101
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Sarmento MJ, Oneto M, Pelicci S, Pesce L, Scipioni L, Faretta M, Furia L, Dellino GI, Pelicci PG, Bianchini P, Diaspro A, Lanzanò L. Exploiting the tunability of stimulated emission depletion microscopy for super-resolution imaging of nuclear structures. Nat Commun 2018; 9:3415. [PMID: 30143630 PMCID: PMC6109149 DOI: 10.1038/s41467-018-05963-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/27/2018] [Indexed: 11/23/2022] Open
Abstract
Imaging of nuclear structures within intact eukaryotic nuclei is imperative to understand the effect of chromatin folding on genome function. Recent developments of super-resolution fluorescence microscopy techniques combine high specificity, sensitivity, and less-invasive sample preparation procedures with the sub-diffraction spatial resolution required to image chromatin at the nanoscale. Here, we present a method to enhance the spatial resolution of a stimulated-emission depletion (STED) microscope based only on the modulation of the STED intensity during the acquisition of a STED image. This modulation induces spatially encoded variations of the fluorescence emission that can be visualized in the phasor plot and used to improve and quantify the effective spatial resolution of the STED image. We show that the method can be used to remove direct excitation by the STED beam and perform dual color imaging. We apply this method to the visualization of transcription and replication foci within intact nuclei of eukaryotic cells.
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Affiliation(s)
- Maria J Sarmento
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the A.S.C.R. v.v.i., Prague, Czech Republic
| | - Michele Oneto
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Simone Pelicci
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Luca Pesce
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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102
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Cai S, Böck D, Pilhofer M, Gan L. The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Mol Biol Cell 2018; 29:2450-2457. [PMID: 30091658 PMCID: PMC6233054 DOI: 10.1091/mbc.e18-05-0331] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.
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Affiliation(s)
- Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Désirée Böck
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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103
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Novais-Cruz M, Alba Abad M, van IJcken WFJ, Galjart N, Jeyaprakash AA, Maiato H, Ferrás C. Mitotic progression, arrest, exit or death relies on centromere structural integrity, rather than de novo transcription. eLife 2018; 7:36898. [PMID: 30080136 PMCID: PMC6128689 DOI: 10.7554/elife.36898] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/03/2018] [Indexed: 12/30/2022] Open
Abstract
Recent studies have challenged the prevailing dogma that transcription is repressed during mitosis. Transcription was also proposed to sustain a robust spindle assembly checkpoint (SAC) response. Here, we used live-cell imaging of human cells, RNA-seq and qPCR to investigate the requirement for de novo transcription during mitosis. Under conditions of persistently unattached kinetochores, transcription inhibition with actinomycin D, or treatment with other DNA-intercalating drugs, delocalized the chromosomal passenger complex (CPC) protein Aurora B from centromeres, compromising SAC signaling and cell fate. However, we were unable to detect significant changes in mitotic transcript levels. Moreover, inhibition of transcription independently of DNA intercalation had no effect on Aurora B centromeric localization, SAC response, mitotic progression, exit or death. Mechanistically, we show that DNA intercalating agents reduce the interaction of the CPC with nucleosomes. Thus, mitotic progression, arrest, exit or death is determined by centromere structural integrity, rather than de novo transcription.
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Affiliation(s)
- Marco Novais-Cruz
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
| | - Maria Alba Abad
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Niels Galjart
- Department of Cell BiologyErasmus Medical CenterRotterdamNetherlands
| | - A Arockia Jeyaprakash
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
| | - Helder Maiato
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
- Cell Division Group, Experimental Biology Unit, Department of Biomedicine, Faculdade de MedicinaUniversidade do PortoPortoPortugal
| | - Cristina Ferrás
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Instituto de Investigação e Inovação em Saúde (i3S)Universidade do PortoPortoPortugal
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104
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Abstract
Maeshima et al. preview work from the Walther et al. imaging Condensin behavior and describing its stoichiometry in mitosis to model chromosome condensation. Condensins are key players in mitotic chromosome condensation. Using an elegant combination of state-of-the-art imaging techniques, Walther et al. (2018. J. Cell Biol.https://doi.org/10.1083/jcb.201801048) counted the number of Condensins, examined their behaviors on human mitotic chromosomes, and integrated the quantitative data to propose a new mechanistic model for chromosome condensation.
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Affiliation(s)
- Kazuhiro Maeshima
- National Institute of Genetics and SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan
| | - Kayo Hibino
- National Institute of Genetics and SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan
| | - Damien F Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
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105
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Cai S, Song Y, Chen C, Shi J, Gan L. Natural chromatin is heterogeneous and self-associates in vitro. Mol Biol Cell 2018; 29:1652-1663. [PMID: 29742050 PMCID: PMC6080658 DOI: 10.1091/mbc.e17-07-0449] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 04/10/2018] [Accepted: 05/04/2018] [Indexed: 11/23/2022] Open
Abstract
The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography (cryo-ET) to study the undigested natural chromatin released from two single-celled organisms in which 30-nm fibers have not been observed in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is condensed into a large mass in vitro. Rare irregular 30-nm fibers, some of which include face-to-face nucleosome interactions, do form at the periphery of this mass. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains condensed, with very few open motifs. Yeast chromatin packing is largely unchanged in the absence of linker histone and mildly decondensed when histones are more acetylated. Natural chromatin is therefore generally nonpermissive of regular motifs, even at the level of oligonucleosomes.
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Affiliation(s)
- Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Yajiao Song
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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106
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Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish Yadav KN, Feng H, Wang R, Zhang P, Zhurkin V, Bai Y. Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures. J Mol Biol 2018; 430:3093-3110. [PMID: 29959925 DOI: 10.1016/j.jmb.2018.06.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 01/23/2023]
Abstract
It has long been suggested that chromatin may form a fiber with a diameter of ~30 nm that suppresses transcription. Despite nearly four decades of study, the structural nature of the 30-nm chromatin fiber and conclusive evidence of its existence in vivo remain elusive. The key support for the existence of specific 30-nm chromatin fiber structures is based on the determination of the structures of reconstituted nucleosome arrays using X-ray crystallography and single-particle cryo-electron microscopy coupled with glutaraldehyde chemical cross-linking. Here we report the characterization of these nucleosome arrays in solution using analytical ultracentrifugation, NMR, and small-angle X-ray scattering. We found that the physical properties of these nucleosome arrays in solution are not consistent with formation of just a few discrete structures of nucleosome arrays. In addition, we obtained a crystal of the nucleosome in complex with the globular domain of linker histone H5 that shows a new form of nucleosome packing and suggests a plausible alternative compact conformation for nucleosome arrays. Taken together, our results challenge the key evidence for the existence of a limited number of structures of reconstituted nucleosome arrays in solution by revealing that the reconstituted nucleosome arrays are actually best described as an ensemble of various conformations with a zigzagged arrangement of nucleosomes. Our finding has implications for understanding the structure and function of chromatin in vivo.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiansheng Jiang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davood Norouzi
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - K N Sathish Yadav
- Laboratory of Structural Biophysics, National Cancer Institute, Frederick, MD 21701, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rui Wang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ping Zhang
- Laboratory of Structural Biophysics, National Cancer Institute, Frederick, MD 21701, USA
| | - Victor Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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107
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Johnson WL, Xie KT, Kwon M, Liu S, Pellman D. How the Genome Folds, Divides, Lives, and Dies. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 82:349-360. [PMID: 29802151 DOI: 10.1101/sqb.2017.82.035527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Whitney L Johnson
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02215
| | - Kathleen T Xie
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02215
| | - Mijung Kwon
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02215
| | - Shiwei Liu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02215
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02215
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
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108
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Bilokapic S, Strauss M, Halic M. Cryo-EM of nucleosome core particle interactions in trans. Sci Rep 2018; 8:7046. [PMID: 29728587 PMCID: PMC5935684 DOI: 10.1038/s41598-018-25429-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/23/2018] [Indexed: 11/09/2022] Open
Abstract
Nucleosomes, the basic unit of chromatin, are repetitively spaced along DNA and regulate genome expression and maintenance. The long linear chromatin molecule is extensively condensed to fit DNA inside the nucleus. How distant nucleosomes interact to build tertiary chromatin structure remains elusive. In this study, we used cryo-EM to structurally characterize different states of long range nucleosome core particle (NCP) interactions. Our structures show that NCP pairs can adopt multiple conformations, but, commonly, two NCPs are oriented with the histone octamers facing each other. In this conformation, the dyad of both nucleosome core particles is facing the same direction, however, the NCPs are laterally shifted and tilted. The histone octamer surface and histone tails in trans NCP pairs remain accessible to regulatory proteins. The overall conformational flexibility of the NCP pair suggests that chromatin tertiary structure is dynamic and allows access of various chromatin modifying machineries to nucleosomes.
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Affiliation(s)
- Silvija Bilokapic
- Department of Biochemistry, Gene Center, University of Munich LMU, 81377, Munich, Germany
| | - Mike Strauss
- Cryo-EM facility, Max Planck for Biochemistry, 82152, Martiensried, Germany
| | - Mario Halic
- Department of Biochemistry, Gene Center, University of Munich LMU, 81377, Munich, Germany.
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109
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Nucleosome-level 3D organization of the genome. Biochem Soc Trans 2018; 46:491-501. [PMID: 29626147 DOI: 10.1042/bst20170388] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/26/2018] [Accepted: 03/01/2018] [Indexed: 01/19/2023]
Abstract
Nucleosomes are the unitary structures of chromosome folding, and their arrangements are intimately coupled to the regulation of genome activities. Conventionally, structural analyses using electron microscopy and X-ray crystallography have been used to study such spatial nucleosome arrangements. In contrast, recent improvements in the resolution of sequencing-based methods allowed investigation of nucleosome arrangements separately at each genomic locus, enabling exploration of gene-dependent regulation mechanisms. Here, we review recent studies on nucleosome folding in chromosomes from these two methodological perspectives: conventional structural analyses and DNA sequencing, and discuss their implications for future research.
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110
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Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes. Biochem Biophys Res Commun 2018; 498:319-326. [DOI: 10.1016/j.bbrc.2017.09.086] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/06/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022]
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111
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Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. A pathway for mitotic chromosome formation. Science 2018; 359:eaao6135. [PMID: 29348367 PMCID: PMC5924687 DOI: 10.1126/science.aao6135] [Citation(s) in RCA: 433] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/09/2018] [Indexed: 12/23/2022]
Abstract
Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central "spiral staircase" condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of condensin I or II shows that nested loops form by differential action of the two condensins, whereas condensin II is required for helical winding.
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Affiliation(s)
- Johan H Gibcus
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Kumiko Samejima
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Anton Goloborodko
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Itaru Samejima
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Natalia Naumova
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Johannes Nuebler
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems, and Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Linfeng Xie
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA
| | - James R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 800 Algoma Boulevard, Oshkosh, WI 54901, USA
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
- Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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112
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Gligoris TG. Chromosome Biology: The Sight of DNA, at Last! Curr Biol 2018; 28:R77-R79. [PMID: 29374450 DOI: 10.1016/j.cub.2017.11.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Chromosomes are shaped by the combined function of the condensin and cohesin Smc-kleisin complexes. After more than two decades of research in this field, a new study finally sheds light on how these machines might interact with their DNA substrates.
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113
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Maeshima K, Matsuda T, Shindo Y, Imamura H, Tamura S, Imai R, Kawakami S, Nagashima R, Soga T, Noji H, Oka K, Nagai T. A Transient Rise in Free Mg 2+ Ions Released from ATP-Mg Hydrolysis Contributes to Mitotic Chromosome Condensation. Curr Biol 2018; 28:444-451.e6. [PMID: 29358072 DOI: 10.1016/j.cub.2017.12.035] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/12/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023]
Abstract
For cell division, negatively charged chromatin, in which nucleosome fibers (10 nm fibers) are irregularly folded [1-5], must be condensed into chromosomes and segregated. While condensin and other proteins are critical for organizing chromatin into the appropriate chromosome shape [6-17], free divalent cations such as Mg2+ and Ca2+, which condense chromatin or chromosomes in vitro [18-28], have long been considered important, especially for local condensation, because the nucleosome fiber has a net negative charge and is by itself stretched like "beads on a string" by electrostatic repulsion. For further folding, other positively charged factors are required to decrease the charge and repulsion [29]. However, technical limitations to measure intracellular free divalent cations, but not total cations [30], especially Mg2+, have prevented us from elucidating their function. Here, we developed a Förster resonance energy transfer (FRET)-based Mg2+ indicator that monitors free Mg2+ dynamics throughout the cell cycle. By combining this indicator with Ca2+ [31] and adenosine triphosphate (ATP) [32] indicators, we demonstrate that the levels of free Mg2+, but not Ca2+, increase during mitosis. The Mg2+ increase is coupled with a decrease in ATP, which is normally bound to Mg2+ in the cell [33]. ATP inhibited Mg2+-dependent chromatin condensation in vitro. Chelating Mg2+ induced mitotic cell arrest and chromosome decondensation, while ATP reduction had the opposite effect. Our results suggest that ATP-bound Mg2+ is released by ATP hydrolysis and contributes to mitotic chromosome condensation with increased rigidity, suggesting a novel regulatory mechanism for higher-order chromatin organization by the intracellular Mg2+-ATP balance.
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Affiliation(s)
- Kazuhiro Maeshima
- Structural Biology Center, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
| | - Tomoki Matsuda
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Yutaka Shindo
- Department of Biosciences & Informatics, Keio University, Hiyoshi, Yokohama 223-8522, Japan
| | - Hiromi Imamura
- Department of Life Science, Kyoto University, Kyoto 606-8501, Japan
| | - Sachiko Tamura
- Structural Biology Center, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Ryosuke Imai
- Structural Biology Center, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Syoji Kawakami
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Ryosuke Nagashima
- Structural Biology Center, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8656, Japan
| | - Kotaro Oka
- Department of Biosciences & Informatics, Keio University, Hiyoshi, Yokohama 223-8522, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.
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114
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Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 2018; 357:357/6349/eaag0025. [PMID: 28751582 DOI: 10.1126/science.aag0025] [Citation(s) in RCA: 505] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 01/11/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022]
Abstract
The chromatin structure of DNA determines genome compaction and activity in the nucleus. On the basis of in vitro structures and electron microscopy (EM) studies, the hierarchical model is that 11-nanometer DNA-nucleosome polymers fold into 30- and subsequently into 120- and 300- to 700-nanometer fibers and mitotic chromosomes. To visualize chromatin in situ, we identified a fluorescent dye that stains DNA with an osmiophilic polymer and selectively enhances its contrast in EM. Using ChromEMT (ChromEM tomography), we reveal the ultrastructure and three-dimensional (3D) organization of individual chromatin polymers, megabase domains, and mitotic chromosomes. We show that chromatin is a disordered 5- to 24-nanometer-diameter curvilinear chain that is packed together at different 3D concentration distributions in interphase and mitosis. Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.
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Affiliation(s)
- Horng D Ou
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andrea Thor
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.,Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Clodagh C O'Shea
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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115
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The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans 2017; 46:67-76. [PMID: 29263138 PMCID: PMC5818668 DOI: 10.1042/bst20170101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023]
Abstract
A chromosome is a single long DNA molecule assembled along its length with nucleosomes and proteins. During interphase, a mammalian chromosome exists as a highly organized supramolecular globule in the nucleus. Here, we discuss new insights into how genomic DNA is packaged and organized within interphase chromosomes. Our emphasis is on the structural principles that underlie chromosome organization, with a particular focus on the intrinsic contributions of the 10-nm chromatin fiber, but not the regular 30-nm fiber. We hypothesize that the hierarchical globular organization of an interphase chromosome is fundamentally established by the self-interacting properties of a 10-nm zig-zag array of nucleosomes, while histone post-translational modifications, histone variants, and chromatin-associated proteins serve to mold generic chromatin domains into specific structural and functional entities.
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116
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Chen P, Li G. Structure and Epigenetic Regulation of Chromatin Fibers. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:25-35. [PMID: 29167282 DOI: 10.1101/sqb.2017.82.033795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In eukaryotes, genomic DNA is hierarchically packaged by histones into chromatin on several levels to fit inside the nucleus. As a central-level structure between nucleosomal arrays and higher-order chromatin organizations, the 30-nm chromatin fiber and its dynamics play a crucial role in gene regulation. However, despite considerable efforts over the past three decades, the fundamental structure and its dynamic regulation of chromatin fibers still remain as a big challenge in molecular biology. Here, we mainly summarize the most recent progress in elucidating the structure of the 30-nm chromatin fiber in vitro and epigenetic regulation of chromatin fibers by chromatin factors, particularly histone variants. In addition, we also discuss recent studies in unraveling the three-dimensional organization of chromatin fibers in situ by genomic approaches and electron microscopy.
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Affiliation(s)
- Ping Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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117
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Le Gros MA, Clowney EJ, Magklara A, Yen A, Markenscoff-Papadimitriou E, Colquitt B, Myllys M, Kellis M, Lomvardas S, Larabell CA. Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. Cell Rep 2017; 17:2125-2136. [PMID: 27851973 DOI: 10.1016/j.celrep.2016.10.060] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 08/28/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
The realization that nuclear distribution of DNA, RNA, and proteins differs between cell types and developmental stages suggests that nuclear organization serves regulatory functions. Understanding the logic of nuclear architecture and how it contributes to differentiation and cell fate commitment remains challenging. Here, we use soft X-ray tomography (SXT) to image chromatin organization, distribution, and biophysical properties during neurogenesis in vivo. Our analyses reveal that chromatin with similar biophysical properties forms an elaborate connected network throughout the entire nucleus. Although this interconnectivity is present in every developmental stage, differentiation proceeds with concomitant increase in chromatin compaction and re-distribution of condensed chromatin toward the nuclear core. HP1β, but not nucleosome spacing or phasing, regulates chromatin rearrangements because it governs both the compaction of chromatin and its interactions with the nuclear envelope. Our experiments introduce SXT as a powerful imaging technology for nuclear architecture.
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Affiliation(s)
- Mark A Le Gros
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; National Center for X-Ray Tomography, University of California San Francisco, San Francisco, CA 94158, USA; Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - E Josephine Clowney
- Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Angeliki Magklara
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Ioannina, Greece
| | - Angela Yen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | | | - Bradley Colquitt
- Program in Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Markko Myllys
- Department of Physics, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Stavros Lomvardas
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Program in Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; National Center for X-Ray Tomography, University of California San Francisco, San Francisco, CA 94158, USA.
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118
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Affiliation(s)
- Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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119
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Kuznetsova MA, Chaban IA, Sheval EV. Visualization of chromosome condensation in plants with large chromosomes. BMC PLANT BIOLOGY 2017; 17:153. [PMID: 28899358 PMCID: PMC5596468 DOI: 10.1186/s12870-017-1102-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/07/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Most data concerning chromosome organization have been acquired from studies of a small number of model organisms, the majority of which are mammals. In plants with large genomes, the chromosomes are significantly larger than the animal chromosomes that have been studied to date, and it is possible that chromosome condensation in such plants was modified during evolution. Here, we analyzed chromosome condensation and decondensation processes in order to find structural mechanisms that allowed for an increase in chromosome size. RESULTS We found that anaphase and telophase chromosomes of plants with large chromosomes (average 2C DNA content exceeded 0.8 pg per chromosome) contained chromatin-free cavities in their axial regions in contrast to well-characterized animal chromosomes, which have high chromatin density in the axial regions. Similar to animal chromosomes, two intermediates of chromatin folding were visible inside condensing (during prophase) and decondensing (during telophase) chromosomes of Nigella damascena: approximately 150 nm chromonemata and approximately 300 nm fibers. The spatial folding of the latter fibers occurs in a fundamentally different way than in animal chromosomes, which leads to the formation of chromosomes with axial chromatin-free cavities. CONCLUSION Different compaction topology, but not the number of compaction levels, allowed for the evolution of increased chromosome size in plants.
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Affiliation(s)
- Maria A Kuznetsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Inna A Chaban
- All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskaja 42, 127550, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
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120
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Ekundayo B, Richmond TJ, Schalch T. Capturing Structural Heterogeneity in Chromatin Fibers. J Mol Biol 2017; 429:3031-3042. [PMID: 28893533 DOI: 10.1016/j.jmb.2017.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/01/2017] [Accepted: 09/03/2017] [Indexed: 10/18/2022]
Abstract
Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context.
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Affiliation(s)
- Babatunde Ekundayo
- Department of Molecular Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Timothy J Richmond
- Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Thomas Schalch
- Department of Molecular Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland; Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, CH-1211 Geneva 4, Switzerland.
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121
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Abstract
Genome architecture is revealed with electron tomography
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Affiliation(s)
- Daniel R Larson
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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122
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Chen B, Yusuf M, Hashimoto T, Estandarte AK, Thompson G, Robinson I. Three-dimensional positioning and structure of chromosomes in a human prophase nucleus. SCIENCE ADVANCES 2017; 3:e1602231. [PMID: 28776025 PMCID: PMC5521992 DOI: 10.1126/sciadv.1602231] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
The human genetic material is packaged into 46 chromosomes. The structure of chromosomes is known at the lowest level, where the DNA chain is wrapped around a core of eight histone proteins to form nucleosomes. Around a million of these nucleosomes, each about 11 nm in diameter and 6 nm in thickness, are wrapped up into the complex organelle of the chromosome, whose structure is mostly known at the level of visible light microscopy to form a characteristic cross shape in metaphase. However, the higher-order structure of human chromosomes, between a few tens and hundreds of nanometers, has not been well understood. We show a three-dimensional (3D) image of a human prophase nucleus obtained by serial block-face scanning electron microscopy, with 36 of the complete set of 46 chromosomes captured within it. The acquired image allows us to extract quantitative 3D structural information about the nucleus and the preserved, intact individual chromosomes within it, including their positioning and full spatial morphology at a resolution of around 50 nm in three dimensions. The chromosome positions were found, at least partially, to follow the pattern of chromosome territories previously observed only in interphase. The 3D conformation shows parallel, planar alignment of the chromatids, whose occupied volumes are almost fully accounted for by the DNA and known chromosomal proteins. We also propose a potential new method of identifying human chromosomes in three dimensions, on the basis of the measurements of their 3D morphology.
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Affiliation(s)
- Bo Chen
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Research Complex at Harwell, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Research Complex at Harwell, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
| | - Teruo Hashimoto
- School of Materials, The University of Manchester, Manchester M13 9PL, UK
| | - Ana Katrina Estandarte
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Research Complex at Harwell, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
| | - George Thompson
- School of Materials, The University of Manchester, Manchester M13 9PL, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Research Complex at Harwell, Harwell Oxford, Didcot, Oxfordshire OX11 0FA, UK
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
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123
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Spichal M, Fabre E. The Emerging Role of the Cytoskeleton in Chromosome Dynamics. Front Genet 2017; 8:60. [PMID: 28580009 PMCID: PMC5437106 DOI: 10.3389/fgene.2017.00060] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/28/2017] [Indexed: 01/15/2023] Open
Abstract
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus. Monomers of these cytoplasmic polymers and related proteins can also enter the nucleus and play different roles in the interior of the nucleus than they do in the cytoplasm. Nuclear cytoskeletal proteins can act as chromatin remodelers alone or in complexes with other nuclear proteins. They can also act as transcription factors. Many of these mechanisms have been conserved during evolution, indicating that the cytoskeletal regulation of chromosome dynamics is an essential process. In this review, we discuss the different influences of cytoskeletal proteins on chromosome dynamics by focusing on the well-studied model organism budding yeast.
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Affiliation(s)
- Maya Spichal
- Department of Genetics, University of North Carolina, Chapel HillNC, United States
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, CNRS UMR 7212, INSERM U944, Hôpital St. Louis 1Paris, France
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124
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Shimamoto Y, Tamura S, Masumoto H, Maeshima K. Nucleosome-nucleosome interactions via histone tails and linker DNA regulate nuclear rigidity. Mol Biol Cell 2017; 28:1580-1589. [PMID: 28428255 PMCID: PMC5449155 DOI: 10.1091/mbc.e16-11-0783] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/15/2017] [Accepted: 04/05/2017] [Indexed: 12/15/2022] Open
Abstract
A force-calibrated microneedle setup and controlled biochemical perturbation reveal that chromatin acts as a spring-like mechanical module that controls the rigidity of cell nuclei. The underlying molecular mechanism involves linker DNA and internucleosomal interaction via histone tails. Cells, as well as the nuclei inside them, experience significant mechanical stress in diverse biological processes, including contraction, migration, and adhesion. The structural stability of nuclei must therefore be maintained in order to protect genome integrity. Despite extensive knowledge on nuclear architecture and components, however, the underlying physical and molecular mechanisms remain largely unknown. We address this by subjecting isolated human cell nuclei to microneedle-based quantitative micromanipulation with a series of biochemical perturbations of the chromatin. We find that the mechanical rigidity of nuclei depends on the continuity of the nucleosomal fiber and interactions between nucleosomes. Disrupting these chromatin features by varying cation concentration, acetylating histone tails, or digesting linker DNA results in loss of nuclear rigidity. In contrast, the levels of key chromatin assembly factors, including cohesin, condensin II, and CTCF, and a major nuclear envelope protein, lamin, are unaffected. Together with in situ evidence using living cells and a simple mechanical model, our findings reveal a chromatin-based regulation of the nuclear mechanical response and provide insight into the significance of local and global chromatin structures, such as those associated with interdigitated or melted nucleosomal fibers.
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Affiliation(s)
- Yuta Shimamoto
- Quantitative Mechanobiology Laboratory, Center for Frontier Research, National Institute of Genetics, Mishima 411-8540, Japan .,Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima 411-8540, Japan.,PRIME, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
| | - Sachiko Tamura
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics, Mishima 411-8540, Japan
| | - Hiroshi Masumoto
- Biomedical Research Support Center, Nagasaki University School of Medicine; Nagasaki 852-8523, Japan
| | - Kazuhiro Maeshima
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima 411-8540, Japan .,PRIME, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
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125
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Singh AK, Rastogi S, Shukla H, Asalam M, Rath SK, Akhtar MS. Cdc15 Phosphorylates the C-terminal Domain of RNA Polymerase II for Transcription during Mitosis. J Biol Chem 2017; 292:5507-5518. [PMID: 28202544 DOI: 10.1074/jbc.m116.761056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/12/2017] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, the basal transcription in interphase is orchestrated through the regulation by kinases (Kin28, Bur1, and Ctk1) and phosphatases (Ssu72, Rtr1, and Fcp1), which act through the post-translational modification of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. The CTD comprises the repeated Tyr-Ser-Pro-Thr-Ser-Pro-Ser motif with potential epigenetic modification sites. Despite the observation of transcription and periodic expression of genes during mitosis with entailing CTD phosphorylation and dephosphorylation, the associated CTD specific kinase(s) and its role in transcription remains unknown. Here we have identified Cdc15 as a potential kinase phosphorylating Ser-2 and Ser-5 of CTD for transcription during mitosis in the budding yeast. The phosphorylation of CTD by Cdc15 is independent of any prior Ser phosphorylation(s). The inactivation of Cdc15 causes reduction of global CTD phosphorylation during mitosis and affects the expression of genes whose transcript levels peak during mitosis. Cdc15 also influences the complete transcription of clb2 gene and phosphorylates Ser-5 at the promoter and Ser-2 toward the 3' end of the gene. The observation that Cdc15 could phosphorylate Ser-5, as well as Ser-2, during transcription in mitosis is in contrast to the phosphorylation marks put by the kinases in interphase (G1, S, and G2), where Cdck7/Kin28 phosphorylates Ser-5 at promoter and Bur1/Ctk1 phosphorylates Ser-2 at the 3' end of the genes.
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Affiliation(s)
| | | | | | - Mohd Asalam
- From the Molecular and Structural Biology Division
| | - Srikanta Kumar Rath
- the Toxicology Division, Council of Scientific and Industrial Research (CSIR)-Central Drug Research Institute, Lucknow PIN 226 031, India and.,the Academy of Scientific and Innovative Research, New Delhi 110025, India
| | - Md Sohail Akhtar
- From the Molecular and Structural Biology Division, .,the Academy of Scientific and Innovative Research, New Delhi 110025, India
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126
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Krzemien KM, Beckers M, Quack S, Michaelis J. Atomic force microscopy of chromatin arrays reveal non-monotonic salt dependence of array compaction in solution. PLoS One 2017; 12:e0173459. [PMID: 28296908 PMCID: PMC5351988 DOI: 10.1371/journal.pone.0173459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/22/2017] [Indexed: 12/03/2022] Open
Abstract
Compaction of DNA in chromatin is a hallmark of the eukaryotic cell and unravelling its structure is required for an understanding of DNA involving processes. Despite strong experimental efforts, many questions concerning the DNA packing are open. In particular, it is heavily debated whether an ordered structure referred to as the “30 nm fibre” exist in vivo. Scanning probe microscopy has become a cutting edge technology for the high-resolution imaging of DNA- protein complexes. Here, we perform high-resolution atomic force microscopy of non-cross-linked chromatin arrays in liquid, under different salt conditions. A statistical analysis of the data reveals that array compaction is salt dependent in a non-monotonic fashion. A simple physical model can qualitatively explain the observed findings due to the opposing effects of salt dependent stiffening of DNA, nucleosome stability and histone-histone interactions. While for different salt concentrations different compaction states are observed, our data do not provide support for the existence of regular chromatin fibres. Our studies add new insights into chromatin structure, and with that contribute to a further understanding of the DNA condensation.
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Affiliation(s)
| | | | - Salina Quack
- Institute of Biophysics, Ulm University, Ulm, Germany
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Ulm, Germany
- * E-mail:
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127
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Kinoshita K, Hirano T. Dynamic organization of mitotic chromosomes. Curr Opin Cell Biol 2017; 46:46-53. [PMID: 28214612 DOI: 10.1016/j.ceb.2017.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/30/2017] [Indexed: 12/19/2022]
Abstract
The assembly of rod-shaped chromosomes during mitosis is an essential prerequisite for faithful segregation of genetic information into daughter cells. Despite the long history of chromosome research, it is only recently that we have acquired powerful approaches and crucial tools that help to unlock the secret of this seemingly complex process. In particular, in vitro assays, mammalian genetics, Hi-C analyses and computer simulations have provided valuable information during the past two years. These studies are now beginning to elucidate how the core components of mitotic chromosomes, namely, histones, topoisomerase IIα and condensins, cooperate with each other to convert very long stretches of DNA into rod-shaped chromosomes.
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Affiliation(s)
- Kazuhisa Kinoshita
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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128
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Condensin, master organizer of the genome. Chromosome Res 2017; 25:61-76. [PMID: 28181049 DOI: 10.1007/s10577-017-9553-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/19/2016] [Accepted: 01/23/2017] [Indexed: 02/06/2023]
Abstract
A fundamental requirement in nature is for a cell to correctly package and divide its replicated genome. Condensin is a mechanical multisubunit complex critical to this process. Condensin uses ATP to power conformational changes in DNA to enable to correct DNA compaction, organization, and segregation of DNA from the simplest bacteria to humans. The highly conserved nature of the condensin complex and the structural similarities it shares with the related cohesin complex have provided important clues as to how it functions in cells. The fundamental requirement for condensin in mitosis and meiosis is well established, yet the precise mechanism of action is still an open question. Mutation or removal of condensin subunits across a range of species disrupts orderly chromosome condensation leading to errors in chromosome segregation and likely death of the cell. There are divergences in function across species for condensin. Once considered to function solely in mitosis and meiosis, an accumulating body of evidence suggests that condensin has key roles in also regulating the interphase genome. This review will examine how condensin organizes our genomes, explain where and how it binds the genome at a mechanical level, and highlight controversies and future directions as the complex continues to fascinate and baffle biologists.
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129
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Bascom G, Schlick T. Linking Chromatin Fibers to Gene Folding by Hierarchical Looping. Biophys J 2017; 112:434-445. [PMID: 28153411 DOI: 10.1016/j.bpj.2017.01.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/16/2022] Open
Abstract
While much is known about DNA structure on the basepair level, this scale represents only a fraction of the structural levels involved in folding the genomic material. With recent advances in experimental and theoretical techniques, a variety of structures have been observed on the fiber, gene, and chromosome levels of genome organization. Here we view chromatin architecture from nucleosomes and fibers to genes and chromosomes, highlighting the rich structural diversity and fiber fluidity emerging from both experimental and theoretical techniques. In this context, we discuss our recently proposed folding mechanism, which we call "hierarchical looping", similar to rope flaking used in mountain climbing, where 10-nm zigzag chromatin fibers are compacted laterally into self-associating loops which then stack and fold in space. We propose that hierarchical looping may act as a bridge between fibers and genes as well as provide a mechanism to relate key features of interphase and metaphase chromosome architecture to genome structural changes. This motif emerged by analysis of ultrastructural internucleosome contact data by electron microscopy-assisted nucleosome interaction capture cross-linking experiments, in combination with mesoscale modeling. We suggest that while the local folding of chromatin can be regulated at the fiber level by adjustment of internal factors such as linker-histone binding affinities, linker DNA lengths, and divalent ion levels, hierarchical looping on the gene level can additionally be controlled by posttranslational modifications and external factors such as polycomb group proteins. From a combination of 3C data and mesoscale modeling, we suggest that hierarchical looping could also play a role in epigenetic gene silencing, as stacked loops may occlude access to transcription start sites. With advances in crystallography, single-molecule in vitro biochemistry, in vivo imaging techniques, and genome-wide contact data experiments, various modeling approaches are allowing for previously unavailable structural interpretation of these data at multiple spatial and temporal scales. An unprecedented level of productivity and opportunity is on the horizon for the chromatin structure field.
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Affiliation(s)
- Gavin Bascom
- Department of Chemistry, New York University, New York, New York
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York; Courant Institute of Mathematical Sciences, New York University, New York, New York; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China.
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130
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Bajpai G, Jain I, Inamdar MM, Das D, Padinhateeri R. Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure. PLoS Comput Biol 2017; 13:e1005365. [PMID: 28135276 PMCID: PMC5305278 DOI: 10.1371/journal.pcbi.1005365] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/13/2017] [Accepted: 01/14/2017] [Indexed: 11/18/2022] Open
Abstract
Why most of the in vivo experiments do not find the 30-nm chromatin fiber, well studied in vitro, is a puzzle. Two basic physical inputs that are crucial for understanding the structure of the 30-nm fiber are the stiffness of the linker DNA and the relative orientations of the DNA entering/exiting nucleosomes. Based on these inputs we simulate chromatin structure and show that the presence of non-histone proteins, which bind and locally bend linker DNA, destroys any regular higher order structures (e.g., zig-zag). Accounting for the bending geometry of proteins like nhp6 and HMG-B, our theory predicts phase-diagram for the chromatin structure as a function of DNA-bending non-histone protein density and mean linker DNA length. For a wide range of linker lengths, we show that as we vary one parameter, that is, the fraction of bent linker region due to non-histone proteins, the steady-state structure will show a transition from zig-zag to an irregular structure-a structure that is reminiscent of what is observed in experiments recently. Our theory can explain the recent in vivo observation of irregular chromatin having co-existence of finite fraction of the next-neighbor (i + 2) and neighbor (i + 1) nucleosome interactions.
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Affiliation(s)
- Gaurav Bajpai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ishutesh Jain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mandar M. Inamdar
- Department of Civil Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail:
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131
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Abstract
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus. Monomers of these cytoplasmic polymers and related proteins can also enter the nucleus and play different roles in the interior of the nucleus than they do in the cytoplasm. Nuclear cytoskeletal proteins can act as chromatin remodelers alone or in complexes with other nuclear proteins. They can also act as transcription factors. Many of these mechanisms have been conserved during evolution, indicating that the cytoskeletal regulation of chromosome dynamics is an essential process. In this review, we discuss the different influences of cytoskeletal proteins on chromosome dynamics by focusing on the well-studied model organism budding yeast.
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Affiliation(s)
- Maya Spichal
- Department of Genetics, University of North Carolina, Chapel HillNC, United States
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, CNRS UMR 7212, INSERM U944, Hôpital St. Louis 1Paris, France
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132
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Hémonnot CYJ, Ranke C, Saldanha O, Graceffa R, Hagemann J, Köster S. Following DNA Compaction During the Cell Cycle by X-ray Nanodiffraction. ACS NANO 2016; 10:10661-10670. [PMID: 28024349 DOI: 10.1021/acsnano.6b05034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
X-ray imaging of intact biological cells is emerging as a complementary method to visible light or electron microscopy. Owing to the high penetration depth and small wavelength of X-rays, it is possible to resolve subcellular structures at a resolution of a few nanometers. Here, we apply scanning X-ray nanodiffraction in combination with time-lapse bright-field microscopy to nuclei of 3T3 fibroblasts and thus relate the observed structures to specific phases in the cell division cycle. We scan the sample at a step size of 250 nm and analyze the individual diffraction patterns according to a generalized Porod's law. Thus, we obtain information on the aggregation state of the nuclear DNA at a real space resolution on the order of the step size and in parallel structural information on the order of few nanometers. We are able to distinguish nucleoli, heterochromatin, and euchromatin in the nuclei and follow the compaction and decompaction during the cell division cycle.
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Affiliation(s)
- Clément Y J Hémonnot
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Christiane Ranke
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Oliva Saldanha
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Rita Graceffa
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Johannes Hagemann
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Sarah Köster
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
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133
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Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. Nature 2016; 541:237-241. [PMID: 28024297 DOI: 10.1038/nature20781] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/10/2016] [Indexed: 12/29/2022]
Abstract
Chromatin structure at the length scale encompassing local nucleosome-nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA. However, this secondary structure of chromatin remains poorly understood compared with the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions. Here we report the first genome-wide map of chromatin conformation in human cells at the 1-3 nucleosome (50-500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq) to identify DNA-DNA contacts that are spatially proximal. Unbiased analysis of RICC-seq signal reveals regional enrichment of DNA fragments characteristic of alternating rather than adjacent nucleosome interactions in tri-nucleosome units, particularly in H3K9me3-marked heterochromatin. We infer differences in the likelihood of nucleosome-nucleosome contacts among open chromatin, H3K27me3-marked, and H3K9me3-marked repressed chromatin regions. After calibrating RICC-seq signal to three-dimensional distances, we show that compact two-start helical fibre structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked chromatin, while non-compact structures and solenoid structures are consistent with open chromatin. Our data support a model of chromatin architecture in intact interphase nuclei consistent with variable longitudinal compaction of two-start helical fibres.
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134
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Izadi S, Anandakrishnan R, Onufriev AV. Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber. J Chem Theory Comput 2016; 12:5946-5959. [PMID: 27748599 PMCID: PMC5649046 DOI: 10.1021/acs.jctc.6b00712] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular dynamics (MD) simulations based on the implicit solvent generalized Born (GB) models can provide significant computational advantages over the traditional explicit solvent simulations. However, the standard GB becomes prohibitively expensive for all-atom simulations of large structures; the model scales poorly, ∼n2, with the number of solute atoms. Here we combine our recently developed optimal point charge approximation (OPCA) with the hierarchical charge partitioning (HCP) approximation to present an ∼n log n multiscale, yet fully atomistic, GB model (GB-HCPO). The HCP approximation exploits the natural organization of biomolecules (atoms, groups, chains, and complexes) to partition the structure into multiple hierarchical levels of components. OPCA approximates the charge distribution for each of these components by a small number of point charges so that the low order multipole moments of these components are optimally reproduced. The approximate charges are then used for computing electrostatic interactions with distant components, while the full set of atomic charges are used for nearby components. We show that GB-HCPO can deliver up to 2 orders of magnitude speedup compared to the standard GB, with minimal impact on its accuracy. For large structures, GB-HCPO can approach the same nominal speed, as in nanoseconds per day, as the highly optimized explicit-solvent simulation based on particle mesh Ewald (PME). The increase in the nominal simulation speed, relative to the standard GB, coupled with substantially faster sampling of conformational space, relative to the explicit solvent, makes GB-HCPO a suitable candidate for MD simulation of large atomistic systems in implicit solvent. As a practical demonstration, we use GB-HCPO simulation to refine a ∼1.16 million atom structure of 30 nm chromatin fiber (40 nucleosomes). The refined structure suggests important details about spatial organization of the linker DNA and the histone tails in the fiber: (1) the linker DNA fills the core region, allowing the H3 histone tails to interact with the linker DNA, which is consistent with experiment; (2) H3 and H4 tails are found mostly in the core of the structure, closer to the helical axis of the fiber, while H2A and H2B are mostly solvent exposed. Potential functional consequences of these findings are discussed. GB-HCPO is implemented in the open source MD software NAB in Amber 2016.
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Affiliation(s)
- Saeed Izadi
- Department of Biomedical Engineering and Mechanics, ‡Biomedical Division, Edward Via College of Osteopathic Medicine, ¶Department of Computer Science and Physics, and §Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University , Blacksburg, Virginia 24061, United States
| | - Ramu Anandakrishnan
- Department of Biomedical Engineering and Mechanics, ‡Biomedical Division, Edward Via College of Osteopathic Medicine, ¶Department of Computer Science and Physics, and §Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University , Blacksburg, Virginia 24061, United States
| | - Alexey V Onufriev
- Department of Biomedical Engineering and Mechanics, ‡Biomedical Division, Edward Via College of Osteopathic Medicine, ¶Department of Computer Science and Physics, and §Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University , Blacksburg, Virginia 24061, United States
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135
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Abstract
Eukaryotic genomes are packaged in chromatin. The higher-order organization of nucleosome core particles is controlled by the association of the intervening linker DNA with either the linker histone H1 or high mobility group box (HMGB) proteins. While H1 is thought to stabilize the nucleosome by preventing DNA unwrapping, the DNA bending imposed by HMGB may propagate to the nucleosome to destabilize chromatin. For metazoan H1, chromatin compaction requires its lysine-rich C-terminal domain, a domain that is buried between globular domains in the previously characterized yeast Saccharomyces cerevisiae linker histone Hho1p. Here, we discuss the functions of S. cerevisiae HMO1, an HMGB family protein unique in containing a terminal lysine-rich domain and in stabilizing genomic DNA. On ribosomal DNA (rDNA) and genes encoding ribosomal proteins, HMO1 appears to exert its role primarily by stabilizing nucleosome-free regions or "fragile" nucleosomes. During replication, HMO1 likewise appears to ensure low nucleosome density at DNA junctions associated with the DNA damage response or the need for topoisomerases to resolve catenanes. Notably, HMO1 shares with the mammalian linker histone H1 the ability to stabilize chromatin, as evidenced by the absence of HMO1 creating a more dynamic chromatin environment that is more sensitive to nuclease digestion and in which chromatin-remodeling events associated with DNA double-strand break repair occur faster; such chromatin stabilization requires the lysine-rich extension of HMO1. Thus, HMO1 appears to have evolved a unique linker histone-like function involving the ability to stabilize both conventional nucleosome arrays as well as DNA regions characterized by low nucleosome density or the presence of noncanonical nucleosomes.
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136
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Ubiquitin utilizes an acidic surface patch to alter chromatin structure. Nat Chem Biol 2016; 13:105-110. [PMID: 27870837 PMCID: PMC5161692 DOI: 10.1038/nchembio.2235] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/07/2016] [Indexed: 02/06/2023]
Abstract
Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with nuclear magnetic resonance spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic “wedge” that prevents the intimate association of neighboring nucleosomes. Using two independent cross-linking strategies and an oligomerization assay, we also showed that ubiquitin-ubiquitin contacts occur in the chromatin environment and are important for the solubilization of the chromatin polymers. Our work highlights a novel, chromatin-related aspect of the “ubiquitin code”, and sheds light on how the information rich ubiquitin modification can orchestrate different biochemical outcomes using different surface features.
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137
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Booth DG, Beckett AJ, Molina O, Samejima I, Masumoto H, Kouprina N, Larionov V, Prior IA, Earnshaw WC. 3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin. Mol Cell 2016; 64:790-802. [PMID: 27840028 PMCID: PMC5128728 DOI: 10.1016/j.molcel.2016.10.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/24/2016] [Accepted: 10/05/2016] [Indexed: 11/20/2022]
Abstract
Recent studies have revealed the importance of Ki-67 and the chromosome periphery in chromosome structure and segregation, but little is known about this elusive chromosome compartment. Here we used correlative light and serial block-face scanning electron microscopy, which we term 3D-CLEM, to model the entire mitotic chromosome complement at ultra-structural resolution. Prophase chromosomes exhibit a highly irregular surface appearance with a volume smaller than metaphase chromosomes. This may be because of the absence of the periphery, which associates with chromosomes only after nucleolar disassembly later in prophase. Indeed, the nucleolar volume almost entirely accounts for the extra volume found in metaphase chromosomes. Analysis of wild-type and Ki-67-depleted chromosomes reveals that the periphery comprises 30%–47% of the entire chromosome volume and more than 33% of the protein mass of isolated mitotic chromosomes determined by quantitative proteomics. Thus, chromatin makes up a surprisingly small percentage of the total mass of metaphase chromosomes. 3D-CLEM combines light and serial block-face scanning electron microscopy The complete architecture of all 46 human chromosomes has been defined A large portion of mitotic chromosomes is not composed of chromatin Chromosome volumes determined by light and electron microscopy differ dramatically
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Affiliation(s)
- Daniel G Booth
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK.
| | - Alison J Beckett
- Biomedical Electron Microscopy Unit, Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, L69 3BX Liverpool, UK
| | - Oscar Molina
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
| | - Itaru Samejima
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
| | - Hiroshi Masumoto
- Department of Frontier Research, Laboratory of Cell Engineering, Kazusa DNA Research Institute, Kisarazu, 292-0818 Chiba, Japan
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4264, USA
| | - Ian A Prior
- Biomedical Electron Microscopy Unit, Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, L69 3BX Liverpool, UK
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK.
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138
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Muskhelishvili G, Travers A. The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity. Biophys Rev 2016; 8:5-22. [PMID: 28510220 PMCID: PMC5425797 DOI: 10.1007/s12551-016-0237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023] Open
Abstract
We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.
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Affiliation(s)
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
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139
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Yi J, Stypula-Cyrus Y, Blaha CS, Roy HK, Backman V. Fractal Characterization of Chromatin Decompaction in Live Cells. Biophys J 2016; 109:2218-26. [PMID: 26636933 DOI: 10.1016/j.bpj.2015.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/15/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022] Open
Abstract
Chromatin organization has a fundamental impact on the whole spectrum of genomic functions. Quantitative characterization of the chromatin structure, particularly at submicron length scales where chromatin fractal globules are formed, is critical to understanding this structure-function relationship. Such analysis is currently challenging due to the diffraction-limited resolution of conventional light microscopy. We herein present an optical approach termed inverse spectroscopic optical coherence tomography to characterize the mass density fractality of chromatin, and we apply the technique to observe chromatin decompaction in live cells. The technique makes it possible for the first time, to our knowledge, to sense intracellular morphology with length-scale sensitivity from ∼30 to 450 nm, thus primarily probing the higher-order chromatin structure, without resolving the actual structures. We used chromatin decompaction due to inhibition of histone deacytelases and measured the subsequent changes in the fractal dimension of the intracellular structure. The results were confirmed by transmission electron microscopy and confocal fluorescence microscopy.
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Affiliation(s)
- Ji Yi
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Boston Medical Center, Department of Medicine, Boston University, Boston, Massachusetts
| | | | - Catherine S Blaha
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois
| | - Hemant K Roy
- Boston Medical Center, Department of Medicine, Boston University, Boston, Massachusetts
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois.
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140
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Dickerson D, Gierliński M, Singh V, Kitamura E, Ball G, Tanaka TU, Owen-Hughes T. High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division. BMC Cell Biol 2016; 17:33. [PMID: 27609610 PMCID: PMC5016949 DOI: 10.1186/s12860-016-0111-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/25/2016] [Indexed: 01/23/2023] Open
Abstract
Background Genomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy. Results We established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs. Conclusions The directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0111-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Dickerson
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vijender Singh
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Etsushi Kitamura
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Graeme Ball
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. .,Wellcome Trust Building, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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141
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Chen C, Lim HH, Shi J, Tamura S, Maeshima K, Surana U, Gan L. Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo. Mol Biol Cell 2016; 27:3357-3368. [PMID: 27605704 PMCID: PMC5170867 DOI: 10.1091/mbc.e16-07-0506] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/01/2016] [Indexed: 11/11/2022] Open
Abstract
Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin-nucleosomes-are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an "open" configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome-nucleosome associations.
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Affiliation(s)
- Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Hong Hwa Lim
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Proteos, Singapore 138673, Singapore.,Bioprocessing Technology Institute, Singapore 138668, Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sachiko Tamura
- National Institute of Genetics and Sokendai, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- National Institute of Genetics and Sokendai, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Proteos, Singapore 138673, Singapore.,Bioprocessing Technology Institute, Singapore 138668, Singapore.,Department of Pharmacology, National University of Singapore, Singapore 117543, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
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142
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143
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Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome. Adv Colloid Interface Sci 2016; 232:36-48. [PMID: 26956528 DOI: 10.1016/j.cis.2016.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 11/23/2022]
Abstract
To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA-protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP-NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed.
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144
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Eslami-Mossallam B, Schiessel H, van Noort J. Nucleosome dynamics: Sequence matters. Adv Colloid Interface Sci 2016; 232:101-113. [PMID: 26896338 DOI: 10.1016/j.cis.2016.01.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 02/06/2023]
Abstract
About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly conserved in evolution, nucleosomes can be very different from each other due to posttranslational modifications of the histones. Another crucial factor in making nucleosomes unique has so far been underappreciated: the sequence of their DNA. This review provides an overview of the experimental and theoretical progress that increasingly points to the importance of the nucleosomal base pair sequence. Specifically, we discuss the role of the underlying base pair sequence in nucleosome positioning, sliding, breathing, force-induced unwrapping, dissociation and partial assembly and also how the sequence can influence higher-order structures. A new view emerges: the physical properties of nucleosomes, especially their dynamical properties, are determined to a large extent by the mechanical properties of their DNA, which in turn depends on DNA sequence.
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145
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Ghirlando R, Felsenfeld G. Chromatin structure outside and inside the nucleus. Biopolymers 2016; 99:225-32. [PMID: 23348669 DOI: 10.1002/bip.22157] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/07/2012] [Indexed: 11/09/2022]
Abstract
The structure of the 30-nm chromatin fiber has provided, over the years, an important reference in chromatin studies. Originally derived from electron microscopic studies of soluble chromatin fibers released by restriction digestion, the gross structural features of such fragments have been supported by biophysical methods such as low angle X-ray and neutron scattering, sedimentation, light scattering, and electric dichroism. Electron microscopy and sedimentation velocity measurements demonstrated that reconstituted chromatin fibers, prepared from repeating arrays of high affinity nucleosome positioning sequences, retain the same overall features as observed for native chromatin fibers. It had been suggested that the 30 nm fiber might be the form assumed in vivo by transcriptionally silent chromatin, but individual gene or genome-wide studies of chromatin released from nuclei do not reveal any such simple correlation. Furthermore, even though the 30 nm fiber has been thought to represent an intermediate in the hierarchical folding of DNA into chromosomes, most analyses of chromatin folding within the nucleus do not detect any regular extended compact structures. However, there are important exceptions in chicken erythroid cell nuclei as well as in transcribed regions that form extended loops. Localized domains within the nucleus, either at the surface of chromosome domains or constrained as a specialized kind of constitutive heterochromatin by specific DNA binding proteins, may adopt 30 nm fiber-like structures.
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Affiliation(s)
- Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0540
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146
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Abstract
SMC (structural maintenance of chromosomes) complexes - which include condensin, cohesin and the SMC5-SMC6 complex - are major components of chromosomes in all living organisms, from bacteria to humans. These ring-shaped protein machines, which are powered by ATP hydrolysis, topologically encircle DNA. With their ability to hold more than one strand of DNA together, SMC complexes control a plethora of chromosomal activities. Notable among these are chromosome condensation and sister chromatid cohesion. Moreover, SMC complexes have an important role in DNA repair. Recent mechanistic insight into the function and regulation of these universal chromosomal machines enables us to propose molecular models of chromosome structure, dynamics and function, illuminating one of the fundamental entities in biology.
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147
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Maeshima K, Rogge R, Tamura S, Joti Y, Hikima T, Szerlong H, Krause C, Herman J, Seidel E, DeLuca J, Ishikawa T, Hansen JC. Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers. EMBO J 2016; 35:1115-32. [PMID: 27072995 PMCID: PMC4868957 DOI: 10.15252/embj.201592660] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
Abstract
The existence of a 30‐nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg2+‐dependent self‐association of linear 12‐mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call “oligomers”, are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10‐nm fibers, rather than folded 30‐nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl2, but became disrupted in the absence of MgCl2, conditions that also dissociated the oligomers in vitro. These results indicate that a 10‐nm array of nucleosomes has the intrinsic ability to self‐assemble into large chromatin globules stabilized by nucleosome–nucleosome interactions, and suggest that the oligomers are a good in vitro model for investigating the structure and organization of interphase chromosomes.
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Affiliation(s)
- Kazuhiro Maeshima
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Japan
| | - Ryan Rogge
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Sachiko Tamura
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Japan XFEL Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Japan
| | | | - Heather Szerlong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Christine Krause
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jake Herman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Erik Seidel
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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148
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Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Curr Opin Struct Biol 2016; 37:29-45. [DOI: 10.1016/j.sbi.2015.11.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/05/2023]
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149
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Liquid-like behavior of chromatin. Curr Opin Genet Dev 2016; 37:36-45. [DOI: 10.1016/j.gde.2015.11.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022]
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150
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Friedman DA, Tait L, Vaughan ATM. Influence of nuclear structure on the formation of radiation-induced lethal lesions. Int J Radiat Biol 2016; 92:229-40. [DOI: 10.3109/09553002.2016.1144941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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