151
|
Wang W, Zhang K, Chen D. From Tunable DNA/Polymer Self-Assembly to Tailorable and Morphologically Pure Core-Shell Nanofibers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15350-15359. [PMID: 30427695 DOI: 10.1021/acs.langmuir.8b02992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In reported experimental studies, DNA/polymer self-assemblies are usually kinetically trapped, leading to the encapsulation and irregular collapse of DNA chains within the resultant assemblies. In striking contrast, eukaryotic cells use tetrasome-to-nucleosome pathways to escape possible kinetic trapping for the formation of well-defined 10 nm chromatin fibers. Here, we report a novel pathway for DNA and amphiphilic diblock copolymer self-assembly inspired by the tetrasome pathway with highly controllable kinetics. The polymer is an A- b-B diblock copolymer with a hydrophilic and noninteractive block A and a hydrophobic and interactive block B. Below the critical water content for the micellization, B blocks wrap the backbone of a DNA chain by weak electrostatic interactions to form a linear DNA/polymer complex. With a gradual increase in the water content, the diblock copolymer unimers in the bulk solution tend to aggregate on the linear DNA/polymer complex, which induces the originally wrapped DNA chain, to change its conformation to wrap around the polymer aggregate, guiding and tailoring the self-assembly. Highly controllable kinetics is achieved via the reduced DNA/polymer electrostatic interactions and the high dynamics of the polymer chains in the system. DNA/polymer self-assembly leads to tailorable and morphologically pure core-shell nanofibers. Compared to the DNA/micelle self-assembly pathway described in our previous study, the present self-assembly pathway exhibits advantages for the fabrication of flexible nanofibers with lengths in micrometers and the potential for unique applications in preparing not only 2D networks at extremely low percolation thresholds but also chemiresistors with large on/off current ratios.
Collapse
Affiliation(s)
- Weichong Wang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science , Fudan University , 2005 Songhu Road , Shanghai 200438 , P.R. China
| | - Kaka Zhang
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science , Fudan University , 2005 Songhu Road , Shanghai 200438 , P.R. China
| | - Daoyong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science , Fudan University , 2005 Songhu Road , Shanghai 200438 , P.R. China
| |
Collapse
|
152
|
Zhou K, Gaullier G, Luger K. Nucleosome structure and dynamics are coming of age. Nat Struct Mol Biol 2018; 26:3-13. [PMID: 30532059 DOI: 10.1038/s41594-018-0166-x] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Since the first high-resolution structure of the nucleosome was reported in 1997, the available information on chromatin structure has increased very rapidly. Here, we review insights derived from cutting-edge biophysical and structural approaches applied to the study of nucleosome dynamics and nucleosome-binding factors, with a focus on the experimental advances driving the research. In addition, we highlight emerging challenges in nucleosome structural biology.
Collapse
Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Guillaume Gaullier
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
| |
Collapse
|
153
|
Huang YC, Su CJ, Korolev N, Berezhnoy NV, Wang S, Soman A, Chen CY, Chen HL, Jeng US, Nordenskiöld L. The effect of linker DNA on the structure and interaction of nucleosome core particles. SOFT MATTER 2018; 14:9096-9106. [PMID: 30215440 DOI: 10.1039/c8sm00998h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In eukaryotes, the compaction of chromatin fibers composed of nucleosome core particles (NCPs) connected by a linker DNA into chromosomes is highly efficient; however, the underlying folding mechanisms remain elusive. We used small angle X-ray scattering (SAXS) to investigate the influence of linker DNA length on the local structure and the interparticle interactions of the NCPs. In the presence of the linker DNA of 30 bp or less in length, the results suggest partial unwrapping of nucleosomal DNA on the NCP irrespective of the linker DNA length. Moreover, the presence of 15 bp linker DNA alleviated the electrostatic repulsion between the NCPs and prevented the formation of an ordered columnar hexagonal phase, demonstrating that the linker DNA plays an active role in chromatin folding.
Collapse
Affiliation(s)
- Yen-Chih Huang
- Department of Chemical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsin-Chu 30013, Taiwan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
154
|
de Jong BE, Brouwer TB, Kaczmarczyk A, Visscher B, van Noort J. Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force. Biophys J 2018; 115:1848-1859. [PMID: 30366627 PMCID: PMC6303278 DOI: 10.1016/j.bpj.2018.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/21/2018] [Accepted: 10/05/2018] [Indexed: 12/30/2022] Open
Abstract
The organization of chromatin in 30 nm fibers remains a topic of debate. Here, we quantify the mechanical properties of the linker DNA and evaluate the impact of these properties on chromatin fiber folding. We extended a rigid basepair DNA model to include (un)wrapping of nucleosomal DNA and (un)stacking of nucleosomes in one-start and two-start chromatin fibers. Monte Carlo simulations that mimic single-molecule force spectroscopy experiments of folded nucleosomal arrays reveal different stages of unfolding as a function of force and are largely consistent with a two-start folding for 167 and one-start folding for 197 nucleosome repeat length fibers. The major insight is that nucleosome unstacking and subsequent unwrapping is not necessary to obtain quantitative agreement with experimental force extension curves up to the overstretching plateau of folded chromatin fibers at 3-5 pN. Nucleosome stacking appears better accommodated in one-start than in two-start conformations, and we suggest that this difference can compensate the increased energy for bending the linker DNA. Overall, these simulations capture the dynamic structure of chromatin fibers while maintaining realistic physical properties of the linker DNA.
Collapse
Affiliation(s)
- Babette E de Jong
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Thomas B Brouwer
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Bert Visscher
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
155
|
Stoddard CI, Feng S, Campbell MG, Liu W, Wang H, Zhong X, Bernatavichute Y, Cheng Y, Jacobsen SE, Narlikar GJ. A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase. Mol Cell 2018; 73:73-83.e6. [PMID: 30415948 DOI: 10.1016/j.molcel.2018.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/22/2018] [Accepted: 10/01/2018] [Indexed: 12/12/2022]
Abstract
DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is poorly understood. The maintenance DNA methyltransferase from Zea mays, ZMET2, recognizes dimethylation of H3K9 via a chromodomain (CD) and a bromo adjacent homology (BAH) domain, which flank the catalytic domain. Here, we show that dinucleosomes are the preferred ZMET2 substrate, with DNA methylation preferentially targeted to linker DNA. Electron microscopy shows one ZMET2 molecule bridging two nucleosomes within a dinucleosome. We find that the CD stabilizes binding, whereas the BAH domain enables allosteric activation by the H3K9me mark. ZMET2 further couples recognition of H3K9me to an increase in the specificity for hemimethylated versus unmethylated DNA. We propose a model in which synergistic coupling between recognition of nucleosome spacing, H3K9 methylation, and DNA modification allows ZMET2 to maintain DNA methylation in heterochromatin with high fidelity.
Collapse
Affiliation(s)
- Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Melody G Campbell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wanlu Liu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Haifeng Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Yana Bernatavichute
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
156
|
Garcia-Saez I, Menoni H, Boopathi R, Shukla MS, Soueidan L, Noirclerc-Savoye M, Le Roy A, Skoufias DA, Bednar J, Hamiche A, Angelov D, Petosa C, Dimitrov S. Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation. Mol Cell 2018; 72:902-915.e7. [PMID: 30392928 DOI: 10.1016/j.molcel.2018.09.027] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/27/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022]
Abstract
Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. The structure reveals a flat two-start helix with uniform nucleosomal stacking interfaces and a nucleosome packing density that is only half that of a twisted 30-nm fiber. Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. Biophysical, cryo-EM, and crosslinking data validate the crystal structure and reveal that a minor change in ionic environment shifts the conformational landscape to a more compact, twisted form. These findings provide insights into the structural plasticity of chromatin and suggest a possible assembly pathway for a 30-nm fiber.
Collapse
Affiliation(s)
- Isabel Garcia-Saez
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Hervé Menoni
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Ramachandran Boopathi
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Manu S Shukla
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Lama Soueidan
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | | | - Aline Le Roy
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Dimitrios A Skoufias
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Jan Bednar
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague 2, Czech Republic.
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS, INSERM, 67404 Illkirch Cedex, France.
| | - Dimitar Angelov
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007 Lyon, France.
| | - Carlo Petosa
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France.
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France; "Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| |
Collapse
|
157
|
Li Z, Kono H. Investigating the Influence of Arginine Dimethylation on Nucleosome Dynamics Using All-Atom Simulations and Kinetic Analysis. J Phys Chem B 2018; 122:9625-9634. [DOI: 10.1021/acs.jpcb.8b05067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zhenhai Li
- Molecular Modeling and Simulation (MMS) Group, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7, Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation (MMS) Group, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7, Umemidai, Kizugawa, Kyoto 619-0215, Japan
| |
Collapse
|
158
|
Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes. Chromosoma 2018; 128:7-13. [PMID: 30175387 PMCID: PMC6394650 DOI: 10.1007/s00412-018-0678-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022]
Abstract
The high-order structure of metaphase chromosomes remains still under investigation, especially the 30-nm structure that is still controversial. Advanced 3D imaging has provided useful information for our understanding of this detailed structure. It is evident that new technologies together with improved sample preparations and image analyses should be adequately combined. This mini review highlights 3D imaging used for chromosome analysis so far with future imaging directions also highlighted.
Collapse
|
159
|
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.
Collapse
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
| |
Collapse
|
160
|
Howell SC, Qiu X, Curtis JE. Monte Carlo simulation algorithm for B-DNA. J Comput Chem 2018; 37:2553-63. [PMID: 27671358 DOI: 10.1002/jcc.24474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/12/2016] [Accepted: 07/23/2016] [Indexed: 01/12/2023]
Abstract
Understanding the structure-function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small-angle X-ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all-atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub-ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B-DNA is represented using a wormlike bead-rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse-grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Steven C Howell
- Neutron Condensed Matter Science Group, NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-8562
| | - Xiangyun Qiu
- Department of Physics, The George Washington University, Washington, District of Columbia, 20052
| | - Joseph E Curtis
- Neutron Condensed Matter Science Group, NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-8562.
| |
Collapse
|
161
|
Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| |
Collapse
|
162
|
Shi X, Prasanna C, Nagashima T, Yamazaki T, Pervushin K, Nordenskiöld L. Structure and Dynamics in the Nucleosome Revealed by Solid-State NMR. Angew Chem Int Ed Engl 2018; 57:9734-9738. [DOI: 10.1002/anie.201804707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Xiangyan Shi
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Toshio Nagashima
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Toshio Yamazaki
- RIKEN Center for Life Science Technologies; Yokohama City Kanagawa 230-0045 Japan
| | - Konstantin Pervushin
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
| |
Collapse
|
163
|
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.
Collapse
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
| |
Collapse
|
164
|
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.
Collapse
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.
| |
Collapse
|
165
|
Banerjee DR, Deckard CE, Elinski MB, Buzbee ML, Wang WW, Batteas JD, Sczepanski JT. Plug-and-Play Approach for Preparing Chromatin Containing Site-Specific DNA Modifications: The Influence of Chromatin Structure on Base Excision Repair. J Am Chem Soc 2018; 140:8260-8267. [PMID: 29883113 DOI: 10.1021/jacs.8b04063] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The genomic DNA of eukaryotic cells exists in the form of chromatin, the structure of which controls the biochemical accessibility of the underlying DNA to effector proteins. In order to gain an in depth molecular understanding of how chromatin structure regulates DNA repair, detailed in vitro biochemical and biophysical studies are required. However, because of challenges associated with reconstituting nucleosome arrays containing site-specifically positioned DNA modifications, such studies have been limited to the use of mono- and dinucleosomes as model in vitro substrates, which are incapable of folding into native chromatin structures. To address this issue, we developed a straightforward and general approach for assembling chemically defined oligonucleosome arrays (i.e., designer chromatin) containing site-specifically modified DNA. Our method takes advantage of nicking endonucleases to excise short fragments of unmodified DNA, which are subsequently replaced with synthetic oligonucleotides containing the desired modification. Using this approach, we prepared several oligonucleosome substrates containing precisely positioned 2'-deoxyuridine (dU) residues and examined the efficiency of base excision repair (BER) within several distinct chromatin architectures. We show that, depending on the translational position of the lesion, the combined catalytic activities of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) can be either inhibited by as much as 20-fold or accelerated by more than 5-fold within compact chromatin (i.e., the 30 nm fiber) relative to naked DNA. Moreover, we demonstrate that digestion of dU by UDG/APE1 proceeds much more rapidly in mononucleosomes than in compacted nucleosome arrays, thereby providing the first direct evidence that internucleosome interactions play an important role in regulating BER within higher-order chromatin structures. Overall, this work highlights the value of performing detailed biochemical studies on precisely modified chromatin substrates in vitro and provides a robust platform for investigating DNA modifications in chromatin biology.
Collapse
Affiliation(s)
- Deb Ranjan Banerjee
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Charles E Deckard
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Meagan B Elinski
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Meridith L Buzbee
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Wesley Wei Wang
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - James D Batteas
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Jonathan T Sczepanski
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| |
Collapse
|
166
|
Öztürk MA, Cojocaru V, Wade RC. Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many. Structure 2018; 26:1050-1057. [PMID: 29937356 DOI: 10.1016/j.str.2018.05.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/31/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022]
Abstract
There is renewed interest in linker histone (LH)-nucleosome binding and how LHs influence eukaryotic DNA compaction. For a long time, the goal was to uncover "the structure of the chromatosome," but recent studies of LH-nucleosome complexes have revealed an ensemble of structures. Notably, the reconstituted LH-nucleosome complexes used in experiments rarely correspond to the sequence combinations present in organisms. For a full understanding of the determinants of the distribution of the chromatosome structural ensemble, studies must include a complete description of the sequences and experimental conditions used, and be designed to enable systematic evaluation of sequence and environmental effects.
Collapse
Affiliation(s)
- Mehmet Ali Öztürk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, 69120 Heidelberg, Germany
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.
| |
Collapse
|
167
|
Schwenger A, Jurkowski TP, Richert C. Capturing and Stabilizing Folded Proteins in Lattices Formed with Branched Oligonucleotide Hybrids. Chembiochem 2018; 19:1523-1530. [DOI: 10.1002/cbic.201800145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Tomasz P. Jurkowski
- Institut für Biochemie und Technische BiochemieUniversität Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| |
Collapse
|
168
|
Fang K, Chen X, Li X, Shen Y, Sun J, Czajkowsky DM, Shao Z. Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure. ACS NANO 2018; 12:4909-4918. [PMID: 29715004 DOI: 10.1021/acsnano.8b01963] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is widely recognized that the higher-order spatial organization of the genome, beyond the nucleosome, plays an important role in many biological processes. However, to date, direct information on even such fundamental structural details as the typical sizes and DNA content of these higher-order structures in situ is poorly characterized. Here, we examine the nanoscopic DNA organization within human nuclei using super-resolution direct stochastic optical reconstruction microscopy (dSTORM) imaging and 5-ethynyl-2'-deoxyuridine click chemistry, studying single fully labeled chromosomes within an otherwise unlabeled nuclei to improve the attainable resolution. We find that, regardless of nuclear position, individual subchromosomal regions consist of three different levels of DNA compaction: (i) dispersed chromatin; (ii) nanodomains of sizes ranging tens of nanometers containing a few kilobases (kb) of DNA; and (iii) clusters of nanodomains. Interestingly, the sizes and DNA content of the nanodomains are approximately the same at the nuclear periphery, nucleolar proximity, and nuclear interior, suggesting that these nanodomains share a roughly common higher-order architecture. Overall, these results suggest that DNA compaction within the eukaryote nucleus occurs via the condensation of DNA into few-kb nanodomains of approximately similar structure, with further compaction occurring via the clustering of nanodomains.
Collapse
|
169
|
Öztürk MA, Cojocaru V, Wade RC. Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification. Biophys J 2018; 114:2363-2375. [PMID: 29759374 PMCID: PMC6129471 DOI: 10.1016/j.bpj.2018.04.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/18/2018] [Accepted: 04/09/2018] [Indexed: 12/20/2022] Open
Abstract
Linker histone (LH) proteins play a key role in higher-order structuring of chromatin for the packing of DNA in eukaryotic cells and in the regulation of genomic function. The common fruit fly (Drosophila melanogaster) has a single somatic isoform of the LH (H1). It is thus a useful model organism for investigating the effects of the LH on nucleosome compaction and the structure of the chromatosome, the complex formed by binding of an LH to a nucleosome. The structural and mechanistic details of how LH proteins bind to nucleosomes are debated. Here, we apply Brownian dynamics simulations to compare the nucleosome binding of the globular domain of D. melanogaster H1 (gH1) and the corresponding chicken (Gallus gallus) LH isoform, gH5, to identify residues in the LH that critically affect the structure of the chromatosome. Moreover, we investigate the effects of posttranslational modifications on the gH1 binding mode. We find that certain single-point mutations and posttranslational modifications of the LH proteins can significantly affect chromatosome structure. These findings indicate that even subtle differences in LH sequence can significantly shift the chromatosome structural ensemble and thus have implications for chromatin structure and transcriptional regulation.
Collapse
Affiliation(s)
- Mehmet Ali Öztürk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany; The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, Heidelberg University, Heidelberg, Germany
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany.
| |
Collapse
|
170
|
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.
Collapse
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.
| |
Collapse
|
171
|
On possible role of DNA electrodynamics in chromatin regulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 134:50-54. [DOI: 10.1016/j.pbiomolbio.2017.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/23/2022]
|
172
|
Kilic S, Boichenko I, Lechner CC, Fierz B. A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage. Chem Sci 2018; 9:3704-3709. [PMID: 29780501 PMCID: PMC5935033 DOI: 10.1039/c8sc00681d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/15/2018] [Indexed: 12/18/2022] Open
Abstract
The cellular response to DNA damage results in a signaling cascade that primes chromatin for repair. Combinatorial post-translational modifications (PTMs) play an important role in this process by altering the physical properties of chromatin and recruiting downstream factors. One key signal integrator is the histone variant H2A.X, which is phosphorylated at a C-terminal serine (S139ph), and ubiquitylated within its N-terminal tail at lysines 13 and 15 (K13/15ub). How these PTMs directly impact chromatin structure and thereby facilitate DNA repair is not well understood. Detailed studies require synthetic access to such N- and C-terminally modified proteins. This is complicated by the requirement for protecting groups allowing multi-fragment assembly. Here, we report a semi-synthetic route to generate simultaneously N- and C-terminally modified proteins using genetically encoded orthogonal masking groups. Applied to H2A.X, expression of a central protein fragment, containing a protected N-terminal cysteine and a C-terminal thioester masked as a split intein, enables sequential C- and N-terminal protein modification and results in the convergent production of H2A.X carrying K15ub and S139ph. Using single-molecule FRET between defined nucleosomes in synthetic chromatin fibers, we then show that K15 ubiquitylation (but not S139ph) impairs nucleosome stacking in tetranucleosome units, opening chromatin during DNA repair.
Collapse
Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Carolin C Lechner
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| |
Collapse
|
173
|
Fernandes V, Teles K, Ribeiro C, Treptow W, Santos G. Fat nucleosome: Role of lipids on chromatin. Prog Lipid Res 2018; 70:29-34. [PMID: 29678609 DOI: 10.1016/j.plipres.2018.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/18/2018] [Accepted: 04/16/2018] [Indexed: 01/01/2023]
Abstract
Structural changes in chromatin regulate gene expression and define phenotypic outcomes. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Most recently, the formation of condensed chromatin regions based on phase-separation in the cell, a basic physical mechanism, was proposed. Increased understanding of the mechanisms of interaction between chromatin and lipids suggest that small lipid molecules, such as cholesterol and short-chain fatty acids, can regulate important nuclear functions. New biophysical data has suggested that cholesterol interacts with nucleosome through multiple binding sites and affects chromatin structure in vitro. Regardless of the mechanism of how lipids bind to chromatin, there is currently little awareness that lipids may be stored in chromatin and influence its state. Focusing on lipids that bind to nuclear receptors, clinically relevant transcription factors, we discuss the potential interactions of the nucleosome with steroid hormones, bile acids and fatty acids, which suggest that other lipid chemotypes may also impact chromatin structure through binding to common sites on the nucleosome. Herein, we review the main impacts of lipids on the nuclear environment, emphasizing its role on chromatin architecture. We postulate that lipids that bind to nucleosomes and affect chromatin states are likely to be worth investigating as tools to modify disease phenotypes at a molecular level.
Collapse
Affiliation(s)
- Vinicius Fernandes
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil; Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF 70910-900, Brasília, Brazil
| | - Kaian Teles
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil
| | - Camyla Ribeiro
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, DF 70910-900, Brasília, Brazil
| | - Guilherme Santos
- Laboratório de Farmacologia Molecular, Departamento de Farmácia, Universidade de Brasília, Brasília 70919-970, Brazil.
| |
Collapse
|
174
|
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.
Collapse
|
175
|
Superresolution microscopy reveals structural mechanisms driving the nanoarchitecture of a viral chromatin tether. Proc Natl Acad Sci U S A 2018; 115:4992-4997. [PMID: 29610353 DOI: 10.1073/pnas.1721638115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
By tethering their circular genomes (episomes) to host chromatin, DNA tumor viruses ensure retention and segregation of their genetic material during cell divisions. Despite functional genetic and crystallographic studies, there is little information addressing the 3D structure of these tethers in cells, issues critical for understanding persistent infection by these viruses. Here, we have applied direct stochastic optical reconstruction microscopy (dSTORM) to establish the nanoarchitecture of tethers within cells latently infected with the oncogenic human pathogen, Kaposi's sarcoma-associated herpesvirus (KSHV). Each KSHV tether comprises a series of homodimers of the latency-associated nuclear antigen (LANA) that bind with their C termini to the tandem array of episomal terminal repeats (TRs) and with their N termini to host chromatin. Superresolution imaging revealed that individual KSHV tethers possess similar overall dimensions and, in aggregate, fold to occupy the volume of a prolate ellipsoid. Using plasmids with increasing numbers of TRs, we found that tethers display polymer power law scaling behavior with a scaling exponent characteristic of active chromatin. For plasmids containing a two-TR tether, we determined the size, separation, and relative orientation of two distinct clusters of bound LANA, each corresponding to a single TR. From these data, we have generated a 3D model of the episomal half of the tether that integrates and extends previously established findings from epifluorescent, crystallographic, and epigenetic approaches. Our findings also validate the use of dSTORM in establishing novel structural insights into the physical basis of molecular connections linking host and pathogen genomes.
Collapse
|
176
|
Liu Z, Tjian R. Visualizing transcription factor dynamics in living cells. J Cell Biol 2018; 217:1181-1191. [PMID: 29378780 PMCID: PMC5881510 DOI: 10.1083/jcb.201710038] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/03/2018] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
The assembly of sequence-specific enhancer-binding transcription factors (TFs) at cis-regulatory elements in the genome has long been regarded as the fundamental mechanism driving cell type-specific gene expression. However, despite extensive biochemical, genetic, and genomic studies in the past three decades, our understanding of molecular mechanisms underlying enhancer-mediated gene regulation remains incomplete. Recent advances in imaging technologies now enable direct visualization of TF-driven regulatory events and transcriptional activities at the single-cell, single-molecule level. The ability to observe the remarkably dynamic behavior of individual TFs in live cells at high spatiotemporal resolution has begun to provide novel mechanistic insights and promises new advances in deciphering causal-functional relationships of TF targeting, genome organization, and gene activation. In this review, we review current transcription imaging techniques and summarize converging results from various lines of research that may instigate a revision of models to describe key features of eukaryotic gene regulation.
Collapse
Affiliation(s)
- Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA
- Howard Hughes Medical Institute, Berkeley, CA
| |
Collapse
|
177
|
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]
|
178
|
Zinchenko A, Berezhnoy NV, Wang S, Rosencrans WM, Korolev N, van der Maarel JR, Nordenskiöld L. Single-molecule compaction of megabase-long chromatin molecules by multivalent cations. Nucleic Acids Res 2018; 46:635-649. [PMID: 29145649 PMCID: PMC5778610 DOI: 10.1093/nar/gkx1135] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 10/18/2017] [Accepted: 10/29/2017] [Indexed: 11/21/2022] Open
Abstract
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo. Variation of HO loading revealed a number of unique features related to the efficiency of chromatin compaction by multivalent cations, the mechanism of compaction, and the character of partly compact chromatin structures. The observations may be relevant for how DNA accessibility in chromatin is maintained. Compaction of saturated chromatin, in turn, is accompanied by an intra-chain segregation at the level of single chromatin molecules, suggesting an intriguing scenario of selective activation/deactivation of DNA as a result of chromatin fiber heterogeneity due to the nucleosome positioning. We suggest that this chromatin, reconstituted on megabase-long DNA because of its large size, is a useful model of eukaryotic chromatin.
Collapse
Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Sai Wang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - William M Rosencrans
- Department of Physics and Astronomy, Colgate University, Hamilton, NY 13346, USA
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| |
Collapse
|
179
|
Korolev N, Lyubartsev AP, Nordenskiöld L. A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Sci Rep 2018; 8:1543. [PMID: 29367745 PMCID: PMC5784010 DOI: 10.1038/s41598-018-19875-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an “NCP-centred” set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.
Collapse
Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
180
|
Kilic S, Felekyan S, Doroshenko O, Boichenko I, Dimura M, Vardanyan H, Bryan LC, Arya G, Seidel CAM, Fierz B. Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. Nat Commun 2018; 9:235. [PMID: 29339721 PMCID: PMC5770380 DOI: 10.1038/s41467-017-02619-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/11/2017] [Indexed: 01/17/2023] Open
Abstract
The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics in chromatin fibers. We show that nucleosomes engage in short-lived (micro- to milliseconds) stacking interactions with one of their neighbors. This results in discrete tetranucleosome units with distinct interaction registers that interconvert within hundreds of milliseconds. Additionally, we find that dynamic chromatin architecture is modulated by the multivalent architectural protein heterochromatin protein 1α (HP1α), which engages methylated histone tails and thereby transiently stabilizes stacked nucleosomes. This compacted state nevertheless remains dynamic, exhibiting fluctuations on the timescale of HP1α residence times. Overall, this study reveals that exposure of internal DNA sites and nucleosome surfaces in chromatin fibers is governed by an intrinsic dynamic hierarchy from micro- to milliseconds, allowing the gene regulation machinery to access compact chromatin. Chromatin fibers undergo continuous structural rearrangements but their dynamic architecture is poorly understood. Here, the authors use single-molecule FRET to determine the structural states and interconversion kinetics of chromatin fibers, monitoring their effector protein-dependent dynamic motions.
Collapse
Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Olga Doroshenko
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Mykola Dimura
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hayk Vardanyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Gaurav Arya
- Pratt School of Engineering, Duke University, 144 Hudson Hall, Box 90300, Durham, NC, 27708, USA
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| |
Collapse
|
181
|
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.
Collapse
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.
| |
Collapse
|
182
|
Abstract
Magnetic tweezers form a unique tool to study the topology and mechanical properties of chromatin fibers. Chromatin is a complex of DNA and proteins that folds the DNA in such a way that meter-long stretches of DNA fit into the micron-sized cell nucleus. Moreover, it regulates accessibility of the genome to the cellular replication, transcription, and repair machinery. However, the structure and mechanisms that govern chromatin folding remain poorly understood, despite recent spectacular improvements in high-resolution imaging techniques. Single-molecule force spectroscopy techniques can directly measure both the extension of individual chromatin fragments with nanometer accuracy and the forces involved in the (un)folding of single chromatin fibers. Here, we report detailed methods that allow one to successfully prepare in vitro reconstituted chromatin fibers for use in magnetic tweezers-based force spectroscopy. The higher-order structure of different chromatin fibers can be inferred from fitting a statistical mechanics model to the force-extension data. These methods for quantifying chromatin folding can be extended to study many other processes involving chromatin, such as the epigenetic regulation of transcription.
Collapse
|
183
|
Brouwer TB, Kaczmarczyk A, Pham C, van Noort J. Unraveling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers. Methods Mol Biol 2018; 1837:317-349. [PMID: 30109618 DOI: 10.1007/978-1-4939-8675-0_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers in particular have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to magnetics bead inside flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleo-protein filaments can be extracted from the data.
Collapse
Affiliation(s)
- Thomas B Brouwer
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - Chi Pham
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands.
| |
Collapse
|
184
|
Ishida H, Kono H. H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes. Biophys J 2017; 113:978-990. [PMID: 28877499 DOI: 10.1016/j.bpj.2017.07.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 11/17/2022] Open
Abstract
Histone tails play an important role in internucleosomal interaction and chromatin compaction. To understand how the H4 tails are involved in the internucleosomal interaction, an adaptively biased molecular dynamics simulation of 63 models of two stacked nucleosomes, each with the H4 tails in different locations, was carried out. This simulation generated a variety of orientations of the separated nucleosomes depending on the formation of the H4 tail bridge between the H4 tails and the DNA of the neighboring nucleosomes. For the models that showed distinctive orientations of the two nucleosomes, the free energies of the separation of the nucleosomes were further investigated using umbrella sampling simulations. The attractive force between the nucleosomes was estimated from the free energies; the force when two H4 tail bridges formed varied from 36 to 63 pN, depending on the formation of the H4 tail-bridge and the interfacial interaction, whereas the force reduced to 15-18 pN after either one of the H4 tail bridges had broken, regardless of the conformation of the H4 tail. Additional simulations of the nucleosomes show that when the H4 tail was truncated, the force between the nucleosomes became repulsive (from-3 to -7 pN). We concluded that the H4 tails potentially produce the diversity in the orientation of the two nucleosomes, which would contribute to the polymorphism of the chromatin structure.
Collapse
Affiliation(s)
- Hisashi Ishida
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, Japan.
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, Japan
| |
Collapse
|
185
|
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.
Collapse
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
| |
Collapse
|
186
|
Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Nat Commun 2017; 8:1489. [PMID: 29138400 PMCID: PMC5686127 DOI: 10.1038/s41467-017-01598-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 10/03/2017] [Indexed: 12/03/2022] Open
Abstract
Combinatorial polyvalent contacts of histone-binding domains or readers commonly mediate localization and activities of chromatin-associated proteins. A pair of readers, the PHD fingers of the protein CHD4, has been shown to bivalently recognize histone H3 tails. Here we describe a mechanism by which these linked but independent readers bind to the intact nucleosome core particle (NCP). Comprehensive NMR, chemical reactivity, molecular dynamics, and fluorescence analyses point to the critical roles of intra-nucleosomal histone-DNA interactions that reduce the accessibility of H3 tails in NCP, the nucleosomal DNA, and the linker between readers in modulating nucleosome- and/or histone-binding activities of the readers. We show that the second PHD finger of CHD4 initiates recruitment to the nucleosome, however both PHDs are required to alter the NCP dynamics. Our findings reveal a distinctive regulatory mechanism for the association of paired readers with the nucleosome that provides an intricate balance between cooperative and individual activities of the readers. The chromatin remodeller CHD4 contains two PHD finger reader domains that have been shown to bivalently recognize H3 histone tails. Here, the authors describe a mechanism by which the PHD fingers bind to the intact nucleosome core particle, revealing both cooperative and individual interactions.
Collapse
|
187
|
Buckwalter JM, Norouzi D, Harutyunyan A, Zhurkin VB, Grigoryev SA. Regulation of chromatin folding by conformational variations of nucleosome linker DNA. Nucleic Acids Res 2017; 45:9372-9387. [PMID: 28934465 PMCID: PMC5766201 DOI: 10.1093/nar/gkx562] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/19/2017] [Indexed: 11/16/2022] Open
Abstract
Linker DNA conformational variability has been proposed to direct nucleosome array folding into more or less compact chromatin fibers but direct experimental evidence for such models are lacking. Here, we tested this hypothesis by designing nucleosome arrays with A-tracts at specific locations in the nucleosome linkers to induce inward (AT-IN) and outward (AT-OUT) bending of the linker DNA. Using electron microscopy and analytical centrifugation techniques, we observed spontaneous folding of AT-IN nucleosome arrays into highly compact structures, comparable to those induced by linker histone H1. In contrast, AT-OUT nucleosome arrays formed less compact structures with decreased nucleosome interactions similar to wild-type nucleosome arrays. Adding linker histone H1 further increased compaction of the A-tract arrays while maintaining structural differences between them. Furthermore, restriction nuclease digestion revealed a strongly reduced accessibility of nucleosome linkers in the compact AT-IN arrays. Electron microscopy analysis and 3D computational Monte Carlo simulations are consistent with a profound zigzag linker DNA configuration and closer nucleosome proximity in the AT-IN arrays due to inward linker DNA bending. We propose that the evolutionary preferred positioning of A-tracts in DNA linkers may control chromatin higher-order folding and thus influence cellular processes such as gene expression, transcription and DNA repair.
Collapse
Affiliation(s)
- Jenna M Buckwalter
- Penn State University College of Medicine, Department of Biochemistry and Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| | - Davood Norouzi
- Laboratory of Cell Biology, CCR, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anna Harutyunyan
- Penn State University College of Medicine, Department of Biochemistry and Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, CCR, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sergei A Grigoryev
- Penn State University College of Medicine, Department of Biochemistry and Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| |
Collapse
|
188
|
Emerging roles of linker histones in regulating chromatin structure and function. Nat Rev Mol Cell Biol 2017; 19:192-206. [PMID: 29018282 DOI: 10.1038/nrm.2017.94] [Citation(s) in RCA: 286] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Together with core histones, which make up the nucleosome, the linker histone (H1) is one of the five main histone protein families present in chromatin in eukaryotic cells. H1 binds to the nucleosome to form the next structural unit of metazoan chromatin, the chromatosome, which may help chromatin to fold into higher-order structures. Despite their important roles in regulating the structure and function of chromatin, linker histones have not been studied as extensively as core histones. Nevertheless, substantial progress has been made recently. The first near-atomic resolution crystal structure of a chromatosome core particle and an 11 Å resolution cryo-electron microscopy-derived structure of the 30 nm nucleosome array have been determined, revealing unprecedented details about how linker histones interact with the nucleosome and organize higher-order chromatin structures. Moreover, several new functions of linker histones have been discovered, including their roles in epigenetic regulation and the regulation of DNA replication, DNA repair and genome stability. Studies of the molecular mechanisms of H1 action in these processes suggest a new paradigm for linker histone function beyond its architectural roles in chromatin.
Collapse
|
189
|
Nikitina T, Norouzi D, Grigoryev SA, Zhurkin VB. DNA topology in chromatin is defined by nucleosome spacing. SCIENCE ADVANCES 2017; 3:e1700957. [PMID: 29098179 PMCID: PMC5659657 DOI: 10.1126/sciadv.1700957] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/27/2017] [Indexed: 06/07/2023]
Abstract
In eukaryotic nucleosomes, DNA makes ~1.7 superhelical turns around histone octamer. However, there is a long-standing discrepancy between the nucleosome core structure determined by x-ray crystallography and measurements of DNA topology in circular minichromosomes, indicating that there is only ~1.0 superhelical turn per nucleosome. Although several theoretical assumptions were put forward to explain this paradox by conformational variability of the nucleosome linker, none was tested experimentally. We analyzed topological properties of DNA in circular nucleosome arrays with precisely positioned nucleosomes. Using topological electrophoretic assays and electron microscopy, we demonstrate that the DNA linking number per nucleosome strongly depends on the nucleosome spacing and varies from -1.4 to -0.9. For the predominant {10n + 5} class of nucleosome repeats found in native chromatin, our results are consistent with the DNA topology observed earlier. Thus, we reconcile the topological properties of nucleosome arrays with nucleosome core structure and provide a simple explanation for the DNA topology in native chromatin with variable DNA linker length. Topological polymorphism of the chromatin fibers described here may reflect a more general tendency of chromosomal domains containing active or repressed genes to acquire different nucleosome spacing to retain topologically distinct higher-order structures.
Collapse
Affiliation(s)
- Tatiana Nikitina
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davood Norouzi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei A. Grigoryev
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Victor B. Zhurkin
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
190
|
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.
Collapse
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.
| |
Collapse
|
191
|
Kaczmarczyk A, Allahverdi A, Brouwer TB, Nordenskiöld L, Dekker NH, van Noort J. Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding. J Biol Chem 2017; 292:17506-17513. [PMID: 28855255 DOI: 10.1074/jbc.m117.791830] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/21/2017] [Indexed: 01/06/2023] Open
Abstract
The eukaryotic genome is highly compacted into a protein-DNA complex called chromatin. The cell controls access of transcriptional regulators to chromosomal DNA via several mechanisms that act on chromatin-associated proteins and provide a rich spectrum of epigenetic regulation. Elucidating the mechanisms that fold chromatin fibers into higher-order structures is therefore key to understanding the epigenetic regulation of DNA accessibility. Here, using histone H4-V21C and histone H2A-E64C mutations, we employed single-molecule force spectroscopy to measure the unfolding of individual chromatin fibers that are reversibly cross-linked through the histone H4 tail. Fibers with covalently linked nucleosomes featured the same folding characteristics as fibers containing wild-type histones but exhibited increased stability against stretching forces. By stabilizing the secondary structure of chromatin, we confirmed a nucleosome repeat length (NRL)-dependent folding. Consistent with previous crystallographic and cryo-EM studies, the obtained force-extension curves on arrays with 167-bp NRLs best supported an underlying structure consisting of zig-zag, two-start fibers. For arrays with 197-bp NRLs, we previously inferred solenoidal folding, which was further corroborated by force-extension curves of the cross-linked fibers. The different unfolding pathways exhibited by these two types of arrays and reported here extend our understanding of chromatin structure and its potential roles in gene regulation. Importantly, these findings imply that chromatin compaction by nucleosome stacking protects nucleosomal DNA from external forces up to 4 piconewtons.
Collapse
Affiliation(s)
- Artur Kaczmarczyk
- From the Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands, and
| | - Abdollah Allahverdi
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
| | - Thomas B Brouwer
- From the Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands, and
| | - John van Noort
- From the Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands,
| |
Collapse
|
192
|
Razin SV, Ulianov SV. Gene functioning and storage within a folded genome. Cell Mol Biol Lett 2017; 22:18. [PMID: 28861108 PMCID: PMC5575855 DOI: 10.1186/s11658-017-0050-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/24/2017] [Indexed: 01/28/2023] Open
Abstract
In mammals, genomic DNA that is roughly 2 m long is folded to fit the size of the cell nucleus that has a diameter of about 10 μm. The folding of genomic DNA is mediated via assembly of DNA-protein complex, chromatin. In addition to the reduction of genomic DNA linear dimensions, the assembly of chromatin allows to discriminate and to mark active (transcribed) and repressed (non-transcribed) genes. Consequently, epigenetic regulation of gene expression occurs at the level of DNA packaging in chromatin. Taking into account the increasing attention of scientific community toward epigenetic systems of gene regulation, it is very important to understand how DNA folding in chromatin is related to gene activity. For many years the hierarchical model of DNA folding was the most popular. It was assumed that nucleosome fiber (10-nm fiber) is folded into 30-nm fiber and further on into chromatin loops attached to a nuclear/chromosome scaffold. Recent studies have demonstrated that there is much less regularity in chromatin folding within the cell nucleus. The very existence of 30-nm chromatin fibers in living cells was questioned. On the other hand, it was found that chromosomes are partitioned into self-interacting spatial domains that restrict the area of enhancers action. Thus, TADs can be considered as structural-functional domains of the chromosomes. Here we discuss the modern view of DNA packaging within the cell nucleus in relation to the regulation of gene expression. Special attention is paid to the possible mechanisms of the chromatin fiber self-assembly into TADs. We discuss the model postulating that partitioning of the chromosome into TADs is determined by the distribution of active and inactive chromatin segments along the chromosome. This article was specially invited by the editors and represents work by leading researchers.
Collapse
Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia.,Lomonosov Moscow State University, Biological Faculty, Leninskie Gory 1, building 12, 119192 Moscow, Russia
| |
Collapse
|
193
|
Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Towards quantitative analysis of gene regulation by enhancers. Epigenomics 2017; 9:1219-1231. [PMID: 28799793 DOI: 10.2217/epi-2017-0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
Collapse
Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Stefjord Todolli
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
194
|
Berezhnoy NV, Liu Y, Allahverdi A, Yang R, Su CJ, Liu CF, Korolev N, Nordenskiöld L. The Influence of Ionic Environment and Histone Tails on Columnar Order of Nucleosome Core Particles. Biophys J 2017; 110:1720-1731. [PMID: 27119633 DOI: 10.1016/j.bpj.2016.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/04/2016] [Accepted: 03/07/2016] [Indexed: 01/08/2023] Open
Abstract
The nucleosome core particle (NCP) is the basic building block of chromatin. Nucleosome-nucleosome interactions are instrumental in chromatin compaction, and understanding NCP self-assembly is important for understanding chromatin structure and dynamics. Recombinant NCPs aggregated by multivalent cations form various ordered phases that can be studied by x-ray diffraction (small-angle x-ray scattering). In this work, the effects on the supramolecular structure of aggregated NCPs due to lysine histone H4 tail acetylations, histone H2A mutations (neutralizing the acidic patch of the histone octamer), and the removal of histone tails were investigated. The formation of ordered mainly hexagonal columnar NCP phases is in agreement with earlier studies; however, the highly homogeneous recombinant NCP systems used in this work display a more compact packing. The long-range order of the NCP columnar phase was found to be abolished or reduced by acetylation of the H4 tails, acidic patch neutralization, and removal of the H3 and H2B tails. Loss of nucleosome stacking upon removal of the H3 tails in combination with other tails was observed. In the absence of the H2A tails, the formation of an unknown highly ordered phase was observed.
Collapse
Affiliation(s)
- Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ying Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Abdollah Allahverdi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| |
Collapse
|
195
|
Wilson MD, Costa A. Cryo-electron microscopy of chromatin biology. Acta Crystallogr D Struct Biol 2017; 73:541-548. [PMID: 28580916 PMCID: PMC5458496 DOI: 10.1107/s2059798317004430] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 11/17/2022] Open
Abstract
The basic unit of chromatin, the nucleosome core particle (NCP), controls how DNA in eukaryotic cells is compacted, replicated and read. Since its discovery, biochemists have sought to understand how this protein-DNA complex can help to control so many diverse tasks. Recent electron-microscopy (EM) studies on NCP-containing assemblies have helped to describe important chromatin transactions at a molecular level. With the implementation of recent technical advances in single-particle EM, our understanding of how nucleosomes are recognized and read looks to take a leap forward. In this review, the authors highlight recent advances in the architectural understanding of chromatin biology elucidated by EM.
Collapse
Affiliation(s)
- Marcus D. Wilson
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| |
Collapse
|
196
|
Cuvier O, Fierz B. Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. Nat Rev Genet 2017; 18:457-472. [DOI: 10.1038/nrg.2017.28] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
197
|
Abstract
Eukaryotic DNA is packaged into regularly spaced nucleosomes, resembling beads on a string. Each bead contains ∼147 bp wrapped around a core histone octamer. Linker histone (H1) binds to the linker DNA to drive chromatin folding. Micrococcal nuclease (MNase) digestion studies reveal 2 mono-nucleosomal intermediates: the core particle (∼147 bp) and the chromatosome (∼160 bp; a core particle with additional DNA protected by H1). We have recently developed an improved method for mapping nucleosomes, using exonuclease III to remove residual linker (MNase-Exo-seq). (1) We discovered 2 new intermediate particles corresponding to core particles with ∼7 bp of linker protruding from one side (∼154 bp) or both sides (∼161 bp), which are formed in the absence of H1. We propose that these "proto-chromatosomes" are stabilized by core histone-DNA contacts in the linker, ∼7 bp from the nucleosome boundaries. These contacts may determine the topography of the H1 binding site.
Collapse
Affiliation(s)
- Josefina Ocampo
- a Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Feng Cui
- b Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology , Rochester , NY , USA
| | - Victor B Zhurkin
- c National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
| | - David J Clark
- a Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health , Bethesda , MD , USA
| |
Collapse
|
198
|
|
199
|
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.
Collapse
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
| |
Collapse
|
200
|
How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017; 101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?
Collapse
|