1
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Wang WJ, Tan CP, Mao ZW. Metals and inorganic molecules in regulating protein and nucleic acid phase separation. Curr Opin Chem Biol 2023; 74:102308. [PMID: 37088005 DOI: 10.1016/j.cbpa.2023.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/25/2023]
Abstract
The realization that liquid-liquid phase separation (LLPS) underlies the formation of membraneless compartments in cells has motivated efforts to modulate the condensation process of biomolecules. Increasing evidence shows that metals and inorganic molecules abundantly distributed in cells play important roles in the regulation of biomolecular condensation. Herein, we briefly reviewed the background of biomacromolecular phase separation and summarized the recent research progress on the roles of metals and inorganic molecules in regulating protein and nucleic acid phase separation in vitro and in cells.
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Affiliation(s)
- Wen-Jin Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510006, PR China
| | - Cai-Ping Tan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510006, PR China.
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510006, PR China.
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2
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Sun T, Minhas V, Mirzoev A, Korolev N, Lyubartsev AP, Nordenskiöld L. A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions. J Chem Theory Comput 2022; 18:3948-3960. [PMID: 35580041 PMCID: PMC9202350 DOI: 10.1021/acs.jctc.2c00083] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(H2O)62+ or Co(NH3)63+) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.
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Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
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3
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Hiltner L, Carme Calderer M, Arsuaga J, Vázquez M. Chromonic liquid crystals and packing configurations of bacteriophage viruses. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200111. [PMID: 34024128 DOI: 10.1098/rsta.2020.0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
We study equilibrium configurations of hexagonal columnar liquid crystals in the context of characterizing packing structures of bacteriophage viruses in a protein capsid. These are viruses that infect bacteria and are currently the focus of intense research efforts, with the goal of finding new therapies for bacteria-resistant antibiotics. The energy that we propose consists of the Oseen-Frank free energy of nematic liquid crystals that penalizes bending of the columnar directions, in addition to the cross-sectional elastic energy accounting for distortions of the transverse hexagonal structure; we also consider the isotropic contribution of the core and the energy of the unknown interface between the outer ordered region of the capsid and the inner disordered core. The problem becomes of free boundary type, with constraints. We show that the concentric, azimuthal, spool-like configuration is the absolute minimizer. Moreover, we present examples of toroidal structures formed by DNA in free solution and compare them with the analogous ones occurring in experiments with other types of lyotropic liquid crystals, such as food dyes and additives. This article is part of the theme issue 'Topics in mathematical design of complex materials'.
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Affiliation(s)
- Lindsey Hiltner
- School of Mathematics, University of Minnesota, Minneapolis, MN 55442, USA
| | - M Carme Calderer
- School of Mathematics, University of Minnesota, Minneapolis, MN 55442, USA
| | - Javier Arsuaga
- Department of Cellular and Molecular Biology, Briggs Hall, Davis, CA 09
- Department of Mathematics, MSB, 2115, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Mariel Vázquez
- Department of Mathematics, MSB, 2150, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
- Department of Microbiology and Molecular Genetics, Briggs Hall, Davis, CA 09
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4
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Daban JR. Soft-matter properties of multilayer chromosomes. Phys Biol 2021; 18. [PMID: 34126606 DOI: 10.1088/1478-3975/ac0aff] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 06/14/2021] [Indexed: 12/17/2022]
Abstract
This perspective aims to identify the relationships between the structural and dynamic properties of chromosomes and the fundamental properties of soft-matter systems. Chromatin is condensed into metaphase chromosomes during mitosis. The resulting structures are elongated cylinders having micrometer-scale dimensions. Our previous studies, using transmission electron microscopy, atomic force microscopy, and cryo-electron tomography, suggested that metaphase chromosomes have a multilayered structure, in which each individual layer has the width corresponding to a mononucleosome sheet. The self-assembly of multilayer chromatin plates from small chromatin fragments suggests that metaphase chromosomes are self-organized hydrogels (in which a single DNA molecule crosslinks the whole structure) with an internal liquid-crystal order produced by the stacking of chromatin layers along the chromosome axis. This organization of chromatin was unexpected, but the spontaneous assembly of large structures has been studied in different soft-matter systems and, according to these studies, the self-organization of chromosomes could be justified by the interplay between weak interactions of repetitive nucleosome building blocks and thermal fluctuations. The low energy of interaction between relatively large building blocks also justifies the easy deformation and structural fluctuations of soft-matter structures and the changes of phase caused by diverse external factors. Consistent with these properties of soft matter, different experimental results show that metaphase chromosomes are easily deformable. Furthermore, at the end of mitosis, condensed chromosomes undergo a phase transition into a more fluid structure, which can be correlated to the decrease in the Mg2+concentration and to the dissociation of condensins from chromosomes. Presumably, the unstacking of layers and chromatin fluctuations driven by thermal energy facilitate gene expression during interphase.
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Affiliation(s)
- Joan-Ramon Daban
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
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5
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King JT, Shakya A. Phase separation of DNA: From past to present. Biophys J 2021; 120:1139-1149. [PMID: 33582138 PMCID: PMC8059212 DOI: 10.1016/j.bpj.2021.01.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/11/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
Phase separation of biological molecules, such as nucleic acids and proteins, has garnered widespread attention across many fields in recent years. For instance, liquid-liquid phase separation has been implicated not only in membraneless intracellular organization but also in many biochemical processes, including transcription, translation, and cellular signaling. Here, we present a historical background of biological phase separation and survey current work on nuclear organization and its connection to DNA phase separation from the perspective of DNA sequence, structure, and genomic context.
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Affiliation(s)
- John T King
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
| | - Anisha Shakya
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
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6
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Lopes JT, Romano F, Grelet E, Franco LFM, Giacometti A. Phase behavior of hard cylinders. J Chem Phys 2021; 154:104902. [PMID: 33722037 DOI: 10.1063/5.0040942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Using isobaric Monte Carlo simulations, we map out the entire phase diagram of a system of hard cylindrical particles of length (L) and diameter (D) using an improved algorithm to identify the overlap condition between two cylinders. Both the prolate L/D > 1 and the oblate L/D < 1 phase diagrams are reported with no solution of continuity. In the prolate L/D > 1 case, we find intermediate nematic N and smectic SmA phases in addition to a low density isotropic I and a high density crystal X phase with I-N-SmA and I-SmA-X triple points. An apparent columnar phase C is shown to be metastable, as in the case of spherocylinders. In the oblate L/D < 1 case, we find stable intermediate cubatic (Cub), nematic (N), and columnar (C) phases with I-N-Cub, N-Cub-C, and I-Cub-C triple points. Comparison with previous numerical and analytical studies is discussed. The present study, accounting for the explicit cylindrical shape, paves the way to more sophisticated models with important biological applications, such as viruses and nucleosomes.
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Affiliation(s)
- Joyce T Lopes
- Universidade Estadual de Campinas, Faculdade de Engenharia Química, Departamento de Engenharia de Sistemas Químicos, Campinas, Brazil
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
| | - Eric Grelet
- Université de Bordeaux, CNRS, Centre de Recherche Paul-Pascal, 115 Avenue Schweitzer, 33600 Pessac, France
| | - Luís F M Franco
- Universidade Estadual de Campinas, Faculdade de Engenharia Química, Departamento de Engenharia de Sistemas Químicos, Campinas, Brazil
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy
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7
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Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Sci Rep 2021; 11:380. [PMID: 33432055 PMCID: PMC7801413 DOI: 10.1038/s41598-020-79654-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023] Open
Abstract
Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.
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Marr LT, Ocampo J, Clark DJ, Hayes JJ. Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes. Epigenetics Chromatin 2021; 14:5. [PMID: 33430969 PMCID: PMC7802155 DOI: 10.1186/s13072-020-00381-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/28/2020] [Indexed: 01/09/2023] Open
Abstract
Background The vast majority of methods available to characterize genome-wide chromatin structure exploit differences in DNA accessibility to nucleases or chemical crosslinking. We developed a novel method to gauge genome-wide accessibility of histone protein surfaces within nucleosomes by assessing reactivity of engineered cysteine residues with a thiol-specific reagent, biotin-maleimide (BM). Results Yeast nuclei were obtained from cells expressing the histone mutant H2B S116C, in which a cysteine resides near the center of the external flat protein surface of the nucleosome. BM modification revealed that nucleosomes are generally equivalently accessible throughout the S. cerevisiae genome, including heterochromatic regions, suggesting limited, higher-order chromatin structures in which this surface is obstructed by tight nucleosome packing. However, we find that nucleosomes within 500 bp of transcription start sites exhibit the greatest range of accessibility, which correlates with the density of chromatin remodelers. Interestingly, accessibility is not well correlated with RNA polymerase density and thus the level of gene expression. We also investigated the accessibility of cysteine mutations designed to detect exposure of histone surfaces internal to the nucleosome thought to be accessible in actively transcribed genes: H3 102, is at the H2A–H2B dimer/H3–H4 tetramer interface, and H3 A110C, resides at the H3–H3 interface. However, in contrast to the external surface site, we find that neither of these internal sites were found to be appreciably exposed. Conclusions Overall, our finding that nucleosomes surfaces within S. cerevisiae chromatin are equivalently accessible genome-wide is consistent with a globally uncompacted chromatin structure lacking substantial higher-order organization. However, we find modest differences in accessibility that correlate with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible than actively transcribed or intergenic regions. In contrast, we find that two internal sites remain inaccessible, suggesting that such non-canonical nucleosome species generated during transcription are rapidly and efficiently converted to canonical nucleosome structure and thus not widely present in native chromatin.
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Affiliation(s)
- Luke T Marr
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI-CONICET), C1428ADN, Buenos Aires, Argentina
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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le Paige UB, Xiang S, Hendrix MMRM, Zhang Y, Folkers GE, Weingarth M, Bonvin AMJJ, Kutateladze TG, Voets IK, Baldus M, van Ingen H. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:187-202. [PMID: 35647606 PMCID: PMC9135053 DOI: 10.5194/mr-2-187-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins with the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ~ 200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein-binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle X-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low-affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.
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Affiliation(s)
- Ulric B. le Paige
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - ShengQi Xiang
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Marco M. R. M. Hendrix
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gert E. Folkers
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Alexandre M. J. J. Bonvin
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Marc Baldus
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Hugo van Ingen
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
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Saurabh S, Jang YH, Lansac Y, Maiti PK. Orientation Dependence of Inter-NCP Interaction: Insights into the Behavior of Liquid Crystal Phase and Chromatin Fiber Organization. J Phys Chem B 2019; 124:314-323. [DOI: 10.1021/acs.jpcb.9b07898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suman Saurabh
- GREMAN, University of Tours, CNRS UMR 7347, 37200 Tours, France
- Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans, France
| | - Yun Hee Jang
- Department of Energy Science and Engineering, DGIST, Daegu 42988, Korea
| | - Yves Lansac
- GREMAN, University of Tours, CNRS UMR 7347, 37200 Tours, France
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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11
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Eltsov M, Grewe D, Lemercier N, Frangakis A, Livolant F, Leforestier A. Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections. Nucleic Acids Res 2019; 46:9189-9200. [PMID: 30053160 PMCID: PMC6158616 DOI: 10.1093/nar/gky670] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/13/2018] [Indexed: 01/04/2023] Open
Abstract
In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. Atomic structures have been obtained from crystallography and single particle cryo-electron microscopy (cryoEM) of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequence and histone content, and little is known about their conformational variability, especially in the cellular context. Using cryoEM and tomography of vitreous sections we analyse native nucleosomes, both in vitro, using purified particles solubilized at physiologically relevant concentrations (25–50%), and in situ, within interphase nuclei. We visualize individual nucleosomes at a level of detail that allows us to measure the distance between the DNA gyres wrapped around. In concentrated solutions, we demonstrate a salt-dependent transition, with a high salt compact conformation resembling the canonical nucleosome and an open low salt one, closer to nuclear nucleosomes. Although further particle characterization and cartography are needed to understand the relationship between this conformational variability and chromatin functional states, this work opens a route to chromatin exploration in situ.
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Affiliation(s)
- Mikhail Eltsov
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Diana Grewe
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Nicolas Lemercier
- Laboratoire de Physique des Solides, UMR 8502 CNRS, Université Paris-Sud, Université Paris-Saclay, Bat 510, 91405 Orsay Cedex, France
| | - Achilleas Frangakis
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Françoise Livolant
- Laboratoire de Physique des Solides, UMR 8502 CNRS, Université Paris-Sud, Université Paris-Saclay, Bat 510, 91405 Orsay Cedex, France
| | - Amélie Leforestier
- Laboratoire de Physique des Solides, UMR 8502 CNRS, Université Paris-Sud, Université Paris-Saclay, Bat 510, 91405 Orsay Cedex, France
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12
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Huang YC, Su CJ, Korolev N, Berezhnoy NV, Wang S, Soman A, Chen CY, Chen HL, Jeng US, Nordenskiöld L. The effect of linker DNA on the structure and interaction of nucleosome core particles. SOFT MATTER 2018; 14:9096-9106. [PMID: 30215440 DOI: 10.1039/c8sm00998h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In eukaryotes, the compaction of chromatin fibers composed of nucleosome core particles (NCPs) connected by a linker DNA into chromosomes is highly efficient; however, the underlying folding mechanisms remain elusive. We used small angle X-ray scattering (SAXS) to investigate the influence of linker DNA length on the local structure and the interparticle interactions of the NCPs. In the presence of the linker DNA of 30 bp or less in length, the results suggest partial unwrapping of nucleosomal DNA on the NCP irrespective of the linker DNA length. Moreover, the presence of 15 bp linker DNA alleviated the electrostatic repulsion between the NCPs and prevented the formation of an ordered columnar hexagonal phase, demonstrating that the linker DNA plays an active role in chromatin folding.
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Affiliation(s)
- Yen-Chih Huang
- Department of Chemical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsin-Chu 30013, Taiwan.
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13
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Brach K, Hatakeyama A, Nogues C, Olesiak-Banska J, Buckle M, Matczyszyn K. Photochemical analysis of structural transitions in DNA liquid crystals reveals differences in spatial structure of DNA molecules organized in liquid crystalline form. Sci Rep 2018. [PMID: 29540820 PMCID: PMC5852169 DOI: 10.1038/s41598-018-22863-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The anisotropic shape of DNA molecules allows them to form lyotropic liquid crystals (LCs) at high concentrations. This liquid crystalline arrangement is also found in vivo (e.g., in bacteriophage capsids, bacteria or human sperm nuclei). However, the role of DNA liquid crystalline organization in living organisms still remains an open question. Here we show that in vitro, the DNA spatial structure is significantly changed in mesophases compared to non-organized DNA molecules. DNA LCs were prepared from pBluescript SK (pBSK) plasmid DNA and investigated by photochemical analysis of structural transitions (PhAST). We reveal significant differences in the probability of UV-induced pyrimidine dimer photoproduct formation at multiple loci on the DNA indicative of changes in major groove architecture.
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Affiliation(s)
- Katarzyna Brach
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wroclaw, 50370, Poland
| | - Akiko Hatakeyama
- LBPA, IDA, ENS Cachan, CNRS, Université Paris-Saclay, Cachan, F-94235, France
| | - Claude Nogues
- LBPA, IDA, ENS Cachan, CNRS, Université Paris-Saclay, Cachan, F-94235, France
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wroclaw, 50370, Poland
| | - Malcolm Buckle
- LBPA, IDA, ENS Cachan, CNRS, Université Paris-Saclay, Cachan, F-94235, France.
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wroclaw, 50370, Poland.
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14
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Korolev N, Lyubartsev AP, Nordenskiöld L. A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Sci Rep 2018; 8:1543. [PMID: 29367745 PMCID: PMC5784010 DOI: 10.1038/s41598-018-19875-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an “NCP-centred” set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.
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Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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15
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Sung B, Kim MH. Liquid-crystalline nanoarchitectures for tissue engineering. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2018; 9:205-215. [PMID: 29441265 PMCID: PMC5789436 DOI: 10.3762/bjnano.9.22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/21/2017] [Indexed: 05/03/2023]
Abstract
Hierarchical orders are found throughout all levels of biosystems, from simple biopolymers, subcellular organelles, single cells, and macroscopic tissues to bulky organs. Especially, biological tissues and cells have long been known to exhibit liquid crystal (LC) orders or their structural analogues. Inspired by those native architectures, there has recently been increased interest in research for engineering nanobiomaterials by incorporating LC templates and scaffolds. In this review, we introduce and correlate diverse LC nanoarchitectures with their biological functionalities, in the context of tissue engineering applications. In particular, the tissue-mimicking LC materials with different LC phases and the regenerative potential of hard and soft tissues are summarized. In addition, the multifaceted aspects of LC architectures for developing tissue-engineered products are envisaged. Lastly, a perspective on the opportunities and challenges for applying LC nanoarchitectures in tissue engineering fields is discussed.
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Affiliation(s)
- Baeckkyoung Sung
- Liquid Crystal Institute and Chemical Physics Interdisciplinary Program, Kent State University, Kent, OH 44242, USA
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Min-Ho Kim
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
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16
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Ishida H, Kono H. H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes. Biophys J 2017; 113:978-990. [PMID: 28877499 DOI: 10.1016/j.bpj.2017.07.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 11/17/2022] Open
Abstract
Histone tails play an important role in internucleosomal interaction and chromatin compaction. To understand how the H4 tails are involved in the internucleosomal interaction, an adaptively biased molecular dynamics simulation of 63 models of two stacked nucleosomes, each with the H4 tails in different locations, was carried out. This simulation generated a variety of orientations of the separated nucleosomes depending on the formation of the H4 tail bridge between the H4 tails and the DNA of the neighboring nucleosomes. For the models that showed distinctive orientations of the two nucleosomes, the free energies of the separation of the nucleosomes were further investigated using umbrella sampling simulations. The attractive force between the nucleosomes was estimated from the free energies; the force when two H4 tail bridges formed varied from 36 to 63 pN, depending on the formation of the H4 tail-bridge and the interfacial interaction, whereas the force reduced to 15-18 pN after either one of the H4 tail bridges had broken, regardless of the conformation of the H4 tail. Additional simulations of the nucleosomes show that when the H4 tail was truncated, the force between the nucleosomes became repulsive (from-3 to -7 pN). We concluded that the H4 tails potentially produce the diversity in the orientation of the two nucleosomes, which would contribute to the polymorphism of the chromatin structure.
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Affiliation(s)
- Hisashi Ishida
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, Japan.
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, Japan
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17
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Berezhnoy NV, Liu Y, Allahverdi A, Yang R, Su CJ, Liu CF, Korolev N, Nordenskiöld L. The Influence of Ionic Environment and Histone Tails on Columnar Order of Nucleosome Core Particles. Biophys J 2017; 110:1720-1731. [PMID: 27119633 DOI: 10.1016/j.bpj.2016.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/04/2016] [Accepted: 03/07/2016] [Indexed: 01/08/2023] Open
Abstract
The nucleosome core particle (NCP) is the basic building block of chromatin. Nucleosome-nucleosome interactions are instrumental in chromatin compaction, and understanding NCP self-assembly is important for understanding chromatin structure and dynamics. Recombinant NCPs aggregated by multivalent cations form various ordered phases that can be studied by x-ray diffraction (small-angle x-ray scattering). In this work, the effects on the supramolecular structure of aggregated NCPs due to lysine histone H4 tail acetylations, histone H2A mutations (neutralizing the acidic patch of the histone octamer), and the removal of histone tails were investigated. The formation of ordered mainly hexagonal columnar NCP phases is in agreement with earlier studies; however, the highly homogeneous recombinant NCP systems used in this work display a more compact packing. The long-range order of the NCP columnar phase was found to be abolished or reduced by acetylation of the H4 tails, acidic patch neutralization, and removal of the H3 and H2B tails. Loss of nucleosome stacking upon removal of the H3 tails in combination with other tails was observed. In the absence of the H2A tails, the formation of an unknown highly ordered phase was observed.
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Affiliation(s)
- Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ying Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Abdollah Allahverdi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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18
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Abstract
Liquid crystals play an important role in biology because the combination of order and mobility is a basic requirement for self-organisation and structure formation in living systems. Cholesteric liquid crystals are omnipresent in living matter under both in vivo and in vitro conditions and address the major types of molecules essential to life. In the animal and plant kingdoms, the cholesteric structure is a recurring design, suggesting a convergent evolution to an optimised left-handed helix. Herein, we review the recent advances in the cholesteric organisation of DNA, chromatin, chitin, cellulose, collagen, viruses, silk and cholesterol ester deposition in atherosclerosis. Cholesteric structures can be found in bacteriophages, archaea, eukaryotes, bacterial nucleoids, chromosomes of unicellular algae, sperm nuclei of many vertebrates, cuticles of crustaceans and insects, bone, tendon, cornea, fish scales and scutes, cuttlebone and squid pens, plant cell walls, virus suspensions, silk produced by spiders and silkworms, and arterial wall lesions. This article specifically aims at describing the consequences of the cholesteric geometry in living matter, which are far from being fully defined and understood, and discusses various perspectives. The roles and functions of biological cholesteric liquid crystals include maximisation of packing efficiency, morphogenesis, mechanical stability, optical information, radiation protection and evolution pressure.
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Affiliation(s)
- Michel Mitov
- Centre d'Elaboration de Matériaux et d'Etudes Structurales (CEMES), CNRS, BP 94347, 29 rue Jeanne-Marvig, F-31055 Toulouse Cedex 4, France.
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19
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Chen Q, Yang R, Korolev N, Liu CF, Nordenskiöld L. Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail-H2A Acidic Patch Interaction. J Mol Biol 2017; 429:2075-2092. [PMID: 28322915 DOI: 10.1016/j.jmb.2017.03.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 01/15/2023]
Abstract
Chromatin folding and dynamics are critically dependent on nucleosome-nucleosome interactions with important contributions from internucleosome binding of the histone H4 N-terminal tail K16-R23 domain to the surface of the H2A/H2B dimer. The H4 Lys16 plays a pivotal role in this regard. Using in vitro reconstituted 12-mer nucleosome arrays, we have investigated the mechanism of the H4 N-terminal tail in maintaining nucleosome-nucleosome stacking and mediating intra- and inter-array chromatin compaction, with emphasis on the role of K16 and the positive charge region, R17-R23. Analytical ultracentrifugation sedimentation velocity experiments and precipitation assays were employed to analyze effects on chromatin folding and self-association, respectively. Effects on chromatin folding caused by various mutations and modifications at position K16 in the H4 histone were studied. Additionally, using charge-quenching mutations, we characterized the importance of the interaction of the residues within the H4 positive charge region R17-R23 with the H2A acidic patch of the adjacent nucleosome. Furthermore, crosslinking experiments were conducted to establish the proximity of the basic tail region to the acidic patch. Our data indicate that the positive charge and length of the side chain of H4 K16 are important for its access to the adjacent nucleosome in the process of nucleosome-nucleosome stacking and array folding. The location and orientation of the H4 R17-R23 domain on the H2A/H2B dimer surface of the neighboring nucleosome core particle (NCP) in the compacted chromatin fiber were established. The dominance of electrostatic interactions in maintaining intra-array interaction was demonstrated.
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Affiliation(s)
- Qinming Chen
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Renliang Yang
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Chuan Fa Liu
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, College of Science, Nanyang Technological University, 60, Nanyang Drive, 637551, Singapore.
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20
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Saurabh S, Glaser MA, Lansac Y, Maiti PK. Atomistic Simulation of Stacked Nucleosome Core Particles: Tail Bridging, the H4 Tail, and Effect of Hydrophobic Forces. J Phys Chem B 2016; 120:3048-60. [DOI: 10.1021/acs.jpcb.5b11863] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suman Saurabh
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Matthew A. Glaser
- Department
of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, United States
| | - Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
- School
of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Prabal K. Maiti
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560012, India
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21
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Lyubartsev AP, Korolev N, Fan Y, Nordenskiöld L. Multiscale modelling of nucleosome core particle aggregation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064111. [PMID: 25563982 DOI: 10.1088/0953-8984/27/6/064111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The nucleosome core particle (NCP) is the basic building block of chromatin. Under the influence of multivalent cations, isolated mononucleosomes exhibit a rich phase behaviour forming various columnar phases with characteristic NCP-NCP stacking. NCP stacking is also a regular element of chromatin structure in vivo. Understanding the mechanism of nucleosome stacking and the conditions leading to self-assembly of NCPs is still incomplete. Due to the complexity of the system and the need to describe electrostatics properly by including the explicit mobile ions, novel modelling approaches based on coarse-grained (CG) methods at the multiscale level becomes a necessity. In this work we present a multiscale CG computer simulation approach to modelling interactions and self-assembly of solutions of NCPs induced by the presence of multivalent cations. Starting from continuum simulations including explicit three-valent cobalt(III)hexammine (CoHex(3+)) counterions and 20 NCPs, based on a previously developed advanced CG NCP model with one bead per amino acid and five beads per two DNA base pair unit (Fan et al 2013 PLoS One 8 e54228), we use the inverse Monte Carlo method to calculate effective interaction potentials for a 'super-CG' NCP model consisting of seven beads for each NCP. These interaction potentials are used in large-scale simulations of up to 5000 NCPs, modelling self-assembly induced by CoHex(3+). The systems of 'super-CG' NCPs form a single large cluster of stacked NCPs without long-range order in agreement with experimental data for NCPs precipitated by the three-valent polyamine, spermidine(3+).
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Affiliation(s)
- Alexander P Lyubartsev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
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22
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Affiliation(s)
- Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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23
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Sebastiani F, Pietrini A, Longo M, Comez L, Petrillo C, Sacchetti F, Paciaroni A. Melting of DNA Nonoriented Fibers: A Wide-Angle X-ray Diffraction Study. J Phys Chem B 2014; 118:3785-92. [DOI: 10.1021/jp411096d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Federico Sebastiani
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alberto Pietrini
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Marialucia Longo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Elettra − Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Lucia Comez
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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24
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Tschierske C. Development of structural complexity by liquid-crystal self-assembly. Angew Chem Int Ed Engl 2013; 52:8828-78. [PMID: 23934786 DOI: 10.1002/anie.201300872] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Indexed: 11/09/2022]
Abstract
Since the discovery of the liquid-crystalline state of matter 125 years ago, this field has developed into a scientific area with many facets. This Review presents recent developments in the molecular design and self-assembly of liquid crystals. The focus is on new exciting soft-matter structures distinct from the usually observed nematic, smectic, and columnar phases. These new structures have enhanced complexity, including multicompartment and cellular structures, periodic and quasiperiodic arrays of spheres, and new emergent properties, such as ferroelctricity and spontaneous achiral symmetry-breaking. Comparisons are made with developments in related fields, such as self-assembled monolayers, multiblock copolymers, and nanoparticle arrays. Measures of structural complexity used herein are the size of the lattice, the number of distinct compartments, the dimensionality, and the logic depth of the resulting supramolecular structures.
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Affiliation(s)
- Carsten Tschierske
- Institut für Chemie, Organische Chemie, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle Saale, Germany.
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25
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Fan Y, Korolev N, Lyubartsev AP, Nordenskiöld L. An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions. PLoS One 2013; 8:e54228. [PMID: 23418426 PMCID: PMC3572162 DOI: 10.1371/journal.pone.0054228] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 12/11/2012] [Indexed: 11/19/2022] Open
Abstract
In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs). The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar) plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+)), divalent (Mg(2+)) or trivalent (Co(NH(3))(6) (3+)) cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+), to partial aggregation with Mg(2+) and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+). The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.
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Affiliation(s)
- Yanping Fan
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (NK); (APL)
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- * E-mail: (NK); (APL)
| | - Lars Nordenskiöld
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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26
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Sun S, Wong JTY, Liu M, Dong F. Counterion-mediated decompaction of liquid crystalline chromosomes. DNA Cell Biol 2012; 31:1657-64. [PMID: 23072628 DOI: 10.1089/dna.2012.1708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Liquid crystalline phases of DNA and nucleosome core particles can be formed in vitro, indicating the crucial roles of these phases in the maintenance and compaction of genomes in vivo. In the present study, sequential levels of liquid crystalline decompaction were identified in highly purified nuclei of Karenia papilionacea in response to the gradual chelation of divalent counterions by ethylenediaminetetraacetic acid (EDTA); the decompaction was observed using polarizing light microscopy, confocal laser scanning microscopy, and transmission electron microscopy and further confirmed utilizing microcalorimetry. Nested fibrous coils in 150 nm arc-like bands of chromatin were observed in the early stages of chromosomal decompaction. The microcalorimetry spectra of isolated nuclei revealed that the dynamic processes of nuclear decompaction occurred in a nonlinear manner; in addition, an EDTA-sensitive thermal transition between 60°C-70°C, corresponding to a liquid-crystalline-phase transition of chromosomes, was found. The results suggested that nested coils of fibrous chromatin filaments are responsible for the establishment and stabilization of the liquid crystalline and birefringence features of the chromosomes of dinoflagellates. The results also indicated that positively charged divalent counterions play significant roles in modulating liquid crystalline phases to compact the chromosomes of dinoflagellates.
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Affiliation(s)
- Shiyong Sun
- Key Laboratory of Solid Waste Treatment and Resource Recycle, Southwest University of Science and Technology, Mianyang, Sichuan, China.
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27
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Structure of metaphase chromosomes: a role for effects of macromolecular crowding. PLoS One 2012; 7:e36045. [PMID: 22540018 PMCID: PMC3335069 DOI: 10.1371/journal.pone.0036045] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 03/29/2012] [Indexed: 12/12/2022] Open
Abstract
In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.
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28
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29
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Olesiak-Banska J, Mojzisova H, Chauvat D, Zielinski M, Matczyszyn K, Tauc P, Zyss J. Liquid crystal phases of DNA: Evaluation of DNA organization by two-photon fluorescence microscopy and polarization analysis. Biopolymers 2011; 95:365-75. [DOI: 10.1002/bip.21583] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Cherstvy AG. Electrostatic interactions in biological DNA-related systems. Phys Chem Chem Phys 2011; 13:9942-68. [DOI: 10.1039/c0cp02796k] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Stehr R, Schöpflin R, Ettig R, Kepper N, Rippe K, Wedemann G. Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams. Biophys J 2010; 98:1028-37. [PMID: 20303860 DOI: 10.1016/j.bpj.2009.11.040] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Revised: 11/21/2009] [Accepted: 11/24/2009] [Indexed: 11/17/2022] Open
Abstract
The three-dimensional structure of chromatin affects DNA accessibility and is therefore a key regulator of gene expression. However, the path of the DNA between consecutive nucleosomes, and the resulting chromatin fiber organization remain controversial. The conformational space available for the folding of the nucleosome chain has been analytically described by phase diagrams with a two-angle model, which describes the chain trajectory by a DNA entry-exit angle at the nucleosome and a torsion angle between consecutive nucleosomes. Here, a novel type of numerical phase diagrams is introduced that relates the geometric phase space to the energy associated with a given chromatin conformation. The resulting phase diagrams revealed differences in the energy landscape that reflect the probability of a given conformation to form in thermal equilibrium. Furthermore, we investigated the effects of entropy and additional degrees of freedom in the dynamic phase diagrams by performing Monte Carlo simulations of the initial chain trajectories. Using our approach, we were able to demonstrate that conformations that initially were geometrically impossible could evolve into energetically favorable states in thermal equilibrium due to DNA bending and torsion. In addition, dynamic phase diagrams were applied to identify chromatin fibers that reflect certain experimentally determined features.
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Affiliation(s)
- René Stehr
- University of Applied Sciences Stralsund, System Engineering and Information Management, Stralsund, Germany
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32
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Birefringence and DNA condensation of liquid crystalline chromosomes. EUKARYOTIC CELL 2010; 9:1577-87. [PMID: 20400466 DOI: 10.1128/ec.00026-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA can self-assemble in vitro into several liquid crystalline phases at high concentrations. The largest known genomes are encoded by the cholesteric liquid crystalline chromosomes (LCCs) of the dinoflagellates, a diverse group of protists related to the malarial parasites. Very little is known about how the liquid crystalline packaging strategy is employed to organize these genomes, the largest among living eukaryotes-up to 80 times the size of the human genome. Comparative measurements using a semiautomatic polarizing microscope demonstrated that there is a large variation in the birefringence, an optical property of anisotropic materials, of the chromosomes from different dinoflagellate species, despite their apparently similar ultrastructural patterns of bands and arches. There is a large variation in the chromosomal arrangements in the nuclei and individual karyotypes. Our data suggest that both macroscopic and ultrastructural arrangements affect the apparent birefringence of the liquid crystalline chromosomes. Positive correlations are demonstrated for the first time between the level of absolute retardance and both the DNA content and the observed helical pitch measured from transmission electron microscopy (TEM) photomicrographs. Experiments that induced disassembly of the chromosomes revealed multiple orders of organization in the dinoflagellate chromosomes. With the low protein-to-DNA ratio, we propose that a highly regulated use of entropy-driven force must be involved in the assembly of these LCCs. Knowledge of the mechanism of packaging and arranging these largest known DNAs into different shapes and different formats in the nuclei would be of great value in the use of DNA as nanostructural material.
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33
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Mojzisova H, Olesiak J, Zielinski M, Matczyszyn K, Chauvat D, Zyss J. Polarization-sensitive two-photon microscopy study of the organization of liquid-crystalline DNA. Biophys J 2010; 97:2348-57. [PMID: 19843467 DOI: 10.1016/j.bpj.2009.07.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 07/07/2009] [Accepted: 07/08/2009] [Indexed: 11/18/2022] Open
Abstract
Highly concentrated DNA solutions exhibit self-ordering properties such as the generation of liquid-crystalline phases. Such organized domains may play an important role in the global chromatin topology but can also be used as a simple model for the study of more complex 3D DNA structures. In this work, using polarized two-photon fluorescence microscopy, we report on the orientation of DNA molecules in liquid-crystalline phases. For this purpose, we analyze the signal emitted by fluorophores that are noncovalently bound to DNA strands. In nonlinear processes, excitation occurs exclusively in the focal volume, which offers advantages such as the reduction of photobleaching of out-of-focus molecules and intrinsic 3D sectioning capability. Propidium iodide and Hoechst, two fluorophores with different DNA binding modes, have been considered. Polarimetric measurements show that the dyes follow the alignment with respect to the DNA strands and allow the determination of the angles between the emission dipoles and the longitudinal axis of the DNA double strand. These results provide a useful starting point toward the application of two-photon polarimetry techniques to determine the local orientation of condensed DNA in physiological conditions.
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Affiliation(s)
- Halina Mojzisova
- Laboratoire de Photonique Quantique et Moléculaire, Institut d'Alembert, Ecole Normale Supérieure de Cachan, Cachan, France.
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Danks MJ, Light ME, Bruce DW. The Preparation, Solution and Mesophase Behaviour of Surfactant Complexes of Cobalt(III). Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mark J. Danks
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, Fax: +44‐1904‐432516
| | - Mark E. Light
- EPSRC Crystallographic Service, Department of Chemistry, University of Southamton, Southampton, SO17 1BJ, United Kingdom
| | - Duncan W. Bruce
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, Fax: +44‐1904‐432516
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Abstract
The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by posttranslational histone modifications and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the Monte Carlo simulation, the nucleosome shape was described as an oblate spherocylinder, and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber.
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Cinacchi G, La Penna G, Perico A. Anisotropic Internucleosome Interactions and Geometrical Constraints in the Organization of Chromatin. Macromolecules 2007. [DOI: 10.1021/ma071343l] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giorgio Cinacchi
- Università di Pisa, Dipartimento di Chimica e Chimica Industriale, Via Risorgimento 35, 56126 Pisa, Italy
| | - Giovanni La Penna
- Consiglio Nazionale delle Ricerche, Istituto per la Chimica dei Composti Organo-Metallici, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
| | - Angelo Perico
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio delle Macromolecole, Via De Marini 6, 16149 Genova, Italy
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Bertin A, Mangenot S, Renouard M, Durand D, Livolant F. Structure and phase diagram of nucleosome core particles aggregated by multivalent cations. Biophys J 2007; 93:3652-63. [PMID: 17693471 PMCID: PMC2072050 DOI: 10.1529/biophysj.107.108365] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The degree of compaction of the eukaryotic chromatin in vivo and in vitro is highly sensitive to the ionic environment. We address the question of the effect of multivalent ions on the interactions and mutual organization of the chromatin structural units, the nucleosome core particles (NCPs). Conditions of precipitation of NCPs in the presence of 10 mM Tris buffer and various amounts of either magnesium (Mg(2+)) or spermidine (Spd(3+)) are explored, compared, and discussed in relation to theoretical models. In addition, the structure of the aggregates is analyzed by complementary techniques: freeze-fracture electron microscopy, cryoelectron microscopy, and x-ray diffraction. In Mg(2+)-NCP aggregates, NCPs tend to stack on top of one another to form columns that are not long-range organized. In the presence of Spd(3+), NCPs precipitate to form a dense isotropic phase, a disordered phase of columns, a two-dimensional columnar hexagonal phase, or a three-dimensional crystal. The more ordered phases (two-dimensional or three-dimensional hexagonal) are found close to the precipitation line, where the number of positive charges carried by cations is slightly larger than the number of available negative charges of the NCPs. All ordered phases coexist with the dense isotropic phases. Formation of hexagonal and columnar phases is prevented by an excess of polycations.
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Affiliation(s)
- Aurélie Bertin
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Orsay-Sud, Paris, France
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Yee J, Tang A, Lau WL, Ritter H, Delport D, Page M, Adam RD, Müller M, Wu G. Core histone genes of Giardia intestinalis: genomic organization, promoter structure, and expression. BMC Mol Biol 2007; 8:26. [PMID: 17425802 PMCID: PMC1872034 DOI: 10.1186/1471-2199-8-26] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 04/10/2007] [Indexed: 11/19/2022] Open
Abstract
Background Giardia intestinalis is a protist found in freshwaters worldwide, and is the most common cause of parasitic diarrhea in humans. The phylogenetic position of this parasite is still much debated. Histones are small, highly conserved proteins that associate tightly with DNA to form chromatin within the nucleus. There are two classes of core histone genes in higher eukaryotes: DNA replication-independent histones and DNA replication-dependent ones. Results We identified two copies each of the core histone H2a, H2b and H3 genes, and three copies of the H4 gene, at separate locations on chromosomes 3, 4 and 5 within the genome of Giardia intestinalis, but no gene encoding a H1 linker histone could be recognized. The copies of each gene share extensive DNA sequence identities throughout their coding and 5' noncoding regions, which suggests these copies have arisen from relatively recent gene duplications or gene conversions. The transcription start sites are at triplet A sequences 1–27 nucleotides upstream of the translation start codon for each gene. We determined that a 50 bp region upstream from the start of the histone H4 coding region is the minimal promoter, and a highly conserved 15 bp sequence called the histone motif (him) is essential for its activity. The Giardia core histone genes are constitutively expressed at approximately equivalent levels and their mRNAs are polyadenylated. Competition gel-shift experiments suggest that a factor within the protein complex that binds him may also be a part of the protein complexes that bind other promoter elements described previously in Giardia. Conclusion In contrast to other eukaryotes, the Giardia genome has only a single class of core histone genes that encode replication-independent histones. Our inability to locate a gene encoding the linker histone H1 leads us to speculate that the H1 protein may not be required for the compaction of Giardia's small and gene-rich genome.
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Affiliation(s)
- Janet Yee
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Anita Tang
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Wei-Ling Lau
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Heather Ritter
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Dewald Delport
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Melissa Page
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Rodney D Adam
- Departments of Immunobiology and Medicine, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | - Miklós Müller
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
- Collegium Budapest, H 1012 Budapest, Hungary
| | - Gang Wu
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
- Haskins Laboratories and Department of Chemistry and Physical Sciences, Pace University, 41 Park Row, New York, NY 10038, USA
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Bruce DW, Goodby JW, Sambles JR, Coles HJ. New directions in liquid crystal science. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2006; 364:2567-71. [PMID: 16973476 DOI: 10.1098/rsta.2006.1840] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
While we are all familiar with liquid crystal displays, an industry currently worth more than US dollars 60 billion yr(-1) and growing rapidly, fewer people are aware of the breadth of the subject of liquid crystals--one that represents the study of the fourth state of matter. Liquid crystals are found as essential elements in biological systems, soaps and detergents, sensor technologies and in the manipulation of electromagnetic radiation of various wavelengths. This meeting was designed to highlight both the truly multidisciplinary nature of liquid crystal science and to feature those areas away from electro-optic displays; these issues are developed and summarized in more detail.
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Affiliation(s)
- Duncan W Bruce
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
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