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Hou Z, Nightingale F, Zhu Y, MacGregor-Chatwin C, Zhang P. Structure of native chromatin fibres revealed by Cryo-ET in situ. Nat Commun 2023; 14:6324. [PMID: 37816746 PMCID: PMC10564948 DOI: 10.1038/s41467-023-42072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
The structure of chromatin plays pivotal roles in regulating gene transcription, DNA replication and repair, and chromosome segregation. This structure, however, remains elusive. Here, using cryo-FIB and cryo-ET, we delineate the 3D architecture of native chromatin fibres in intact interphase human T-lymphoblasts and determine the in situ structures of nucleosomes in different conformations. These chromatin fibres are not structured as uniform 30 nm one-start or two-start filaments but are composed of relaxed, variable zigzag organizations of nucleosomes connected by straight linker DNA. Nucleosomes with little H1 and linker DNA density are distributed randomly without any spatial preference. This work will inspire future high-resolution investigations on native chromatin structures in situ at both a single-nucleosome level and a population level under many different cellular conditions in health and disease.
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Affiliation(s)
- Zhen Hou
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Frank Nightingale
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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2
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Kundu S, Chowdhury A, Nandi S, Bhattacharyya K, Patra A. Deciphering the evolution of supramolecular nanofibers in solution and solid-state: a combined microscopic and spectroscopic approach. Chem Sci 2021; 12:5874-5882. [PMID: 34168812 PMCID: PMC8179674 DOI: 10.1039/d0sc07050e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/17/2021] [Indexed: 12/21/2022] Open
Abstract
Supramolecular self-assembly of small organic molecules has emerged as a powerful tool to construct well-defined micro- and nanoarchitecture through fine-tuning a range of intermolecular interactions. The size, shape, and optical properties of these nanostructures largely depend on the specific assembly of the molecular building units, temperature and polarity of the medium, and external stimuli. The engineering of supramolecular self-assembled nanostructures with morphology-dependent tunable emission is in high demand due to the promising scope in nanodevices and molecular machines. However, probing the evolution of molecular aggregates from the solution and directing the self-assembly process in a pre-defined fashion are challenging. In the present study, we have deciphered the sequential evolution of supramolecular nanofibers from solution to spherical and oblong-shaped nanoparticles through the variation of solvent polarity, tuning the hydrophobic-hydrophilic interactions. An intriguing case of molecular self-assembly has been elucidated employing a newly designed π-conjugated thiophene derivative (TPAn) through a combination of steady-state absorption, emission measurements, fluorescence correlation spectroscopy (FCS), and electron microscopy. The FCS analysis and microscopy results revealed that the small-sized nanofibers in the dispersion further agglomerated upon solvent evaporation, resulting in a network of nanofibers. Stimuli-responsive reversible interconversion between a network of nanofibers and spherical nanoaggregates was probed both in dispersion and solvent-evaporated state. The evolution of organic nanofibers and a subtle control over the self-assembly process demonstrated in the current investigation provide a general paradigm to correlate the size, shape, and emission properties of fluorescent molecular aggregates in complex heterogeneous media, including a human cell.
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Affiliation(s)
- Subhankar Kundu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Arkaprava Chowdhury
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Somen Nandi
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Kankan Bhattacharyya
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
| | - Abhijit Patra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhopal By-Pass Road, Bhauri Bhopal 462066 Madhya Pradesh India
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Sartsanga C, Phengchat R, Fukui K, Wako T, Ohmido N. Surface structures consisting of chromatin fibers in isolated barley (Hordeum vulgare) chromosomes revealed by helium ion microscopy. Chromosome Res 2021; 29:81-94. [PMID: 33615407 DOI: 10.1007/s10577-021-09649-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
The chromosome compaction of chromatin fibers results in the formation of the nucleosome, which consists of a DNA unit coiled around a core of histone molecules associated with linker histone. The compaction of chromatin fibers has been a topic of controversy since the discovery of chromosomes in the 19th century. Although chromatin fibers were first identified using electron microscopy, the chromatin fibers on the surface of chromosome structures in plants remain unclear due to shrinking and breaking caused by prior chromosome isolation or preparation with alcohol and acid fixation, and critical point drying occurred into dehydration and denatured chromosomal proteins. This study aimed to develop a high-quality procedure for the isolation and preparation of plant chromosomes, maintaining the native chromosome structure, to elucidate the organization of chromatin fibers on the surface of plant chromosomes by electron microscopy. A simple technique to isolate intact barley (Hordeum vulgare) chromosomes with a high yield was developed, allowing chromosomes to be observed with a high-resolution scanning ion microscopy and helium ion microscopy (HIM) imaging technology, based on a scanning helium ion beam. HIM images from the surface chromatin fibers were analyzed to determine the size and alignment of the chromatin fibers. The unit size of the chromatin fibers was 11.6 ± 3.5 nm and was closely aligned to the chromatin network model. Our findings indicate that compacting the surface structure of barley via a chromatin network and observation via HIM are powerful tools for investigating the structure of chromatin.
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Affiliation(s)
- Channarong Sartsanga
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Rinyaporn Phengchat
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshiyuki Wako
- Institute of Crop Sciences, National Agriculture and Food Research Organization, 2-1-1 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan.
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Zhou Z, Yan R, Jiang W, Irudayaraj JMK. Chromatin hierarchical branching visualized at the nanoscale by electron microscopy. NANOSCALE ADVANCES 2021; 3:1019-1028. [PMID: 34381959 PMCID: PMC8323808 DOI: 10.1039/d0na00359j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/12/2020] [Indexed: 06/13/2023]
Abstract
Chromatin is spatially organized in a hierarchical manner by virtue of single nucleosomes condensing into higher order chromatin structures, conferring various mechanical properties and biochemical signals. These higher order chromatin structures regulate genomic function by organization of the heterochromatin and euchromatin landscape. Less is known about its transition state from higher order heterochromatin to the lower order nucleosome form, and there is no information on its physical properties. We have developed a facile method of electron microscopy visualization to reveal the interphase chromatin in eukaryotic cells and its organization into hierarchical branching structures. We note that chromatin hierarchical branching can be distinguished at four levels, clearly indicating the stepwise transition from heterochromatin to euchromatin. The protein-DNA density across the chromatin fibers decreases during the transition from compacted heterochromatin to dispersed euchromatin. Moreover, the thickness of the chromatin ranges between 10 to 270 nm, and the controversial 30 nm chromatin fiber exists as a prominent intermediate structure. This study provides important insights into higher order chromatin organization which plays a key role in diseases such as cancer.
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Affiliation(s)
- Zhongwu Zhou
- Bindley Bioscience Center, Department of Agricultural and Biological Engineering, Purdue University West Lafayette IN 47907 USA
- The University of Texas at Austin NHB 4.120, 100 E. 24th St. Austin TX 78712 USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University West Lafayette IN 47907 USA
- Howard Hughes Medical Institute, Janelia Research Campus 19700 Helix Drive Asburn Virginia 20147 USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University West Lafayette IN 47907 USA
| | - Joseph M K Irudayaraj
- Bindley Bioscience Center, Department of Agricultural and Biological Engineering, Purdue University West Lafayette IN 47907 USA
- Cancer Center at Illinois, Department of Bioengineering, College of Engineering, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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Hayashida M, Phengchat R, Malac M, Harada K, Akashi T, Ohmido N, Fukui K. Higher-Order Structure of Human Chromosomes Observed by Electron Diffraction and Electron Tomography. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:149-155. [PMID: 33213601 DOI: 10.1017/s1431927620024666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
It is well known that two DNA molecules are wrapped around histone octamers and folded together to form a single chromosome. However, the nucleosome fiber folding within a chromosome remains an enigma, and the higher-order structure of chromosomes also is not understood. In this study, we employed electron diffraction which provides a noninvasive analysis to characterize the internal structure of chromosomes. The results revealed the presence of structures with 100–200 nm periodic features directionally perpendicular to the chromosome axis in unlabeled isolated human chromosomes. We also visualized the 100–200 nm periodic features perpendicular to the chromosome axis in an isolated chromosome whose DNA molecules were specifically labeled with OsO4 using electron tomography in 300 keV and 1 MeV transmission electron microscopes.
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Affiliation(s)
- Misa Hayashida
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada
| | - Rinyaporn Phengchat
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe657-8501, Japan
| | - Marek Malac
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, AB, T6G 2M9, Canada
- Department of Physics, University of Alberta, EdmontonT6G 2E1, Canada
| | - Ken Harada
- Center for Emergent Matter Science (CEMS), RIKEN, Hatoyama, Saitama350-0395, Japan
| | - Tetsuya Akashi
- Research & Development Group, HITACHI, Ltd., Hatoyama, Saitama350-0395, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe657-8501, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka565-0871, Japan
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Yusuf M, Farooq S, Robinson I, Lalani EN. Cryo-nanoscale chromosome imaging-future prospects. Biophys Rev 2020; 12:1257-1263. [PMID: 33006727 PMCID: PMC7575669 DOI: 10.1007/s12551-020-00757-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 01/30/2023] Open
Abstract
The high-order structure of mitotic chromosomes remains to be fully elucidated. How nucleosomes compact at various structural levels into a condensed mitotic chromosome is unclear. Cryogenic preservation and imaging have been applied for over three decades, keeping biological structures close to the native in vivo state. Despite being extensively utilized, this field is still wide open for mitotic chromosome research. In this review, we focus specifically on cryogenic efforts for determining the mitotic nanoscale chromatin structures. We describe vitrification methods, current status, and applications of advanced cryo-microscopy including future tools required for resolving the native architecture of these fascinating structures that hold the instructions to life.
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Affiliation(s)
- Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan.
| | - Safana Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Brookhaven National Lab, Upton, NY, 11973, USA
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
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Boopathi R, Dimitrov S, Hamiche A, Petosa C, Bednar J. Cryo-electron microscopy of the chromatin fiber. Curr Opin Struct Biol 2020; 64:97-103. [PMID: 32717688 DOI: 10.1016/j.sbi.2020.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023]
Abstract
The three-dimensional (3D) organization of chromatin plays a crucial role in the regulation of gene expression. Chromatin conformation is strongly affected by the composition, structural features and dynamic properties of the nucleosome, which in turn determine the nature and geometry of interactions that can occur between neighboring nucleosomes. Understanding how chromatin is spatially organized above the nucleosome level is thus essential for understanding how gene regulation is achieved. Towards this end, great effort has been made to understand how an array of nucleosomes folds into a regular chromatin fiber. This review summarizes new insights into the 3D structure of the chromatin fiber that were made possible by recent advances in cryo-electron microscopy.
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Affiliation(s)
- Ramachandran Boopathi
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante´ - Allée des Alpes, 38700 La Tronche, France; 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 Sante´ - Allée des Alpes, 38700 La Tronche, France; Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - 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
| | - Carlo Petosa
- 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 Sante´ - 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.
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