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Xu W, Zhang H, Guo W, Jiang L, Zhao Y, Peng Y. Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis. Brief Bioinform 2024; 25:bbad532. [PMID: 38329268 PMCID: PMC10851104 DOI: 10.1093/bib/bbad532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/30/2023] [Accepted: 12/23/2023] [Indexed: 02/09/2024] Open
Abstract
Nucleosomes represent hubs in chromatin organization and gene regulation and interact with a plethora of chromatin factors through different modes. In addition, alterations in histone proteins such as cancer mutations and post-translational modifications have profound effects on histone/nucleosome interactions. To elucidate the principles of histone interactions and the effects of those alterations, we developed histone interactomes for comprehensive mapping of histone-histone interactions (HHIs), histone-DNA interactions (HDIs), histone-partner interactions (HPIs) and DNA-partner interactions (DPIs) of 37 organisms, which contains a total of 3808 HPIs from 2544 binding proteins and 339 HHIs, 100 HDIs and 142 DPIs across 110 histone variants. With the developed networks, we explored histone interactions at different levels of granularities (protein-, domain- and residue-level) and performed systematic analysis on histone interactions at a large scale. Our analyses have characterized the preferred binding hotspots on both nucleosomal/linker DNA and histone octamer and unraveled diverse binding modes between nucleosome and different classes of binding partners. Last, to understand the impact of histone cancer-associated mutations on histone/nucleosome interactions, we complied one comprehensive cancer mutation dataset including 7940 cancer-associated histone mutations and further mapped those mutations onto 419,125 histone interactions at the residue level. Our quantitative analyses point to histone cancer-associated mutations' strongly disruptive effects on HHIs, HDIs and HPIs. We have further predicted 57 recurrent histone cancer mutations that have large effects on histone/nucleosome interactions and may have driver status in oncogenesis.
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Affiliation(s)
- Wang Xu
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
| | - Houfang Zhang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
| | - Wenhan Guo
- Computational Science Program, University of Texas at El Paso, El Paso, TX 79902, USA
| | - Lijun Jiang
- Hubei Key Laboratory of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
| | - Yunhui Peng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
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2
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Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
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Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
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Hausmann M, Hildenbrand G, Pilarczyk G. Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology : (A Hypothesis and Experimental Verification Hints). Results Probl Cell Differ 2022; 70:3-34. [PMID: 36348103 DOI: 10.1007/978-3-031-06573-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The cell nucleus is a complex biological system in which simultaneous reactions and functions take place to keep the cell as an individualized, specialized system running well. The cell nucleus contains chromatin packed in various degrees of density and separated in volumes of chromosome territories and subchromosomal domains. Between the chromatin, however, there is enough "free" space for floating RNA, proteins, enzymes, ATPs, ions, water molecules, etc. which are trafficking by super- and supra-diffusion to the interaction points where they are required. It seems that this trafficking works somehow automatically and drives the system perfectly. After exposure to ionizing radiation causing DNA damage from single base damage up to chromatin double-strand breaks, the whole system "cell nucleus" responds, and repair processes are starting to recover the fully functional and intact system. In molecular biology, many individual epigenetic pathways of DNA damage response or repair of single and double-strand breaks are described. How these responses are embedded into the response of the system as a whole is often out of the focus of consideration. In this article, we want to follow the hypothesis of chromatin architecture's impact on epigenetic pathways and vice versa. Based on the assumption that chromatin acts like an "aperiodic solid state within a limited volume," functionally determined networks and local topologies ("islands") can be defined that drive the appropriate repair process at a given damage site. Experimental results of investigations of the chromatin nano-architecture and DNA repair clusters obtained by means of single-molecule localization microscopy offer hints and perspectives that may contribute to verifying the hypothesis.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
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4
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Grigoriev SV, Iashina EG, Wu B, Pipich V, Lang C, Radulescu A, Bairamukov VY, Filatov MV, Pantina RA, Varfolomeeva EY. Observation of nucleic acid and protein correlation in chromatin of HeLa nuclei using small-angle neutron scattering with D_{2}O-H_{2}O contrast variation. Phys Rev E 2021; 104:044404. [PMID: 34781557 DOI: 10.1103/physreve.104.044404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023]
Abstract
The small-angle neutron scattering (SANS) on HeLa nuclei demonstrates the bifractal nature of the chromatin structural organization. The border line between two fractal structures is detected as a crossover point at Q_{c}≈4×10^{-2}nm^{-1} in the momentum transfer dependence Q^{-D}. The use of contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals clear similarity in the large scale structural organizations of nucleic acids (NA) and proteins. Both NA and protein structures have a mass fractal arrangement with the fractal dimension of D≈2.5 at scales smaller than 150 nm down to 20 nm. Both NA and proteins show a logarithmic fractal behavior with D≈3 at scales larger than 150 nm up to 6000 nm. The combined analysis of the SANS and atomic force microscopy data allows one to conclude that chromatin and its constitutes (DNA and proteins) are characterized as soft, densely packed, logarithmic fractals on the large scale and as rigid, loosely packed, mass fractals on the smaller scale. The comparison of the partial cross sections from NA and proteins with one from chromatin as a whole demonstrates spatial correlation of two chromatin's components in the range up to 900 nm. Thus chromatin in HeLa nuclei is built as the unified structure of the NA and proteins entwined through each other. Correlation between two components is lost upon scale increases toward 6000 nm. The structural features at the large scale, probably, provide nuclei with the flexibility and chromatin-free space to build supercorrelations on the distance of 10^{3} nm resembling cycle cell activity, such as an appearance of nucleoli and a DNA replication.
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Affiliation(s)
- S V Grigoriev
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia.,Saint-Petersburg State University, Ulyanovskaya 1, Saint-Petersburg 198504, Russia
| | - E G Iashina
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia.,Saint-Petersburg State University, Ulyanovskaya 1, Saint-Petersburg 198504, Russia
| | - B Wu
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - V Pipich
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - Ch Lang
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - A Radulescu
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - V Yu Bairamukov
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - M V Filatov
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
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Erenpreisa J, Krigerts J, Salmina K, Gerashchenko BI, Freivalds T, Kurg R, Winter R, Krufczik M, Zayakin P, Hausmann M, Giuliani A. Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis). Cells 2021; 10:1582. [PMID: 34201566 PMCID: PMC8304199 DOI: 10.3390/cells10071582] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.
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Affiliation(s)
- Jekaterina Erenpreisa
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Bogdan I. Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine;
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia;
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia;
| | - Ruth Winter
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
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6
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Hedley JG, Teif VB, Kornyshev AA. Nucleosome-induced homology recognition in chromatin. J R Soc Interface 2021; 18:20210147. [PMID: 34129789 PMCID: PMC8205524 DOI: 10.1098/rsif.2021.0147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
One of the least understood properties of chromatin is the ability of its similar regions to recognize each other through weak interactions. Theories based on electrostatic interactions between helical macromolecules suggest that the ability to recognize sequence homology is an innate property of the non-ideal helical structure of DNA. However, this theory does not account for the nucleosomal packing of DNA. Can homologous DNA sequences recognize each other while wrapped up in the nucleosomes? Can structural homology arise at the level of nucleosome arrays? Here, we present a theoretical model for the recognition potential well between chromatin fibres sliding against each other. This well is different from the one predicted for bare DNA; the minima in energy do not correspond to literal juxtaposition, but are shifted by approximately half the nucleosome repeat length. The presence of this potential well suggests that nucleosome positioning may induce mutual sequence recognition between chromatin fibres and facilitate the formation of chromatin nanodomains. This has implications for nucleosome arrays enclosed between CTCF-cohesin boundaries, which may form stiffer stem-like structures instead of flexible entropically favourable loops. We also consider switches between chromatin states, e.g. through acetylation/deacetylation of histones, and discuss nucleosome-induced recognition as a precursory stage of genetic recombination.
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Affiliation(s)
- Jonathan G. Hedley
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Vladimir B. Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Alexei A. Kornyshev
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
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7
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Anatskaya OV, Vinogradov AE, Vainshelbaum NM, Giuliani A, Erenpreisa J. Phylostratic Shift of Whole-Genome Duplications in Normal Mammalian Tissues towards Unicellularity Is Driven by Developmental Bivalent Genes and Reveals a Link to Cancer. Int J Mol Sci 2020; 21:ijms21228759. [PMID: 33228223 PMCID: PMC7699474 DOI: 10.3390/ijms21228759] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
Tumours were recently revealed to undergo a phylostratic and phenotypic shift to unicellularity. As well, aggressive tumours are characterized by an increased proportion of polyploid cells. In order to investigate a possible shared causation of these two features, we performed a comparative phylostratigraphic analysis of ploidy-related genes, obtained from transcriptomic data for polyploid and diploid human and mouse tissues using pairwise cross-species transcriptome comparison and principal component analysis. Our results indicate that polyploidy shifts the evolutionary age balance of the expressed genes from the late metazoan phylostrata towards the upregulation of unicellular and early metazoan phylostrata. The up-regulation of unicellular metabolic and drug-resistance pathways and the downregulation of pathways related to circadian clock were identified. This evolutionary shift was associated with the enrichment of ploidy with bivalent genes (p < 10−16). The protein interactome of activated bivalent genes revealed the increase of the connectivity of unicellulars and (early) multicellulars, while circadian regulators were depressed. The mutual polyploidy-c-MYC-bivalent genes-associated protein network was organized by gene-hubs engaged in both embryonic development and metastatic cancer including driver (proto)-oncogenes of viral origin. Our data suggest that, in cancer, the atavistic shift goes hand-in-hand with polyploidy and is driven by epigenetic mechanisms impinging on development-related bivalent genes.
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Affiliation(s)
- Olga V. Anatskaya
- Department of Bioinformatics and Functional Genomics, Institute of Cytology, Russian Academy of sciences, 194064 St. Petersburg, Russia
- Correspondence: (O.V.A.); (A.E.V.); (J.E.)
| | - Alexander E. Vinogradov
- Department of Bioinformatics and Functional Genomics, Institute of Cytology, Russian Academy of sciences, 194064 St. Petersburg, Russia
- Correspondence: (O.V.A.); (A.E.V.); (J.E.)
| | - Ninel M. Vainshelbaum
- Department of Oncology, Latvian Biomedical Research and Study Centre, Cancer Research Division, LV-1067 Riga, Latvia;
- Faculty of Biology, University of Latvia, LV-1586 Riga, Latvia
| | | | - Jekaterina Erenpreisa
- Department of Oncology, Latvian Biomedical Research and Study Centre, Cancer Research Division, LV-1067 Riga, Latvia;
- Correspondence: (O.V.A.); (A.E.V.); (J.E.)
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8
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Zinchenko A, Hiramatsu H, Yamaguchi H, Kubo K, Murata S, Kanbe T, Hazemoto N, Yoshikawa K, Akitaya T. Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription. Biophys J 2019; 116:1836-1844. [PMID: 31076102 PMCID: PMC6531782 DOI: 10.1016/j.bpj.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Accepted: 04/12/2019] [Indexed: 02/04/2023] Open
Abstract
Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan.
| | - Hiroyuki Hiramatsu
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | | | - Koji Kubo
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Shizuaki Murata
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Toshio Kanbe
- Laboratory of Medical Mycology, Research Institute for Disease Mechanism and Control, School of Medicine, Nagoya University, Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Norio Hazemoto
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Tatsuo Akitaya
- Department of Chemistry, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.
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9
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Tang SJ. Potential Role of Phase Separation of Repetitive DNA in Chromosomal Organization. Genes (Basel) 2017; 8:genes8100279. [PMID: 29057826 PMCID: PMC5664129 DOI: 10.3390/genes8100279] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/07/2017] [Accepted: 10/13/2017] [Indexed: 01/19/2023] Open
Abstract
The basic principles of chromosomal organization in eukaryotic cells remain elusive. Current mainstream research efforts largely concentrate on searching for critical packaging proteins involved in organizing chromosomes. I have taken a different perspective, by considering the role of genomic information in chromatins. In particular, I put forward the concept that repetitive DNA elements are key chromosomal packaging modules, and their intrinsic property of homology-based interaction can drive chromatin folding. Many repetitive DNA families have high copy numbers and clustered distribution patterns in the linear genomes. These features may facilitate the interactions among members in the same repeat families. In this paper, the potential liquid–liquid phase transition of repetitive DNAs that is induced by their extensive interaction in chromosomes will be considered. I propose that the interaction among repetitive DNAs may lead to phase separation of interacting repetitive DNAs from bulk chromatins. Phase separation of repetitive DNA may provide a physical mechanism that drives rapid massive changes of chromosomal conformation.
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Affiliation(s)
- Shao-Jun Tang
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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10
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Dutta R, Pyne A, Kundu S, Banerjee P, Sarkar N. Concentration-Driven Fascinating Vesicle-Fibril Transition Employing Merocyanine 540 and 1-Octyl-3-methylimidazolium Chloride. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9811-9821. [PMID: 28849933 DOI: 10.1021/acs.langmuir.7b02136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this article, anionic lipophilic dye merocyanine 540(MC540) and cationic surface-active ionic liquid (SAIL) 1-octyl-3-methylimidazolium chloride (C8mimCl) are employed to construct highly ordered fibrillar and vesicular aggregates exploiting an ionic self-assembly (ISA) strategy. It is noteworthy that the concentration of the counterions has exquisite control over the morphology, in which lowering the concentration of both the building blocks in a stoichiometric ratio of 1:1 provides a vesicle to fibril transition. Here, we have reported the concentration-controlled fibril-vesicle transition utilizing the emerging fluorescence lifetime imaging microscopy (FLIM) technique. Furthermore, we have detected this morphological transformation by means of other microscopic techniques such as field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), and cryogenic-transmission electron microscopy (cryo-TEM) to gain additional support. Besides, multiwavelength FLIM (MW-FLIM) and atomic force microscopy (AFM) techniques assist us in knowing the microheterogeneity and the height profile of the vesicles, respectively. We have replaced the SAIL, C8mimCl, by an analogous traditional surfactant, n-octyltrimethylammonium bromide (OTAB), and it provides a discernible change in morphology similar to that of C8mimCl, whereas 1-octanol is unable to exhibit any structural aggregation and thus reveals the importance of electrostatic interaction in supramolecular aggregate formation. However, the SAILs having the same imidazolium headgroup with different chain lengths other than C8mimCl are unable to display any structural transition and determine the importance of the correct chain length for efficient packing of the counterions to form a specific self-assembly. Therefore, this study reveals the synergistic interplay of electrostatic, hydrophobic, and π-π stacking interactions to construct the self-assembly and their concentration-dependent morphological transition.
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Affiliation(s)
- Rupam Dutta
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
| | - Arghajit Pyne
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
| | - Sangita Kundu
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB India
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11
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Tang SJ. New Evidence for the Theory of Chromosome Organization by Repetitive Elements (CORE). Genes (Basel) 2017; 8:genes8020081. [PMID: 28230735 PMCID: PMC5333070 DOI: 10.3390/genes8020081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 02/17/2017] [Indexed: 11/16/2022] Open
Abstract
Repetitive DNA elements were proposed to coordinate chromatin folding and interaction in chromosomes by their intrinsic homology-based clustering ability. A recent analysis of the data sets from chromosome-conformation-capture experiments confirms the spatial clustering of DNA repeats of the same family in the nuclear space, and thus provides strong new support for the CORE theory.
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Affiliation(s)
- Shao-Jun Tang
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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Li J, Li X, Xu J, Wang Y, Wu L, Wang Y, Wang L, Lee M, Li W. Engineering the Ionic Self-Assembly of Polyoxometalates and Facial-Like Peptides. Chemistry 2016; 22:15751-15759. [DOI: 10.1002/chem.201602449] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Jingfang Li
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Xiaodong Li
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Jing Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Yang Wang
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Yanqiu Wang
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Liyan Wang
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Myongsoo Lee
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry; Jilin University; Qianjin Avenue 2699 Changchun 130012 P.R. China
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13
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A repetitive DNA-directed program of chromosome packaging during mitosis. J Genet Genomics 2016; 43:471-6. [PMID: 27567067 DOI: 10.1016/j.jgg.2016.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/26/2016] [Accepted: 04/04/2016] [Indexed: 11/20/2022]
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Tang SJ. The R-Operon: A Model of Repetitive DNA-Organized Transcriptional Compartmentation of Eukaryotic Chromosomes for Coordinated Gene Expression. Genes (Basel) 2016; 7:genes7040016. [PMID: 27110825 PMCID: PMC4846846 DOI: 10.3390/genes7040016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/20/2016] [Accepted: 04/05/2016] [Indexed: 11/29/2022] Open
Abstract
In eukaryotic genomes, it is essential to coordinate the activity of genes that function together to fulfill the same biological processes. Genomic organization likely plays a key role in coordinating transcription of different genes. However, little is known about how co-regulated genes are organized in the cell nucleus and how the chromosomal organization facilitates the co-regulation of different genes. I propose that eukaryotic genomes are organized into repeat assembly (RA)-based structural domains (“R-operons”) in the nuclear space. R-operons result from the interaction of homologous DNA repeats. In an R-operon, genes in different loci of the linear genome are brought into spatial vicinity and co-regulated by the same pool of transcription factors. This type of large-scale chromosomal organization may provide a mechanism for functional compartmentation of chromosomes to facilitate the transcriptional coordination of gene expression.
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Affiliation(s)
- Shao-Jun Tang
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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16
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A computational study of dsDNA pairs and vibrational resonance in separating water. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 8:329-35. [PMID: 26396657 DOI: 10.1007/s11693-014-9157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/19/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
Abstract
This article investigates the relationship between molecular sequence and dependent interacting behavior of molecular segment pairs and secondly, sequence dependent, vibrational resonance in surrounding normal saline, protein-free water. The development of a molecular model to explore these systems phenomena, the results of several nanoscale molecular dynamics simulations, and analysis of behavior of interacting ΦX174 double-stranded DNA segment pair models in various configurations are presented. Fourier analysis revealed intriguing vibration frequencies within the solvent plane between the segments, while subsequent frequency domain transformation of the time domain waveforms revealed statistically significant resonating harmonic signals in the THz range.
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17
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Liu Y, Liang X, Yang R. Identification of peculiar and common effects of histone modifications on transcription. J Theor Biol 2015; 380:24-39. [PMID: 26002420 DOI: 10.1016/j.jtbi.2015.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/05/2015] [Accepted: 04/29/2015] [Indexed: 11/16/2022]
Abstract
Histone modifications (HMs) play an important role in controlling eukaryotic gene expression and next generation sequencing (NGS) has greatly advanced the research on this topic with generating many high-resolution maps for HMs. Here, we use these maps to analyze the relationship between HMs and transcription. By incorporating various segments of genes into analysis without restricting the scope only in the promoter region, we have collected more comprehensive data and captured some details of this process. A position effect of gene regions has been revealed and it can even inverse the property of some HMs from activating to repressing genes such as the cases of H3K4me3, H3K36me3 and H3K14ac. Especially H3K36me3, its dual character on gene transcription makes it able to serve as a criterion to distinguish high and low expressed genes. We also study the general property of different HMs based on the comprehensive data. Using exploratory factor analysis (EFA), we have extracted 4 latent structures underlying the HMs, which are able to represent their activating and repressing effects concisely. These 4 factors have fine properties in the aspects of distinguishing high and low expressed genes, predicting transcription level and identifying genes with unique attributes such as stable RNA generating genes found to have a close relationship with lifespan of organisms here. In summary, while the position effect associated HM peculiarities demonstrate some details of the complex HM regulation network divergently, the common factors catch the nature of the network convergently. This deepens our understanding on the HM-transcription relationship.
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Affiliation(s)
- Yu Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, PR China
| | - Xue Liang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, PR China
| | - Rongcun Yang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, PR China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, PR China.
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18
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Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C. The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett 2015; 589:2931-43. [PMID: 26028501 DOI: 10.1016/j.febslet.2015.05.037] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 02/04/2023]
Abstract
Recent methodological advancements in microscopy and DNA sequencing-based methods provide unprecedented new insights into the spatio-temporal relationships between chromatin and nuclear machineries. We discuss a model of the underlying functional nuclear organization derived mostly from electron and super-resolved fluorescence microscopy studies. It is based on two spatially co-aligned, active and inactive nuclear compartments (ANC and INC). The INC comprises the compact, transcriptionally inactive core of chromatin domain clusters (CDCs). The ANC is formed by the transcriptionally active periphery of CDCs, called the perichromatin region (PR), and the interchromatin compartment (IC). The IC is connected to nuclear pores and serves nuclear import and export functions. The ANC is the major site of RNA synthesis. It is highly enriched in epigenetic marks for transcriptionally competent chromatin and RNA Polymerase II. Marks for silent chromatin are enriched in the INC. Multi-scale cross-correlation spectroscopy suggests that nuclear architecture resembles a random obstacle network for diffusing proteins. An increased dwell time of proteins and protein complexes within the ANC may help to limit genome scanning by factors or factor complexes to DNA exposed within the ANC.
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Affiliation(s)
- Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany.
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Hilmar Strickfaden
- University of Alberta, Cross Cancer Institute Dept. of Oncology, Edmonton, AB, Canada
| | - Daniel Smeets
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Jens Popken
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Michael Sterr
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) & BioQuant Center, Research Group Genome Organization & Function, Heidelberg, Germany.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Mainz and Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Germany.
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19
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Mulligan PJ, Koslover EF, Spakowitz AJ. Thermodynamic model of heterochromatin formation through epigenetic regulation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064109. [PMID: 25563699 DOI: 10.1088/0953-8984/27/6/064109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Gene regulation in eukaryotes requires the segregation of silenced genomic regions into densely packed heterochromatin, leaving the active genes in euchromatin regions more accessible. We introduce a model that connects the presence of epigenetically inherited histone marks, methylation at histone 3 lysine-9, to the physical compaction of chromatin fibers via the binding of heterochromatin protein 1 (HP1). Our model demonstrates some of the key physical features that are necessary to explain experimental observations. In particular, we demonstrate that strong cooperative interactions among the HP1 proteins are necessary to see the phase segregation of heterochromatin and euchromatin regions. We also explore how the cell can use the concentration of HP1 to control condensation and under what circumstances there is a threshold of methylation over which the fibers will compact. Finally, we consider how different potential in vivo fiber structures as well as the flexibility of the histone 3 tail can affect the bridging of HP1. Many of the observations that we make about the HP1 system are guided by general thermodynamics principles and thus could play a role in other DNA organizational processes such as the binding of linker histones.
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Affiliation(s)
- Peter J Mulligan
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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20
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Shin J, Cherstvy AG, Metzler R. Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size. SOFT MATTER 2015; 11:472-88. [PMID: 25413029 DOI: 10.1039/c4sm02007c] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.
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Affiliation(s)
- Jaeoh Shin
- Institute for Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany.
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21
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Cherstvy AG, Teif VB. Electrostatic effect of H1-histone protein binding on nucleosome repeat length. Phys Biol 2014; 11:044001. [PMID: 25078656 DOI: 10.1088/1478-3975/11/4/044001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Within a simple biophysical model we describe the effect of electrostatic binding of H1 histone proteins on the nucleosome repeat length in chromatin. The length of wrapped DNA optimizes its binding energy to the histone core and the elastic energy penalty of DNA wrapping. The magnitude of the effect predicted from our model is in agreement with the systematic experimental data on the linear variation of nucleosome repeat lengths with H1/nucleosome ratio (Woodcock C L et al 2006 Chromos. Res. 14 17-25). We compare our model to the data for different cell types and organisms, with a widely varying ratio of bound H1 histones per nucleosome. We underline the importance of this non-specific histone-DNA charge-balance mechanism in regulating the positioning of nucleosomes and the degree of compaction of chromatin fibers in eukaryotic cells.
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Affiliation(s)
- Andrey G Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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Beshnova DA, Cherstvy AG, Vainshtein Y, Teif VB. Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions. PLoS Comput Biol 2014; 10:e1003698. [PMID: 24992723 PMCID: PMC4081033 DOI: 10.1371/journal.pcbi.1003698] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/16/2014] [Indexed: 12/12/2022] Open
Abstract
The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.
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Affiliation(s)
- Daria A. Beshnova
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Heidelberg, Germany
| | - Andrey G. Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, Potsdam-Golm, Germany
| | - Yevhen Vainshtein
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Heidelberg, Germany
| | - Vladimir B. Teif
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Heidelberg, Germany
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