregulated genes. Cell 2013; 155:606-20. [PMID: 24243018 DOI: 10.1016/j.cell.2013.09.051] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/18/2013] [Accepted: 09/23/2013] [Indexed: 12/11/2022]
Abstract
Transcription of coregulated genes occurs in the context of long-range chromosomal contacts that form multigene complexes. Such contacts and transcription are lost in knockout studies of transcription factors and structural chromatin proteins. To ask whether chromosomal contacts are required for cotranscription in multigene complexes, we devised a strategy using TALENs to cleave and disrupt gene loops in a well-characterized multigene complex. Monitoring this disruption using RNA FISH and immunofluorescence microscopy revealed that perturbing the site of contact had a direct effect on transcription of other interacting genes. Unexpectedly, this effect on cotranscription was hierarchical, with dominant and subordinate members of the multigene complex engaged in both intra- and interchromosomal contact. This observation reveals the profound influence of these chromosomal contacts on the transcription of coregulated genes in a multigene complex.
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Přikrylová T, Pacherník J, Kozubek S, Bártová E. Epigenetics and chromatin plasticity in embryonic stem cells. World J Stem Cells 2013; 5:73-85. [PMID: 23951389 PMCID: PMC3744133 DOI: 10.4252/wjsc.v5.i3.73] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/18/2013] [Accepted: 06/05/2013] [Indexed: 02/06/2023] Open
Abstract
The study of embryonic stem cells is in the spotlight in many laboratories that study the structure and function of chromatin and epigenetic processes. The key properties of embryonic stem cells are their capacity for self-renewal and their pluripotency. Pluripotent stem cells are able to differentiate into the cells of all three germ layers, and because of this property they represent a promising therapeutic tool in the treatment of diseases such as Parkinson's disease and diabetes, or in the healing of lesions after heart attack. As the basic nuclear unit, chromatin is responsible for the regulation of the functional status of cells, including pluripotency and differentiation. Therefore, in this review we discuss the functional changes in chromatin during differentiation and the correlation between epigenetics events and the differentiation potential of embryonic stem cells. In particular we focus on post-translational histone modification, DNA methylation and the heterochromatin protein HP1 and its unique function in mouse and human embryonic stem cells.
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Affiliation(s)
- Terézia Přikrylová
- Terézia Přikrylová, Stanislav Kozubek, Eva Bártová, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
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Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell 2013; 49:773-82. [PMID: 23473598 DOI: 10.1016/j.molcel.2013.02.011] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/17/2012] [Accepted: 02/06/2013] [Indexed: 12/21/2022]
Abstract
Mammalian genomes encode genetic information in their linear sequence, but appropriate expression of their genes requires chromosomes to fold into complex three-dimensional structures. Transcriptional control involves the establishment of physical connections among genes and regulatory elements, both along and between chromosomes. Recent technological innovations in probing the folding of chromosomes are providing new insights into the spatial organization of genomes and its role in gene regulation. It is emerging that folding of large complex chromosomes involves a hierarchy of structures, from chromatin loops that connect genes and enhancers to larger chromosomal domains and nuclear compartments. The larger these structures are along this hierarchy, the more stable they are within cells, while becoming more stochastic between cells. Here, we review the experimental and theoretical data on this hierarchy of structures and propose a key role for the recently discovered topologically associating domains.
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Affiliation(s)
- Johan H Gibcus
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
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