1
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Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
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Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
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2
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Shi X, Kannaian B, Prasanna C, Soman A, Nordenskiöld L. Structural and dynamical investigation of histone H2B in well-hydrated nucleosome core particles by solid-state NMR. Commun Biol 2023; 6:672. [PMID: 37355718 PMCID: PMC10290710 DOI: 10.1038/s42003-023-05050-3] [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: 02/19/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
H2A-H2B dimer is a key component of nucleosomes and an important player in chromatin biology. Here, we characterized the structure and dynamics of H2B in precipitated nucleosome core particles (NCPs) with a physiologically relevant concentration using solid-state NMR. Our recent investigation of H3-H4 tetramer determined its unique dynamic properties and the present work provides a deeper understanding of the previously observed dynamic networks in NCP that is potentially functionally significant. Nearly complete 13C, 15N assignments were obtained for H2B R30-A121, which permit extracting unprecedented detailed structural and amino-acid site-specific dynamics. The derived structure of H2B in the well-hydrated NCP sample agrees well with that of X-ray crystals. Dynamics at different timescales were determined semi-quantitatively for H2B in a site-specific manner. Particularly, higher millisecond-microsecond dynamics are observed for H2B core regions including partial α1, L1, partial α2, and partial L3. The analysis of these regions in the context of the tertiary structure reveals the clustering of dynamical residues. Overall, this work fills a gap to a complete resonance assignment of all four histones in nucleosomes and delineates that the dynamic networks in NCP extend to H2B, which suggests a potential mechanism to couple histone core with distant DNA to modulate the DNA activities.
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Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province, China.
| | - Bhuvaneswari Kannaian
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Aghil Soman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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3
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Datta S, Patel M, Kashyap S, Patel D, Singh U. Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1. Oncotarget 2022; 13:136-155. [PMID: 35070079 PMCID: PMC8765472 DOI: 10.18632/oncotarget.28174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Genomes of somatic cells in culture are prone to spontaneous mutations due to errors in replication and DNA repair. Some of these errors, such as chromosomal fusions, are not rectifiable and subject to selection or elimination in growing cultures. Somatic cell cultures are thus expected to generate background levels of potentially stable chromosomal chimeras. A description of the landscape of such spontaneously generated chromosomal chimeras in cultured cells will help understand the factors affecting somatic mosaicism. Here we show that short homology-associated non-homologous chromosomal chimeras occur in normal human fibroblasts and HEK293T cells at genomic repeats. The occurrence of chromosomal chimeras is enhanced by heat stress and depletion of a repeat regulatory protein CGGBP1. We also present evidence of homologous chromosomal chimeras between allelic copies in repeat-rich DNA obtained by methylcytosine immunoprecipitation. The formation of homologous chromosomal chimeras at Alu and L1 repeats increases upon depletion of CGGBP1. Our data are derived from de novo sequencing from three different cell lines under different experimental conditions and our chromosomal chimera detection pipeline is applicable to long as well as short read sequencing platforms. These findings present significant information about the generation, sensitivity and regulation of somatic mosaicism in human cell cultures.
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Affiliation(s)
- Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Manthan Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - Sukesh Kashyap
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Divyesh Patel
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
- Current address: Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki 00290, Finland
| | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
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4
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Bubak G, Kwapiszewska K, Kalwarczyk T, Bielec K, Andryszewski T, Iwan M, Bubak S, Hołyst R. Quantifying Nanoscale Viscosity and Structures of Living Cells Nucleus from Mobility Measurements. J Phys Chem Lett 2021; 12:294-301. [PMID: 33346672 DOI: 10.1021/acs.jpclett.0c03052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the mobility of nano-objects in the eukaryotic cell nucleus, at multiple length-scales, is essential for dissecting nuclear structure-function relationships both in space and in time. Here, we demonstrate, using single-molecule fluorescent correlation spectroscopies, that motion of inert probes (proteins, polymers, or nanoparticles) with diameters ranging from 2.6 to 150 nm is mostly unobstructed in a nucleus. Supported by the analysis of electron tomography images, these results advocate the ∼150 nm-wide interchromosomal channels filled with the aqueous diluted protein solution. The nucleus is percolated by these channels to allow various cargos to migrate freely at the nanoscale. We determined the volume of interchromosomal channels in the HeLa cell nucleus to 237 ± 61 fL, which constitutes 34% of the cell nucleus volume. The volume fraction of mobile proteins in channels equals 16% ± 4%, and the concentration is 1 mM.
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Affiliation(s)
- Grzegorz Bubak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Andryszewski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michalina Iwan
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Szymon Bubak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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5
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A biomimetic model of 3D fluid extracellular macromolecular crowding microenvironment fine-tunes ovarian cancer cells dissemination phenotype. Biomaterials 2020; 269:120610. [PMID: 33388691 DOI: 10.1016/j.biomaterials.2020.120610] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/21/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022]
Abstract
An early fundamental step in ovarian cancer progression is the dissemination of cancer cells through liquid environments, one of them being cancer ascites accumulated in the peritoneal cavity. These biological fluids are highly crowded with a high total macromolecule concentration. This biophysical property of fluids is widely used in tissue engineering for a few decades now, yet is largely underrated in cancer biomimetic models. To unravel the role of fluids extracellular macromolecular crowding (MMC), we exposed ovarian cancer cells (OCC) to high molecular weight inert polymer solutions. High macromolecular composition of extracellular liquid presented a differential effect: i) it impeded non-adherent OCC aggregation in suspension and, decreased their adhesion; ii) it promoted adherent OCC migration by decreasing extracellular matrix deposition. Besides, there seemed to be a direct link between the extracellular MMC and intracellular processes, especially the actin cytoskeleton organization and the nucleus morphology. In conclusion, extracellular fluid MMC orients OCC dissemination phenotype. Integrating MMC seems crucial to produce more relevant mimetic 3D in vitro fluid models to study ovarian dissemination but also to screen drugs.
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6
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Elbaum M. Quantitative Cryo-Scanning Transmission Electron Microscopy of Biological Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706681. [PMID: 29748979 DOI: 10.1002/adma.201706681] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/01/2018] [Indexed: 06/08/2023]
Abstract
Electron tomography provides a detailed view into the 3D structure of biological cells and tissues. Physical fixation by vitrification of the aqueous medium provides the most faithful preservation of biological specimens in the native, fully hydrated state. Cryo-microscopy is challenging, however, because of the sensitivity to electron irradiation and due to the weak electron scattering of organic material. Tomography is even more challenging because of the dependence on multiple exposures of the same area. Tomographic imaging is typically performed in wide-field transmission electron microscopy (TEM) mode with phase contrast generated by defocus. Scanning transmission electron microscopy (STEM) is an alternative mode based on detection of scattering from a focused probe beam, without imaging optics following the specimen. While careful configuration of the illumination and detectors is required to generate useful contrast, STEM circumvents the major restrictions of phase contrast TEM to very thin specimens and provides a signal that is more simply interpreted in terms of local composition and density. STEM has gained popularity in recent years for materials science. The extension of STEM to cryomicroscopy and tomography of cells and macromolecules is summarized herein.
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Affiliation(s)
- Michael Elbaum
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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7
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Nave C. A comparison of absorption and phase contrast for X-ray imaging of biological cells. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1490-1504. [PMID: 30179189 PMCID: PMC6140389 DOI: 10.1107/s1600577518009566] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 07/04/2018] [Indexed: 05/04/2023]
Abstract
X-ray imaging allows biological cells to be examined at a higher resolution than possible with visible light and without some of the preparation difficulties associated with electron microscopy of thick samples. The most used and developed technique is absorption contrast imaging in the water window which exploits the contrast between carbon and oxygen at an energy of around 500 eV. A variety of phase contrast techniques are also being developed. In general these operate at a higher energy, enabling thicker cells to be examined and, in some cases, can be combined with X-ray fluorescence imaging to locate specific metals. The various methods are based on the differences between the complex refractive indices of the cellular components and the surrounding cytosol or nucleosol, the fluids present in the cellular cytoplasm and nucleus. The refractive indices can be calculated from the atomic composition and density of the components. These in turn can be obtained from published measurements using techniques such as chemical analysis, scanning electron microscopy and X-ray imaging at selected energies. As examples, the refractive indices of heterochromatin, inner mitochondrial membranes, the neutral core of lipid droplets, starch granules, cytosol and nucleosol are calculated. The refractive index calculations enable the required doses and fluences to be obtained to provide images with sufficient statistical significance, for X-ray energies between 200 and 4000 eV. The statistical significance (e.g. the Rose criterion) for various requirements is discussed. The calculations reveal why some cellular components are more visible by absorption contrast and why much greater exposure times are required to see some cellular components. A comparison of phase contrast as a function of photon energy with absorption contrast in the water window is provided and it is shown that much higher doses are generally required for the phase contrast measurements. This particularly applies to those components with a high carbon content but with a mass density similar to the surrounding cytosol or nucleosol. The results provide guidance for the most appropriate conditions for X-ray imaging of individual cellular components within cells of various thicknesses.
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Affiliation(s)
- Colin Nave
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Correspondence e-mail:
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8
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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9
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Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018; 57:9734-9738. [DOI: 10.1002/anie.201804707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
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10
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Fang K, Chen X, Li X, Shen Y, Sun J, Czajkowsky DM, Shao Z. Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure. ACS NANO 2018; 12:4909-4918. [PMID: 29715004 DOI: 10.1021/acsnano.8b01963] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is widely recognized that the higher-order spatial organization of the genome, beyond the nucleosome, plays an important role in many biological processes. However, to date, direct information on even such fundamental structural details as the typical sizes and DNA content of these higher-order structures in situ is poorly characterized. Here, we examine the nanoscopic DNA organization within human nuclei using super-resolution direct stochastic optical reconstruction microscopy (dSTORM) imaging and 5-ethynyl-2'-deoxyuridine click chemistry, studying single fully labeled chromosomes within an otherwise unlabeled nuclei to improve the attainable resolution. We find that, regardless of nuclear position, individual subchromosomal regions consist of three different levels of DNA compaction: (i) dispersed chromatin; (ii) nanodomains of sizes ranging tens of nanometers containing a few kilobases (kb) of DNA; and (iii) clusters of nanodomains. Interestingly, the sizes and DNA content of the nanodomains are approximately the same at the nuclear periphery, nucleolar proximity, and nuclear interior, suggesting that these nanodomains share a roughly common higher-order architecture. Overall, these results suggest that DNA compaction within the eukaryote nucleus occurs via the condensation of DNA into few-kb nanodomains of approximately similar structure, with further compaction occurring via the clustering of nanodomains.
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11
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Szczurek A, Klewes L, Xing J, Gourram A, Birk U, Knecht H, Dobrucki JW, Mai S, Cremer C. Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations. Nucleic Acids Res 2017; 45:e56. [PMID: 28082388 PMCID: PMC5416826 DOI: 10.1093/nar/gkw1301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions.
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Affiliation(s)
| | - Ludger Klewes
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Jun Xing
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Amine Gourram
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Udo Birk
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Hans Knecht
- Département de Médecine, CHUS, Université de Sherbrooke, 3001-12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada.,Department of Medicine, Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, Québec H3T 1E2, Canada
| | - Jurek W Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sabine Mai
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Christoph Cremer
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany.,Kirchhoff Institute of Physics (KIP), and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Germany
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12
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Dong B, Almassalha LM, Soetikno BT, Chandler JE, Nguyen TQ, Urban BE, Sun C, Zhang HF, Backman V. Stochastic fluorescence switching of nucleic acids under visible light illumination. OPTICS EXPRESS 2017; 25:7929-7944. [PMID: 28380910 PMCID: PMC5810907 DOI: 10.1364/oe.25.007929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 05/20/2023]
Abstract
We report detailed characterizations of stochastic fluorescence switching of unmodified nucleic acids under visible light illumination. Although the fluorescent emission from nucleic acids under the visible light illumination has long been overlooked due to their apparent low absorption cross section, our quantitative characterizations reveal the high quantum yield and high photon count in individual fluorescence emission events of nucleic acids at physiological concentrations. Owing to these characteristics, the stochastic fluorescence switching of nucleic acids could be comparable to that of some of the most potent exogenous fluorescence probes for localization-based super-resolution imaging. Therefore, utilizing the principle of single-molecule photon-localization microscopy, native nucleic acids could be ideal candidates for optical label-free super-resolution imaging.
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Affiliation(s)
- Biqin Dong
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
- Mechanical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Luay M. Almassalha
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Brian T. Soetikno
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - John E. Chandler
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - The-Quyen Nguyen
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Ben E. Urban
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Cheng Sun
- Mechanical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Hao F. Zhang
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Vadim Backman
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
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13
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Wu W, Radosevich AJ, Eshein A, Nguyen TQ, Yi J, Cherkezyan L, Roy HK, Szleifer I, Backman V. Using electron microscopy to calculate optical properties of biological samples. BIOMEDICAL OPTICS EXPRESS 2016; 7:4749-4762. [PMID: 27896013 PMCID: PMC5119613 DOI: 10.1364/boe.7.004749] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 05/26/2023]
Abstract
The microscopic structural origins of optical properties in biological media are still not fully understood. Better understanding these origins can serve to improve the utility of existing techniques and facilitate the discovery of other novel techniques. We propose a novel analysis technique using electron microscopy (EM) to calculate optical properties of specific biological structures. This method is demonstrated with images of human epithelial colon cell nuclei. The spectrum of anisotropy factor g, the phase function and the shape factor D of the nuclei are calculated. The results show strong agreement with an independent study. This method provides a new way to extract the true phase function of biological samples and provides an independent validation for optical property measurement techniques.
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Affiliation(s)
- Wenli Wu
- Applied Physics Program, Northwestern University, Evanston, Illinois 60208, USA
| | - Andrew J. Radosevich
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Adam Eshein
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - The-Quyen Nguyen
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Ji Yi
- Department of Medicine, Boston University, Boston, Massachusetts 02118, USA
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Hemant K. Roy
- Section of Gastroenterology, Boston Medical Center/Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
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14
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Abstract
How is the bacterial chromosome organized within the bacterial cell? Over the last 60 years, a variety of approaches have been used to investigate this question. More recently, the parallel development of epifluorescence microscopy and genetic tools has enabled the direct visualization of the intracellular positioning of DNA sequences in live cells and has consequently revolutionized our view of the architecture of the nucleoid in vivo. In this chapter I present a comprehensive methodology designed to characterize the architecture of the nucleoid DNA and the positioning of specific DNA sequences in live Escherichia coli cells. DNA localization systems, preparation of stable agarose-mounted microscopy slides, and basic image analysis tools are mentioned.
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Affiliation(s)
- Christian Lesterlin
- MMSB - Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, UMR 5086, 7 Passage du Vercors, 69 367, Lyon Cedex 07, France.
| | - Nelly Duabrry
- MMSB - Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, UMR 5086, 7 Passage du Vercors, 69 367, Lyon Cedex 07, France.
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15
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Pliss A, Peng X, Liu L, Kuzmin A, Wang Y, Qu J, Li Y, Prasad PN. Single Cell Assay for Molecular Diagnostics and Medicine: Monitoring Intracellular Concentrations of Macromolecules by Two-photon Fluorescence Lifetime Imaging. Theranostics 2015; 5:919-30. [PMID: 26155309 PMCID: PMC4493531 DOI: 10.7150/thno.11863] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/03/2015] [Indexed: 02/01/2023] Open
Abstract
Molecular organization of a cell is dynamically transformed along the course of cellular physiological processes, pathologic developments or derived from interactions with drugs. The capability to measure and monitor concentrations of macromolecules in a single cell would greatly enhance studies of cellular processes in heterogeneous populations. In this communication, we introduce and experimentally validate a bio-analytical single-cell assay, wherein the overall concentration of macromolecules is estimated in specific subcellular domains, such as structure-function compartments of the cell nucleus as well as in nucleoplasm. We describe quantitative mapping of local biomolecular concentrations, either intrinsic relating to the functional and physiological state of a cell, or altered by a therapeutic drug action, using two-photon excited fluorescence lifetime imaging (FLIM). The proposed assay utilizes a correlation between the fluorescence lifetime of fluorophore and the refractive index of its microenvironment varying due to changes in the concentrations of macromolecules, mainly proteins. Two-photon excitation in Near-Infra Red biological transparency window reduced the photo-toxicity in live cells, as compared with a conventional single-photon approach. Using this new assay, we estimated average concentrations of proteins in the compartments of nuclear speckles and in the nucleoplasm at ~150 mg/ml, and in the nucleolus at ~284 mg/ml. Furthermore, we show a profound influence of pharmaceutical inhibitors of RNA synthesis on intracellular protein density. The approach proposed here will significantly advance theranostics, and studies of drug-cell interactions at the single-cell level, aiding development of personal molecular medicine.
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16
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Verdian Doghaei A, Housaindokht M, Bozorgmehr M. Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: Insights from molecular dynamics simulation. J Theor Biol 2015; 364:103-12. [DOI: 10.1016/j.jtbi.2014.09.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 07/14/2014] [Accepted: 09/10/2014] [Indexed: 11/25/2022]
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17
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Ausió J, González-Romero R, Woodcock CL. Comparative structure of vertebrate sperm chromatin. J Struct Biol 2014; 188:142-55. [PMID: 25264147 DOI: 10.1016/j.jsb.2014.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 09/11/2014] [Accepted: 09/17/2014] [Indexed: 12/11/2022]
Abstract
A consistent feature of sperm nuclei is its exceptionally compact state in comparison with somatic nuclei. Here, we have examined the structural organization of sperm chromatin from representatives of three vertebrate lineages, bony fish (Danio rerio), birds (Gallus gallus domesticus) and mammals (Mus musculus) using light and transmission electron microscopy (TEM). Although the three sperm nuclei are all highly compact, they differ in morphology and in the complement of compaction-inducing proteins. Whereas zebrafish sperm retain somatic histones and a nucleosomal organization, in the rooster and mouse, histones are largely replaced by small, arginine-rich protamines. In contrast to the mouse, the rooster protamine contains no cysteine residues and lacks the potential stabilizing effects of S-S bonds. Protamine driven chromatin compaction results in a stable, highly condensed chromatin, markedly different from the somatic nucleosome-based beads-on-a-string architecture, but its structure remains poorly understood. When prepared gently for whole mount TEM, the rooster and mouse sperm chromatin reveal striking rod-like units 40-50 nm in width. Also present in the mouse, which has very flattened sperm nuclei, but not rooster, where nuclei take the form of elongated cylinders, are toroidal shaped structures, with an external diameter of about 90 nm. In contrast, similarly prepared zebrafish sperm exhibit nucleosomal chromatin. We also examined the early stages in the binding of salmine (the salmon protamine) to defined sequence DNA. These images suggest an initial side-by-side binding of linear DNA-protamine complexes leading to the nucleation of thin, flexible rods with the potential to bend, allowing the ends to come into contact and fuse to form toroidal structures. We discuss the relationship between these in vitro observations and the rods and toroids seen in nuclei, and suggest an explanation for the apparent absence of these structures in TEM images of fully condensed sperm nuclei.
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Affiliation(s)
- Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Rodrigo González-Romero
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
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Abstract
The principles that determine the organization of the nucleus have become clearer in recent years, largely because of new insights into polymer, colloid, and soft-matter science. Macromolecules, together with the giant linear polymers that form the chromosomes, are confined at high concentrations within the nuclear envelope and their interactions are influenced strongly by short-range depletion or entropic forces which are negligible in dilute systems, in addition to the more familiar van der Waals, electrostatic, steric, hydrogen bonding, and hydrophobic forces. The studies described in this volume are consistent with the model that this complex and concentrated mixture of macromolecules is maintained in a delicate equilibrium by quite simple although unsuspected physicochemical principles. The sensitivity of this equilibrium to perturbation may underlie the controversies about the existence of a nuclear matrix or scaffold. In this volume, we underline the importance for cell biologists of being familiar with current work in colloid, polymer, soft matter, and nanoscience. This chapter presents a brief background to the aspects of the nucleus that are considered in detail in subsequent chapters.
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Affiliation(s)
- Ronald Hancock
- Laval University Cancer Research Centre, CRCHUQ-Oncology, Québec, Canada; Biosystems Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland.
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Nolin F, Michel J, Wortham L, Tchelidze P, Balossier G, Banchet V, Bobichon H, Lalun N, Terryn C, Ploton D. Changes to cellular water and element content induced by nucleolar stress: investigation by a cryo-correlative nano-imaging approach. Cell Mol Life Sci 2013; 70:2383-94. [PMID: 23385351 PMCID: PMC11113571 DOI: 10.1007/s00018-013-1267-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/10/2013] [Accepted: 01/14/2013] [Indexed: 01/01/2023]
Abstract
The cell is a crowded volume, with estimated mean mass percentage of macromolecules and of water ranging from 7.5 to 45 and 55 to 92.5 %, respectively. However, the concentrations of macromolecules and water at the nanoscale within the various cell compartments are unknown. We recently developed a new approach, correlative cryo-analytical scanning transmission electron microscopy, for mapping the quantity of water within compartments previously shown to display GFP-tagged protein fluorescence on the same ultrathin cryosection. Using energy-dispersive X-ray spectrometry (EDXS), we then identified various elements (C, N, O, P, S, K, Cl, Mg) in these compartments and quantified them in mmol/l. Here, we used this new approach to quantify water and elements in the cytosol, mitochondria, condensed chromatin, nucleoplasm, and nucleolar components of control and stressed cancerous cells. The water content of the control cells was between 60 and 83 % (in the mitochondria and nucleolar fibrillar centers, respectively). Potassium was present at concentrations of 128-462 mmol/l in nucleolar fibrillar centers and condensed chromatin, respectively. The induction of nucleolar stress by treatment with a low dose of actinomycin-D to inhibit rRNA synthesis resulted in both an increase in water content and a decrease in the elements content in all cell compartments. We generated a nanoscale map of water and elements within the cell compartments, providing insight into their changes induced by nucleolar stress.
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Affiliation(s)
- Frédérique Nolin
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Jean Michel
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Laurence Wortham
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Pavel Tchelidze
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
| | - Gérard Balossier
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Vincent Banchet
- Laboratoire de Recherche en Nanosciences, Université de Reims Champagne Ardenne, Reims, France
| | - Hélène Bobichon
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
| | - Nathalie Lalun
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
| | - Christine Terryn
- Plate-forme IBISA, SFR CAP-SANTE, Université de Reims Champagne Ardenne, Reims, France
| | - Dominique Ploton
- CNRS FRE 3481, Université de Reims Champagne Ardenne, Reims, France
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Bancaud A, Lavelle C, Huet S, Ellenberg J. A fractal model for nuclear organization: current evidence and biological implications. Nucleic Acids Res 2012; 40:8783-92. [PMID: 22790985 PMCID: PMC3467038 DOI: 10.1093/nar/gks586] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin is a multiscale structure on which transcription, replication, recombination and repair of the genome occur. To fully understand any of these processes at the molecular level under physiological conditions, a clear picture of the polymorphic and dynamic organization of chromatin in the eukaryotic nucleus is required. Recent studies indicate that a fractal model of chromatin architecture is consistent with both the reaction-diffusion properties of chromatin interacting proteins and with structural data on chromatin interminglement. In this study, we provide a critical overview of the experimental evidence that support a fractal organization of chromatin. On this basis, we discuss the functional implications of a fractal chromatin model for biological processes and propose future experiments to probe chromatin organization further that should allow to strongly support or invalidate the fractal hypothesis.
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Affiliation(s)
- Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, Toulouse F-31077, France.
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21
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Culurgioni S, Muñoz IG, Moreno A, Palacios A, Villate M, Palmero I, Montoya G, Blanco FJ. Crystal structure of inhibitor of growth 4 (ING4) dimerization domain reveals functional organization of ING family of chromatin-binding proteins. J Biol Chem 2012; 287:10876-84. [PMID: 22334692 DOI: 10.1074/jbc.m111.330001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The protein ING4 binds to histone H3 trimethylated at Lys-4 (H3K4me3) through its C-terminal plant homeodomain, thus recruiting the HBO1 histone acetyltransferase complex to target promoters. The structure of the plant homeodomain finger bound to an H3K4me3 peptide has been described, as well as the disorder and flexibility in the ING4 central region. We report the crystal structure of the ING4 N-terminal domain, which shows an antiparallel coiled-coil homodimer with each protomer folded into a helix-loop-helix structure. This arrangement suggests that ING4 can bind simultaneously two histone tails on the same or different nucleosomes. Dimerization has a direct impact on ING4 tumor suppressor activity because monomeric mutants lose the ability to induce apoptosis after genotoxic stress. Homology modeling based on the ING4 structure suggests that other ING dimers may also exist.
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22
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Pliss A, Kuzmin AN, Kachynski AV, Prasad PN. Nonlinear optical imaging and Raman microspectrometry of the cell nucleus throughout the cell cycle. Biophys J 2011; 99:3483-91. [PMID: 21081098 DOI: 10.1016/j.bpj.2010.06.069] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 06/28/2010] [Accepted: 06/30/2010] [Indexed: 11/17/2022] Open
Abstract
Fundamental understanding of cellular processes at molecular level is of considerable importance in cell biology as well as in biomedical disciplines for early diagnosis of infection and cancer diseases, and for developing new molecular medicine-based therapies. Modern biophotonics offers exclusive capabilities to obtain information on molecular composition, organization, and dynamics in a cell by utilizing a combination of optical spectroscopy and optical imaging. We introduce here a combination of Raman microspectrometry, together with coherent anti-Stokes Raman scattering (CARS) and two-photon excited fluorescence (TPEF) nonlinear optical microscopy, to study macromolecular organization of the nucleus throughout the cell cycle. Site-specific concentrations of proteins, DNA, RNA, and lipids were determined in nucleoli, nucleoplasmic transcription sites, nuclear speckles, constitutive heterochromatin domains, mitotic chromosomes, and extrachromosomal regions of mitotic cells by quantitative confocal Raman microspectrometry. A surprising finding, obtained in our study, is that the local concentration of proteins does not increase during DNA compaction. We also demonstrate that postmitotic DNA decondensation is a gradual process, continuing for several hours. The quantitative Raman spectroscopic analysis was corroborated with CARS/TPEF multimodal imaging to visualize the distribution of protein, DNA, RNA, and lipid macromolecules throughout the cell cycle.
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Affiliation(s)
- Artem Pliss
- University at Buffalo, State University of New York, Buffalo, NY, USA
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24
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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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25
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Telomere maintenance in liquid crystalline chromosomes of dinoflagellates. Chromosoma 2010; 119:485-93. [DOI: 10.1007/s00412-010-0272-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 03/11/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
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26
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Bancaud A, Huet S, Daigle N, Mozziconacci J, Beaudouin J, Ellenberg J. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J 2010; 28:3785-98. [PMID: 19927119 DOI: 10.1038/emboj.2009.340] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 10/19/2009] [Indexed: 11/09/2022] Open
Abstract
The nucleus of eukaryotes is organized into functional compartments, the two most prominent being heterochromatin and nucleoli. These structures are highly enriched in DNA, proteins or RNA, and thus thought to be crowded. In vitro, molecular crowding induces volume exclusion, hinders diffusion and enhances association, but whether these effects are relevant in vivo remains unclear. Here, we establish that volume exclusion and diffusive hindrance occur in dense nuclear compartments by probing the diffusive behaviour of inert fluorescent tracers in living cells. We also demonstrate that chromatin-interacting proteins remain transiently trapped in heterochromatin due to crowding induced enhanced affinity. The kinetic signatures of these crowding consequences allow us to derive a fractal model of chromatin organization, which explains why the dynamics of soluble nuclear proteins are affected independently of their size. This model further shows that the fractal architecture differs between heterochromatin and euchromatin, and predicts that chromatin proteins use different target-search strategies in the two compartments. We propose that fractal crowding is a fundamental principle of nuclear organization, particularly of heterochromatin maintenance.
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27
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Quantitative biological imaging by ptychographic x-ray diffraction microscopy. Proc Natl Acad Sci U S A 2009; 107:529-34. [PMID: 20018650 DOI: 10.1073/pnas.0905846107] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent advances in coherent x-ray diffractive imaging have paved the way to reliable and quantitative imaging of noncompact specimens at the nanometer scale. Introduced a year ago, an advanced implementation of ptychographic coherent diffractive imaging has removed much of the previous limitations regarding sample preparation and illumination conditions. Here, we apply this recent approach toward structure determination at the nanoscale to biological microscopy. We show that the projected electron density of unstained and unsliced freeze-dried cells of the bacterium Deinococcus radiodurans can be derived from the reconstructed phase in a straightforward and reproducible way, with quantified and small errors. Thus, the approach may contribute in the future to the understanding of the highly disputed nucleoid structure of bacterial cells. In the present study, the estimated resolution for the cells was 85 nm (half-period length), whereas 50-nm resolution was demonstrated for lithographic test structures. With respect to the diameter of the pinhole used to illuminate the samples, a superresolution of about 15 was achieved for the cells and 30 for the test structures, respectively. These values should be assessed in view of the low dose applied on the order of approximately 1.3x10(5) Gy, and were shown to scale with photon fluence.
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28
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de Nooijer S, Wellink J, Mulder B, Bisseling T. Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei. Nucleic Acids Res 2009; 37:3558-68. [PMID: 19359359 PMCID: PMC2699506 DOI: 10.1093/nar/gkp219] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The organization of the eukaryote nucleus into functional compartments arises by self-organization both through specific protein-protein and protein-DNA interactions and non-specific interactions that lead to entropic effects, such as e.g. depletion attraction. While many specific interactions have so far been demonstrated, the contributions of non-specific interactions are still unclear. We used coarse-grained molecular dynamics simulations of previously published models for Arabidopsis thaliana chromatin organization to show that non-specific interactions can explain the in vivo localization of nucleoli and chromocenters. Also, we quantitatively demonstrate that chromatin looping contributes to the formation of chromosome territories. Our results are consistent with the previously published Rosette model for Arabidopsis chromatin organization and suggest that chromocenter-associated loops play a role in suppressing chromocenter clustering.
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Affiliation(s)
- S de Nooijer
- Laboratory for Molecular Biology, Wageningen University, Drovendaalsesteeg 1, 6708PB Wageningen, Netherlands
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29
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Abstract
Histone modifications modulate chromatin structure and function. A posttranslational modification-randomized, combinatorial library based on the first 21 residues of histone H4 was designed for systematic examination of proteins that interpret a histone code. The 800-member library represented all permutations of most known modifications within the N-terminal tail of histone H4. To determine its utility in a protein binding assay, the on-bead library was screened with an antibody directed against phosphoserine 1 of H4. Among the hits, 59 of 60 sequences were phosphorylated at S1, while 30 of 30 of those selected from the nonhits were unphosphorylated. A 512-member version of the library was then used to determine the binding specificity of the double tudor domain of hJMJD2A, a histone demethylase involved in transcriptional repression. Global linear least-squares fitting of modifications from the identified peptides (40 hits and 34 nonhits) indicated that methylation of K20 was the primary determinant for binding, but that phosphorylation and acetylation of neighboring sites attenuated the interaction. To validate the on-bead screen, isothermal titration calorimetry was performed with 13 H4 peptides. Dissociation constants ranged from 1 mM to 1 microM and corroborated the screening results. The general approach should be useful for probing the specificity of any histone-binding protein.
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Affiliation(s)
- Adam L Garske
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706-1532, USA
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30
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Sousa AA, Hohmann-Marriott M, Aronova MA, Zhang G, Leapman RD. Determination of quantitative distributions of heavy-metal stain in biological specimens by annular dark-field STEM. J Struct Biol 2008; 162:14-28. [PMID: 18359249 PMCID: PMC2705981 DOI: 10.1016/j.jsb.2008.01.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 01/16/2008] [Accepted: 01/17/2008] [Indexed: 11/24/2022]
Abstract
It is shown that dark-field images collected in the scanning transmission electron microscope (STEM) at two different camera lengths yield quantitative distributions of both the heavy and light atoms in a stained biological specimen. Quantitative analysis of the paired STEM images requires knowledge of the elastic scattering cross sections, which are calculated from the NIST elastic scattering cross section database. The results reveal quantitative information about the distribution of fixative and stain within the biological matrix, and provide a basis for assessing detection limits for heavy-metal clusters used to label intracellular proteins. In sectioned cells that have been stained only with osmium tetroxide, we find an average of 1.2+/-0.1 Os atom per nm(3), corresponding to an atomic ratio of Os:C atoms of approximately 0.02, which indicates that small heavy atom clusters of Undecagold and Nanogold can be detected in lightly stained specimens.
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Affiliation(s)
- A. A. Sousa
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - M. Hohmann-Marriott
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - M. A. Aronova
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - G. Zhang
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - R. D. Leapman
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Self-association of polynucleosome chains by macromolecular crowding. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1059-64. [PMID: 18259740 DOI: 10.1007/s00249-008-0276-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 10/22/2022]
Abstract
The crowding of macromolecules in the cell nucleus, where their concentration is in the range of 100 mg/ml, is predicted to result in strong entropic forces between them. Here the effects of crowding on polynucleosome chains in vitro were studied to evaluate if these forces could contribute to the packing of chromatin in the nucleus in vivo. Soluble polynucleosomes approximately 20 nucleosomes in length formed fast-sedimenting complexes in the presence of inert, volume-occupying agents poly(ethylene glycol) (PEG) or dextran. This self-association was reversible and consistent with the effect of macromolecular crowding. In the presence of these crowding agents, polynucleosomes formed large assemblies as seen by fluorescence microscopy after labelling DNA with the fluorescent stain DAPI, and formed rods and sheets at a higher concentration of crowding agent. Self-association caused by crowding does not require exogenous cations. Single, approximately 800 nucleosome-long chains prepared in 100 microM Hepes buffer with no added cations, labelled with the fluorescent DNA stain YOYO-1, and spread on a polylysine-coated surface formed compact 3-D clusters in the presence of PEG or dextran. This reversible packing of polynucleosome chains by crowding may help to understand their compact conformations in the nucleus. These results, together with the known collapse of linear polymers in crowded milieux, suggest that entropic forces due to crowding, which have not been considered previously, may be an important factor in the packing of nucleosome chains in the nucleus.
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32
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Hancock R. Packing of the polynucleosome chain in interphase chromosomes: evidence for a contribution of crowding and entropic forces. Semin Cell Dev Biol 2007; 18:668-75. [PMID: 17904880 DOI: 10.1016/j.semcdb.2007.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 08/22/2007] [Indexed: 11/23/2022]
Abstract
In the crowded intranuclear environment, entropic depletion forces between macromolecules are expected to be strong. A review of simulations of linear polymers leads to several predictions about probable conformations of a polynucleosome chain in these conditions. These include a globular conformation, variable compaction due to different local rigidity or curvature of the mosaic of isochores, satellite sequences, and nucleosomes containing different histone variants, and the possibility that chromosomes represent separate phases like those seen in heterogeneous particle mixtures by experiment and simulation. Experimental results which show that macromolecular crowding alone, in the absence of exogenous cations, can stabilise interphase chromosomes and cause self-association of polynucleosome chains are presented. Together, these considerations suggest that macromolecular crowding and entropic forces are major factors in packing polynucleosome chains in vivo.
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Affiliation(s)
- Ronald Hancock
- Laval University Cancer Research Centre, Hôtel-Dieu Hospital, 9 rue MacMahon, Québec, QC, Canada G1R 2J6.
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33
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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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34
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Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Mol Biol 2007; 8:44. [PMID: 17531098 PMCID: PMC1904230 DOI: 10.1186/1471-2199-8-44] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 05/25/2007] [Indexed: 01/11/2023] Open
Abstract
Background The genetic code imposes a dilemma for cells. The DNA must be long enough to encode for the complexity of an organism, yet thin and flexible enough to fit within the cell. The combination of these properties greatly favors DNA collisions, which can knot and drive recombination of the DNA. Despite the well-accepted propensity of cellular DNA to collide and react with itself, it has not been established what the physiological consequences are. Results Here we analyze the effects of recombined and knotted plasmids in E. coli using the Hin site-specific recombination system. We show that Hin-mediated DNA knotting and recombination (i) promote replicon loss by blocking DNA replication; (ii) block gene transcription; and (iii) cause genetic rearrangements at a rate three to four orders of magnitude higher than the rate for an unknotted, unrecombined plasmid. Conclusion These results show that DNA reactivity leading to recombined and knotted DNA is potentially toxic and may help drive genetic evolution.
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35
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Marenduzzo D, Finan K, Cook PR. The depletion attraction: an underappreciated force driving cellular organization. ACTA ACUST UNITED AC 2007; 175:681-6. [PMID: 17145959 PMCID: PMC2064666 DOI: 10.1083/jcb.200609066] [Citation(s) in RCA: 257] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cellular structures are shaped by hydrogen and ionic bonds, plus van der Waals and hydrophobic forces. In cells crowded with macromolecules, a little-known and distinct force—the “depletion attraction”—also acts. We review evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes.
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Affiliation(s)
- Davide Marenduzzo
- School of Physics, University of Edinburgh, Edinburgh, EH9 3JZ, Scotland, UK
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Molecular Crowding Induces Telomere G-Quadruplex Formation under Salt-Deficient Conditions and Enhances its Competition with Duplex Formation. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502960] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kan ZY, Yao Y, Wang P, Li XH, Hao YH, Tan Z. Molecular Crowding Induces Telomere G-Quadruplex Formation under Salt-Deficient Conditions and Enhances its Competition with Duplex Formation. Angew Chem Int Ed Engl 2006; 45:1629-32. [PMID: 16470760 DOI: 10.1002/anie.200502960] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhong-Yuan Kan
- Laboratory of Biochemistry and Biophysics, College of Life Sciences, Wuhan University, Wuhan 430072, P.R. China
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38
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Mak CKM, Hung VKL, Wong JTY. Type II topoisomerase activities in both the G1 and G2/M phases of the dinoflagellate cell cycle. Chromosoma 2005; 114:420-31. [PMID: 16252092 DOI: 10.1007/s00412-005-0027-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 08/31/2005] [Accepted: 09/01/2005] [Indexed: 11/28/2022]
Abstract
Dinoflagellate genomes are large (up to 200 pg) and are encoded in histoneless chromosomes that are quasi-permanently condensed. This unique combination of chromosomal characteristics presents additional topological and cell cycle control problems for a eukaryotic cell, potentially exhibiting novel regulatory requirements of topoisomerase II. The heterotrophic dinoflagellate Crypthecodinium cohnii was used in this study. The topoisomerase II activities throughout its cell cycle were investigated by DNA flow cytometry following enzyme deactivation. Fluorescence microscopy was also used for studying the chromosome morphology of the treated cells. Two classes of topoisomerase II inhibitors were applied in our study, both of which caused G1 delay as well as G2/M arrest in the C. cohnii cell cycle. At high doses, the topoisomerase poisons amsacrine and ellipticine induced DNA fragmentation in C. cohnii cells. Topoisomerase II activities, as measured by the ability to decatenate kinetoplastid DNA (kDNA), are normally detected throughout the cell cycle in C. cohnii. Our results suggest that the requirement of type II topoisomerase activities during the G1 phase of the cell cycle may relate to the unwinding of quasi-permanently condensed chromosomes for the purpose of transcription. This was also the first time that topoisomerase II activity in dinoflagellate cells was detected.
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Affiliation(s)
- Carmen K M Mak
- Biology Department, Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong SAR, People's Republic of China
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39
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Sandman K, Reeve JN. Archaeal chromatin proteins: different structures but common function? Curr Opin Microbiol 2005; 8:656-61. [PMID: 16256418 DOI: 10.1016/j.mib.2005.10.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Accepted: 10/11/2005] [Indexed: 10/25/2022]
Abstract
Chromatin proteins promote chromosome flexibility in vivo, maintaining a compact yet decondensed template that permits polymerase accessibility. All Archaea have at least two types of chromatin proteins, and diversity in the chromatin protein population appears to prevent polymerization of a single type of protein. Of the numerous chromatin proteins that have been described in Archaea, only two--histones and Alba homologs--are present in all archaeal phyla. Although their structures and complexes with DNA have no similarities, their functions probably overlap as mutants that lack single chromatin proteins are viable.
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Affiliation(s)
- Kathleen Sandman
- Department of Microbiology, Ohio State University, 484W. 12th Avenue, Columbus, OH 43210, USA.
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40
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Triple helix-tetraplex equilibrium for G-rich oligonucleotide N3′→P5′ phosphoramidates: role of molecular concentration and counterions. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2005.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Costas E, Goyanes V. Architecture and evolution of dinoflagellate chromosomes: an enigmatic origin. Cytogenet Genome Res 2005; 109:268-75. [PMID: 15753586 DOI: 10.1159/000082409] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2003] [Accepted: 02/19/2004] [Indexed: 11/19/2022] Open
Abstract
Dinoflagellates are a highly diversified group of unicellular protists that present fascinating nuclear features which have intrigued researchers for many years. As examples, a dense nuclear matrix accommodates permanently condensed chromosomes that are composed of fibers organized without histones and nucleosomes in stacked rows of parallel nested arches. The macromolecular chromosome structure corresponds to cholesteric liquid crystals with a constant left-handed twist. RNA acts to maintain the chromosome structure. Whole mounted chromosomes have a left-handed screw-like configuration with coils which progressively increase their pitch. This helical arrangement seems to be the result of a couple of narrow strands coiling together. Chromosomes do not show Q, G and C banding patterns. However, a roughly spherical differentiated upper end (primitive kinetochore?) and two differentiated coiling regions, the upper one composed of two to three coils where a couple of sister strands run together and parallel to each other, and the lower one where sister strands run out of phase by 180 degrees angular difference along the immediate next turns, can be distinguished. The chromosome segregation into two daughter chromatids begins at the telomere that attaches to the nuclear envelope, follows along the chromosome axis constituting first a Y-shaped and afterwards a V-shaped chromosome, which packs the newly synthesized DNA inside the "old" chromosome. Dividing chromosomes remain highly condensed, and the diameters of the new chromatids and the undivided chromosome are similar, but the number of arches is twice as large in G1 as in G2. The nuclear envelope remains through the cell cycle and shows spindle fibers, which penetrate intranuclear cytoplasmic channels during mitosis constituting an extra nuclear spindle. These and other cytogenetic features suggest that dinoflagellates are a group of enigmatic protists, unique and different from the usual eukaryotes. In contrast, DNA sequence studies propose that dinoflagellates are true eukaryotes, closely related to Apicomplexa, and ciliates (Alveolata), suggesting that the unusual features of chromosome and nuclear organization are not primitive but derived characters. Nevertheless, dinoflagellates have reached enigmatic specific nuclear and chromosome solutions, extremely far from those of other living beings.
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Affiliation(s)
- E Costas
- Genetica (Produccion Animal), Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.
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Engelhardt M. Condensation of chromatin in situ by cation-dependent charge shielding and aggregation. Biochem Biophys Res Commun 2005; 324:1210-4. [PMID: 15504343 DOI: 10.1016/j.bbrc.2004.09.175] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Indexed: 10/26/2022]
Abstract
Binding of di- or polyvalent cations is necessary to maintain the chromatin in isolated nuclei and metaphase chromosomes in a condensed state. We here show that the native, porous structure of the heterochromatin in the interphase nucleus requires both K(+) and Mg(2+) in concentrations, which are known to support transcription in isolated nuclei, thus providing a functional state of the chromatin. When these cations are acting separately, the chromatin is more condensed by Mg(2+) and decondensed by K(+). Comparison with published values of the free electrostatic energy of DNA in chromatin shows that this state of compaction is the result of a balance between the different aggregative properties of K(+) and Mg(2+) at a high degree of charge shielding.
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Affiliation(s)
- Mogens Engelhardt
- Department of Medical Biochemistry and Genetics,Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3c, 2200 Copenhagen N, Denmark.
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Hancock R. A role for macromolecular crowding effects in the assembly and function of compartments in the nucleus. J Struct Biol 2005; 146:281-90. [PMID: 15099570 DOI: 10.1016/j.jsb.2003.12.008] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2003] [Revised: 12/18/2003] [Indexed: 11/29/2022]
Abstract
The mechanisms which cause macromolecules to form discrete compartments within the nucleus are not understood. Here, two ubiquitous compartments, nucleoli, and PML bodies, are shown to disassemble when K562 cell nuclei expand in medium of low monovalent cation concentration; their major proteins dispersed as seen by immunofluorescence and immunoelectron microscopy, and nucleolar transcript elongation fell by approximately 85%. These compartments reassembled and nucleolar transcription recovered in the same medium after adding inert, penetrating macromolecules (8 kDa polyethylene glycol (PEG), or 10.5 kDa dextran) to 12% w/v, showing that disassembly was not caused by the low cation concentration. These responses satisfy the criteria for crowding or volume exclusion effects which occur in concentrated mixtures of macromolecules; upon expansion the macromolecular concentration within the nucleus falls, and can be restored by PEG or dextran. These observations, together with evidence of a high concentration of macromolecules in the nucleus (in the range of 100mg/ml) which must cause strong crowding forces, suggest strongly that these forces play an essential role in driving the formation, and maintaining the function of nuclear compartments. This view is consistent with their dynamic and mobile nature and can provide interpretations of several unexplained observations in nuclear biology.
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Affiliation(s)
- Ronald Hancock
- Laval University Cancer Research Centre, Hôtel-Dieu Hospital, 9 rue MacMahon, Que., P.Q., Canada G1R 2J6.
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Abstract
Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.
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Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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Abstract
We present a phase diagram of the nucleosome core particle (NCP) as a function of the monovalent salt concentration and applied osmotic pressure. Above a critical pressure, NCPs stack on top of each other to form columns that further organize into multiple columnar phases. An isotropic (and in some cases a nematic) phase of columns is observed in the moderate pressure range. Under higher pressure conditions, a lamello-columnar phase and an inverse hexagonal phase form under low salt conditions, whereas a 2D hexagonal phase or a 3D orthorhombic phase is found at higher salt concentration. For intermediate salt concentrations, microphase separation occurs. The richness of the phase diagram originates from the heterogeneous distribution of charges at the surface of the NCP, which makes the particles extremely sensitive to small ionic variations of their environment, with consequences on their interactions and supramolecular organization. We discuss how the polymorphism of NCP supramolecular organization may be involved in chromatin changes in the cellular context.
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Affiliation(s)
- S Mangenot
- Laboratoire de Physique des Solides, CNRS UMR 8502, Bât 510, Université Paris-Sud, 91405 Orsay Cedex, France
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Abstract
The lengths of the DNA molecules of eukaryotic genomes are much greater than the dimensions of the metaphase chromosomes in which they are contained during mitosis. From this observation it has been generally assumed that the linear packing ratio of DNA is an adequate measure of the degree of DNA compaction. This review summarizes the evidence suggesting that the local concentration of DNA is more appropriate than the linear packing ratio for the study of chromatin condensation. The DNA concentrations corresponding to most of the models proposed for the 30-40 nm chromatin fiber are not high enough for the construction of metaphase chromosomes. The interdigitated solenoid model has a higher density because of the stacking of nucleosomes in secondary helices and, after further folding into chromatids, it yields a final concentration of DNA that approaches the experimental value found for condensed chromosomes. Since recent results have shown that metaphase chromosomes contain high concentrations of the chromatin packing ions Mg2+ and Ca2+, it is discussed that dynamic rather than rigid models are required to explain the condensation of the extended fibers observed in the absence of these cations. Finally, considering the different lines of evidence demonstrating the stacking of nucleosomes in different chromatin complexes, it is suggested that the face-to-face interactions between nucleosomes may be the driving force for the formation of higher order structures with a high local concentration of DNA.
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Affiliation(s)
- Joan-Ramon Daban
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Universitat Autòma de Barcelona, Bellaterra, Spain.
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Abstract
In the scanning transmission electron microscope (STEM) an electron beam of a few angstroms diameter is raster scanned over a thin sample and the scattered electrons are sequentially measured for each sample element irradiated. The mass, the elemental composition and the structure of a protein can be simultaneously assessed if all detector systems of the STEM are used. Aspects affecting the accuracy of the mass measurement technique and the demands placed on the instrument's dark-field detector system are outlined. In addition, the influences of some sample preparation techniques are noted and the mass-loss induced at ambient temperatures by the incidence of 80kV electrons on various biological samples is reported. Finally, the importance of the STEM for the structural analysis of proteins is documented by examples.
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Affiliation(s)
- S A Müller
- Maurice E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056, Basel, Switzerland
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Abstract
In concentrated solution and in the presence of high concentrations of monovalent cations, nucleosome core particles order into a discotic columnar mesophase. This phase is limited to finite-sized hexagonal germs that further divide into six coiled branches, following an iterative process. We show how the structure of the germs comes from the competition between hexagonal packing and chirality with a combination of dendritic facetting and double-twist configurations. Geometrical considerations lead us to suspect that the chirality of the eukaryotic chromosomes may originate from the same competition.
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Affiliation(s)
- F Livolant
- Laboratoire de Physique des Solides, Université Paris Sud, 91405 Orsay Cedex, France.
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Kuzminov A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol Biol Rev 1999; 63:751-813, table of contents. [PMID: 10585965 PMCID: PMC98976 DOI: 10.1128/mmbr.63.4.751-813.1999] [Citation(s) in RCA: 719] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although homologous recombination and DNA repair phenomena in bacteria were initially extensively studied without regard to any relationship between the two, it is now appreciated that DNA repair and homologous recombination are related through DNA replication. In Escherichia coli, two-strand DNA damage, generated mostly during replication on a template DNA containing one-strand damage, is repaired by recombination with a homologous intact duplex, usually the sister chromosome. The two major types of two-strand DNA lesions are channeled into two distinct pathways of recombinational repair: daughter-strand gaps are closed by the RecF pathway, while disintegrated replication forks are reestablished by the RecBCD pathway. The phage lambda recombination system is simpler in that its major reaction is to link two double-stranded DNA ends by using overlapping homologous sequences. The remarkable progress in understanding the mechanisms of recombinational repair in E. coli over the last decade is due to the in vitro characterization of the activities of individual recombination proteins. Putting our knowledge about recombinational repair in the broader context of DNA replication will guide future experimentation.
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Affiliation(s)
- A Kuzminov
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA.
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Leforestier A, Fudaley S, Livolant F. Spermidine-induced aggregation of nucleosome core particles: evidence for multiple liquid crystalline phases. J Mol Biol 1999; 290:481-94. [PMID: 10390346 DOI: 10.1006/jmbi.1999.2895] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigate the effect of the addition of a trivalent cation, spermidine, to dilute solutions of nucleosome core particles (NCP). In the presence of spermidine, part of the NCP segregates from the initial homogeneous solution, forming dense aggregates. We follow this precipitation process over a wide range of spermidine and NaCl concentrations and determine the conditions of aggregation of the particles. The structure of the dense phases is analyzed by means of polarizing light microscopy and cryo-electron microscopy. We report the existence of multiple supramolecular organizations. According to the relative concentrations of spermidine, monovalent salt and NCP, the particles may aggregate into amorphous phases, stack into randomly oriented columns, or form liquid crystalline phases. Two discotic liquid crystalline phases are identified and analyzed: a columnar nematic corresponding to columns of NCP simply aligned in parallel, and a columnar hexagonal phase in which the columns order into a transversal 2D hexagonal array. We discuss the nature and origin of the interactions possibly involved in the formation and maintenance of these different types of order.
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Affiliation(s)
- A Leforestier
- Laboratoire de Physique des Solides, Bât. 510, Université Paris-Sud, F-91405, France
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