1
|
Neděla V, Tihlaříková E, Cápal P, Doležel J. Advanced environmental scanning electron microscopy reveals natural surface nano-morphology of condensed mitotic chromosomes in their native state. Sci Rep 2024; 14:12998. [PMID: 38844535 PMCID: PMC11156959 DOI: 10.1038/s41598-024-63515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
The challenge of in-situ handling and high-resolution low-dose imaging of intact, sensitive and wet samples in their native state at nanometer scale, including live samples is met by Advanced Environmental Scanning Electron Microscopy (A-ESEM). This new generation of ESEM utilises machine learning-based optimization of thermodynamic conditions with respect to sample specifics to employ a low temperature method and an ionization secondary electron detector with an electrostatic separator. A modified electron microscope was used, equipped with temperature, humidity and gas pressure sensors for in-situ and real-time monitoring of the sample. A transparent ultra-thin film of ionic liquid is used to increase thermal and electrical conductivity of the samples and to minimize sample damage by free radicals. To validate the power of the new method, we analyze condensed mitotic metaphase chromosomes to reveal new structural features of their perichromosomal layer, and the organization of chromatin fibers, not observed before by any microscopic technique. The ability to resolve nano-structural details of chromosomes using A-ESEM is validated by measuring gold nanoparticles with achievable resolution in the lower nanometre units.
Collapse
Affiliation(s)
- Vilém Neděla
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic.
| | - Eva Tihlaříková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
| |
Collapse
|
2
|
Câmara AS, Kubalová I, Schubert V. Helical chromonema coiling is conserved in eukaryotes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1284-1300. [PMID: 37840457 DOI: 10.1111/tpj.16484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
Efficient chromatin condensation is required to transport chromosomes during mitosis and meiosis, forming daughter cells. While it is well accepted that these processes follow fundamental rules, there has been a controversial debate for more than 140 years on whether the higher-order chromatin organization in chromosomes is evolutionarily conserved. Here, we summarize historical and recent investigations based on classical and modern methods. In particular, classical light microscopy observations based on living, fixed, and treated chromosomes covering a wide range of plant and animal species, and even in single-cell eukaryotes suggest that the chromatids of large chromosomes are formed by a coiled chromatin thread, named the chromonema. More recently, these findings were confirmed by electron and super-resolution microscopy, oligo-FISH, molecular interaction data, and polymer simulation. Altogether, we describe common and divergent features of coiled chromonemata in different species. We hypothesize that chromonema coiling in large chromosomes is a fundamental feature established early during the evolution of eukaryotes to handle increasing genome sizes.
Collapse
Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| |
Collapse
|
3
|
Zhang M, Díaz-Celis C, Liu J, Tao J, Ashby PD, Bustamante C, Ren G. Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography. Nat Commun 2024; 15:4395. [PMID: 38782894 PMCID: PMC11116431 DOI: 10.1038/s41467-024-48305-1] [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: 01/09/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.
Collapse
Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - César Díaz-Celis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinhui Tao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Ashby
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carlos Bustamante
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Department of Physics, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, USA.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
4
|
Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis T, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Structural mechanism of HP1α-dependent transcriptional repression and chromatin compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569387. [PMID: 38076844 PMCID: PMC10705452 DOI: 10.1101/2023.11.30.569387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. In this study, we employed a multidisciplinary approach to unravel the interactions between human HP1α and nucleosomes. We have elucidated the cryo-EM structure of an HP1α dimer bound to an H2A.Z nucleosome, revealing that the HP1α dimer interfaces with nucleosomes at two distinct sites. The primary binding site is located at the N-terminus of histone H3, specifically at the trimethylated K9 (K9me3) region, while a novel secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. This study offers a model that explains how HP1α functions in heterochromatin maintenance and gene silencing, particularly in the context of H3K9me-dependent mechanisms. Additionally, it sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
Collapse
Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Jacob Miratsky
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Vant
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Tyler Lewis
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Kelly Dryden
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903 USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Shayan Sarkar
- Department of Pathology, Stony Brook University; Stony Brook, New York, 11794 USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| |
Collapse
|
5
|
García Fernández F, Huet S, Miné-Hattab J. Multi-Scale Imaging of the Dynamic Organization of Chromatin. Int J Mol Sci 2023; 24:15975. [PMID: 37958958 PMCID: PMC10649806 DOI: 10.3390/ijms242115975] [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: 09/19/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution imaging, among other new technologies developed in the last decade. In addition to challenging early assumptions of chromatin being regular and static, high spatiotemporal resolution imaging made it possible to visualize and characterize different chromatin structures such as clutches, domains and compartments. More specifically, super-resolution microscopy facilitates the study of different cellular processes at a nucleosome scale, providing a multi-scale view of chromatin behavior within the nucleus in different environments. In this review, we describe recent imaging techniques to study the dynamic organization of chromatin at high spatiotemporal resolution. We also discuss recent findings, elucidated by these techniques, on the chromatin landscape during different cellular processes, with an emphasis on the DNA damage response.
Collapse
Affiliation(s)
- Fabiola García Fernández
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, 35000 Rennes, France;
- Institut Universitaire de France, 75231 Paris, France
| | - Judith Miné-Hattab
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
| |
Collapse
|
6
|
Li Y, Zhang H, Li X, Wu W, Zhu P. Cryo-ET study from in vitro to in vivo revealed a general folding mode of chromatin with two-start helical architecture. Cell Rep 2023; 42:113134. [PMID: 37708029 DOI: 10.1016/j.celrep.2023.113134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/19/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
The organization and dynamics of chromatin fiber play crucial roles in regulating DNA accessibility for gene expression. Here we combine cryoelectron tomography (cryo-ET), sub-volume averaging, and 3D segmentation to visualize the in vitro and in vivo chromatin fibers folding by linker histone. We discover that an increased nucleosome repeat length and prolonged fiber length do not change the two-start helical architecture in reconstituted chromatin of homogeneous composition. Additionally, an isolated chromatin fiber with heterogeneous composition was observed, which includes short-range regions compatible with two-start helix. In vivo, sub-volume averaging reveals similar subunits of two-start helical architecture in transcriptionally inactive chromatin in frog erythrocyte nuclei. Strikingly, unambiguous DNA trajectories that displayed a zigzag pattern universally between alternate N/N+2 nucleosomes were further determined by cryo-ET with voltage phase plate. Therefore, these structural similarities suggest a general folding mode of chromatin induced by linker histone, and heterogeneous compositions mainly affect local conformation rather than changing the overall architecture.
Collapse
Affiliation(s)
- Yan Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China
| | - Haonan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyu Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
7
|
Spicer MFD, Gerlich DW. The material properties of mitotic chromosomes. Curr Opin Struct Biol 2023; 81:102617. [PMID: 37279615 PMCID: PMC10448380 DOI: 10.1016/j.sbi.2023.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023]
Abstract
Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.
Collapse
Affiliation(s)
- Maximilian F D Spicer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. https://twitter.com/Spicer__Max
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria.
| |
Collapse
|
8
|
Kadam S, Kumari K, Manivannan V, Dutta S, Mitra MK, Padinhateeri R. Predicting scale-dependent chromatin polymer properties from systematic coarse-graining. Nat Commun 2023; 14:4108. [PMID: 37433821 PMCID: PMC10336007 DOI: 10.1038/s41467-023-39907-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
Collapse
Affiliation(s)
- Sangram Kadam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Kiran Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Vinoth Manivannan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Shuvadip Dutta
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| |
Collapse
|
9
|
Nozaki T, Shinkai S, Ide S, Higashi K, Tamura S, Shimazoe MA, Nakagawa M, Suzuki Y, Okada Y, Sasai M, Onami S, Kurokawa K, Iida S, Maeshima K. Condensed but liquid-like domain organization of active chromatin regions in living human cells. SCIENCE ADVANCES 2023; 9:eadf1488. [PMID: 37018405 PMCID: PMC10075990 DOI: 10.1126/sciadv.adf1488] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/07/2023] [Indexed: 05/31/2023]
Abstract
In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains, for various cellular functions. However, their physical nature in living cells remains unclear (e.g., condensed domains or extended fiber loops; liquid-like or solid-like). Using novel approaches combining genomics, single-nucleosome imaging, and computational modeling, we investigated the physical organization and behavior of early DNA replicated regions in human cells, which correspond to Hi-C contact domains with active chromatin marks. Motion correlation analysis of two neighbor nucleosomes shows that nucleosomes form physically condensed domains with ~150-nm diameters, even in active chromatin regions. The mean-square displacement analysis between two neighbor nucleosomes demonstrates that nucleosomes behave like a liquid in the condensed domain on the ~150 nm/~0.5 s spatiotemporal scale, which facilitates chromatin accessibility. Beyond the micrometers/minutes scale, chromatin seems solid-like, which may contribute to maintaining genome integrity. Our study reveals the viscoelastic principle of the chromatin polymer; chromatin is locally dynamic and reactive but globally stable.
Collapse
Affiliation(s)
- Tadasu Nozaki
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Soya Shinkai
- Laboratory for Developmental Dynamics, Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Hyogo 650-0047, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Koichi Higashi
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masa A. Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Masaki Nakagawa
- Department of Computer Science and Engineering, Fukuoka Institute of Technology, Fukuoka, Fukuoka 811-0295, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, University of Tokyo, 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562, Japan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka 565-0874, Japan
| | - Masaki Sasai
- Department of Complex Systems Science, Nagoya University, Nagoya 464-8601, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Shuichi Onami
- Laboratory for Developmental Dynamics, Center for Biosystems Dynamics Research (BDR), RIKEN, Kobe, Hyogo 650-0047, Japan
| | - Ken Kurokawa
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
10
|
Burgers TCQ, Vlijm R. Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma 2023:10.1007/s00412-023-00792-9. [PMID: 37000292 PMCID: PMC10356683 DOI: 10.1007/s00412-023-00792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]
Abstract
Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.
Collapse
Affiliation(s)
- Thomas C Q Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
| |
Collapse
|
11
|
Sitmukhambetov S, Dinh B, Lai Y, Banigan EJ, Pan Z, Jia X, Chi Y. Development and implementation of a metaphase DNA model for ionizing radiation induced DNA damage calculation. Phys Med Biol 2022; 68:10.1088/1361-6560/aca5ea. [PMID: 36533598 PMCID: PMC9969557 DOI: 10.1088/1361-6560/aca5ea] [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: 08/02/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Objective. To develop a metaphase chromosome model representing the complete genome of a human lymphocyte cell to support microscopic Monte Carlo (MMC) simulation-based radiation-induced DNA damage studies.Approach. We first employed coarse-grained polymer physics simulation to obtain a rod-shaped chromatid segment of 730 nm in diameter and 460 nm in height to match Hi-C data. We then voxelized the segment with a voxel size of 11 nm per side and connected the chromatid with 30 types of pre-constructed nucleosomes and 6 types of linker DNAs in base pair (bp) resolutions. Afterward, we piled different numbers of voxelized chromatid segments to create 23 pairs of chromosomes of 1-5μm long. Finally, we arranged the chromosomes at the cell metaphase plate of 5.5μm in radius to create the complete set of metaphase chromosomes. We implemented the model in gMicroMC simulation by denoting the DNA structure in a four-level hierarchical tree: nucleotide pairs, nucleosomes and linker DNAs, chromatid segments, and chromosomes. We applied the model to compute DNA damage under different radiation conditions and compared the results to those obtained with G0/G1 model and experimental measurements. We also performed uncertainty analysis for relevant simulation parameters.Main results. The chromatid segment was successfully voxelized and connected in bps resolution, containing 26.8 mega bps (Mbps) of DNA. With 466 segments, we obtained the metaphase chromosome containing 12.5 Gbps of DNA. Applying it to compute the radiation-induced DNA damage, the obtained results were self-consistent and agreed with experimental measurements. Through the parameter uncertainty study, we found that the DNA damage ratio between metaphase and G0/G1 phase models was not sensitive to the chemical simulation time. The damage was also not sensitive to the specific parameter settings in the polymer physics simulation, as long as the produced metaphase model followed a similar contact map distribution.Significance. Experimental data reveal that ionizing radiation induced DNA damage is cell cycle dependent. Yet, DNA chromosome models, except for the G0/G1 phase, are not available in the state-of-the-art MMC simulation. For the first time, we successfully built a metaphase chromosome model and implemented it into MMC simulation for radiation-induced DNA damage computation.
Collapse
Affiliation(s)
| | - Bryan Dinh
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Youfang Lai
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Edward J. Banigan
- Institute for Medical Engineering & Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zui Pan
- Graduate Nursing, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Xun Jia
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, MD 21231, USA
| | - Yujie Chi
- Department of Physics, the University of Texas at Arlington, Arlington, TX 76019, USA
| |
Collapse
|
12
|
Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
Collapse
Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| |
Collapse
|
13
|
Fleming M, Nelson F, Wallace I, Eskiw CH. Genome Tectonics: Linking Dynamic Genome Organization with Cellular Nutrients. Lifestyle Genom 2022; 16:21-34. [PMID: 36446341 DOI: 10.1159/000528011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/06/2022] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Our daily intake of food provides nutrients for the maintenance of health, growth, and development. The field of nutrigenomics aims to link dietary intake/nutrients to changes in epigenetic status and gene expression. SUMMARY Although the relationship between our diet and our genes in under intense investigation, there is still a significant aspect of our genome that has received little attention with regard to this. In the past 15 years, the importance of genome organization has become increasingly evident, with research identifying small-scale local changes to large segments of the genome dynamically repositioning within the nucleus in response to/or mediating change in gene expression. The discovery of these dynamic processes and organization maybe as significant as dynamic plate tectonics is to geology, there is little information tying genome organization to specific nutrients or dietary intake. KEY MESSAGES Here, we detail key principles of genome organization and structure, with emphasis on genome folding and organization, and link how these contribute to our future understand of nutrigenomics.
Collapse
Affiliation(s)
- Morgan Fleming
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Fina Nelson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- 21st Street Brewery Inc., Saskatoon, Saskatchewan, Canada
| | - Iain Wallace
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Proxima Research and Development, Saskatoon, Saskatchewan, Canada
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| |
Collapse
|
14
|
Takizawa Y, Kurumizaka H. Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194851. [PMID: 35952957 DOI: 10.1016/j.bbagrm.2022.194851] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Chromatin is a dynamic molecular complex composed of DNA and proteins that package the DNA in the nucleus of eukaryotic cells. The basic structural unit of chromatin is the nucleosome core particle, composed of ~150 base pairs of genomic DNA wrapped around a histone octamer containing two copies each of four histones, H2A, H2B, H3, and H4. Individual nucleosome core particles are connected by short linker DNAs, forming a nucleosome array known as a beads-on-a-string fiber. Higher-order structures of chromatin are closely linked to nuclear events such as replication, transcription, recombination, and repair. Recently, a variety of chromatin structures have been determined by single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), and their structural details have provided clues about the chromatin architecture functions in the cell. In this review, we highlight recent cryo-EM structural studies of a fundamental chromatin unit to clarify the functions of chromatin.
Collapse
Affiliation(s)
- Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| |
Collapse
|
15
|
Zhang M, Díaz-Celis C, Onoa B, Cañari-Chumpitaz C, Requejo KI, Liu J, Vien M, Nogales E, Ren G, Bustamante C. Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography. Mol Cell 2022; 82:3000-3014.e9. [PMID: 35907400 DOI: 10.1016/j.molcel.2022.06.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/09/2022] [Accepted: 06/28/2022] [Indexed: 12/16/2022]
Abstract
It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.
Collapse
Affiliation(s)
- Meng Zhang
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - César Díaz-Celis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Bibiana Onoa
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Katherinne I Requejo
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael Vien
- Department of Physics, University of California, Berkeley, CA, USA
| | - Eva Nogales
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos Bustamante
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA; Department of Physics, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, USA.
| |
Collapse
|
16
|
Williams MR, Xiaokang Y, Hathaway NA, Kireev D. A simulation model of heterochromatin formation at submolecular detail. iScience 2022; 25:104590. [PMID: 35800764 PMCID: PMC9254115 DOI: 10.1016/j.isci.2022.104590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/16/2021] [Accepted: 06/08/2022] [Indexed: 11/15/2022] Open
Abstract
Heterochromatin is a physical state of the chromatin fiber that maintains gene repression during cell development. Although evidence exists on molecular mechanisms involved in heterochromatin formation, a detailed structural mechanism of heterochromatin formation needs a better understanding. We made use of a simple Monte Carlo simulation model with explicit representation of key molecular events to observe molecular self-organization leading to heterochromatin formation. Our simulations provide a structural interpretation of several important traits of the heterochromatinization process. In particular, this study provides a depiction of how small amounts of HP1 are able to induce a highly condensed chromatin state through HP1 dimerization and bridging of sequence-remote nucleosomes. It also elucidates structural roots of a yet poorly understood phenomenon of a nondeterministic nature of heterochromatin formation and subsequent gene repression. Experimental chromatin in vivo assay provides an unbiased estimate of time scale of repressive response to a heterochromatin-triggering event.
Collapse
Affiliation(s)
- Michael R. Williams
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
| | - Yan Xiaokang
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
17
|
Higher-order structure of barley chromosomes observed by electron tomography. Micron 2022; 160:103328. [PMID: 35905587 DOI: 10.1016/j.micron.2022.103328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022]
Abstract
The higher order structure of the metaphase chromosome has been an enigma for over a century and several different models have been presented based on results obtained by a variety of techniques. Some disagreements in the results between methods have possibly arisen from artifacts caused during sample preparation such as staining and dehydration. Therefore, we treated barley chromosomes with ionic liquid to minimize the effects of dehydration. We also observed chromosomes on a film with holes to keep pristine chromosome structure from being flattened as seen when placed on a continuous support film. A chromosome placed over a hole in a thin carbon film was mounted on a tomography holder, and its structure was observed in three dimensions (3D) using electron tomography. We found that there are periodic structures with 300-400 nm pitch along the axis in barley chromosomes. The pitch sizes are larger than those observed in human chromosomes.
Collapse
|
18
|
Razin SV, Zhegalova IV, Kantidze OL. Domain Model of Eukaryotic Genome Organization: From DNA Loops Fixed on the Nuclear Matrix to TADs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:667-680. [PMID: 36154886 DOI: 10.1134/s0006297922070082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 06/16/2023]
Abstract
The article reviews the development of ideas on the domain organization of eukaryotic genome, with special attention on the studies of DNA loops anchored to the nuclear matrix and their role in the emergence of the modern model of eukaryotic genome spatial organization. Critical analysis of results demonstrating that topologically associated chromatin domains are structural-functional blocks of the genome supports the notion that these blocks are fundamentally different from domains whose existence was proposed by the domain hypothesis of eukaryotic genome organization formulated in the 1980s. Based on the discussed evidence, it is concluded that the model postulating that eukaryotic genome is built from uniformly organized structural-functional blocks has proven to be untenable.
Collapse
Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Zhegalova
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Kharkevich Institute for Information Transmission Problems, Moscow, 127051, Russia
| | - Omar L Kantidze
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| |
Collapse
|
19
|
Iida S, Shinkai S, Itoh Y, Tamura S, Kanemaki MT, Onami S, Maeshima K. Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. SCIENCE ADVANCES 2022; 8:eabn5626. [PMID: 35658044 PMCID: PMC9166292 DOI: 10.1126/sciadv.abn5626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Dynamic chromatin behavior plays a critical role in various genome functions. However, it remains unclear how chromatin behavior changes during interphase, where the nucleus enlarges and genomic DNA doubles. While the previously reported chromatin movements varied during interphase when measured using a minute or longer time scale, we unveil that local chromatin motion captured by single-nucleosome imaging/tracking on a second time scale remained steady throughout G1, S, and G2 phases in live human cells. This motion mode appeared to change beyond this time scale. A defined genomic region also behaved similarly. Combined with Brownian dynamics modeling, our results suggest that this steady-state chromatin motion was mainly driven by thermal fluctuations. Steady-state motion temporarily increased following a DNA damage response. Our findings support the viscoelastic properties of chromatin. We propose that the observed steady-state chromatin motion allows cells to conduct housekeeping functions, such as transcription and DNA replication, under similar environments during interphase.
Collapse
Affiliation(s)
- Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
| | - Soya Shinkai
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Masato T. Kanemaki
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
| | - Shuichi Onami
- Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI, Mishima, Japan
- Corresponding author.
| |
Collapse
|
20
|
Ide S, Tamura S, Maeshima K. Chromatin behavior in living cells: Lessons from single‐nucleosome imaging and tracking. Bioessays 2022; 44:e2200043. [DOI: 10.1002/bies.202200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
| |
Collapse
|
21
|
Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy. Sci Rep 2022; 12:8582. [PMID: 35595799 PMCID: PMC9122977 DOI: 10.1038/s41598-022-12568-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.
Collapse
|
22
|
Razin SV, Kantidze OL. The twisted path of the 3D genome: where does it lead? Trends Biochem Sci 2022; 47:736-744. [DOI: 10.1016/j.tibs.2022.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/19/2022] [Accepted: 04/11/2022] [Indexed: 01/01/2023]
|
23
|
Naor T, Nogin Y, Nehme E, Ferdman B, Weiss LE, Alalouf O, Shechtman Y. Quantifying cell-cycle-dependent chromatin dynamics during interphase by live 3D tracking. iScience 2022; 25:104197. [PMID: 35494233 PMCID: PMC9051635 DOI: 10.1016/j.isci.2022.104197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/02/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
The study of cell cycle progression and regulation is important to our understanding of fundamental biophysics, aging, and disease mechanisms. Local chromatin movements are generally considered to be constrained and relatively consistent during all interphase stages, although recent advances in our understanding of genome organization challenge this claim. Here, we use high spatiotemporal resolution, 4D (x, y, z and time) localization microscopy by point-spread-function (PSF) engineering and deep learning-based image analysis, for live imaging of mouse embryonic fibroblast (MEF 3T3) and MEF 3T3 double Lamin A Knockout (LmnaKO) cell lines, to characterize telomere diffusion during the interphase. We detected varying constraint levels imposed on chromatin, which are prominently decreased during G0/G1. Our 4D measurements of telomere diffusion offer an effective method to investigate chromatin dynamics and reveal cell-cycle-dependent motion constraints, which may be caused by various cellular processes. PSF engineering allows scan-free, high spatiotemporal live 3D telomere tracking During the G0/G1 phase, telomere motion is less constrained than in other phases There is observable difference between lateral (xy) and axial (z) chromatin motion In Lamin A-depleted cells, motion constraint was reduced
Collapse
|
24
|
Foe VE. Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation? Integr Org Biol 2022; 4:obac008. [PMID: 36827645 PMCID: PMC8998493 DOI: 10.1093/iob/obac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This essay aims to explain two biological puzzles: why eukaryotic transcription units are composed of short segments of coding DNA interspersed with long stretches of non-coding (intron) DNA, and the near ubiquity of sexual reproduction. As is well known, alternative splicing of its coding sequences enables one transcription unit to produce multiple variants of each encoded protein. Additionally, padding transcription units with non-coding DNA (often many thousands of base pairs long) provides a readily evolvable way to set how soon in a cell cycle the various mRNAs will begin being expressed and the total amount of mRNA that each transcription unit can make during a cell cycle. This regulation complements control via the transcriptional promoter and facilitates the creation of complex eukaryotic cell types, tissues, and organisms. However, it also makes eukaryotes exceedingly vulnerable to double-strand DNA breaks, which end-joining break repair pathways can repair incorrectly. Transcription units cover such a large fraction of the genome that any mis-repair producing a reorganized chromosome has a high probability of destroying a gene. During meiosis, the synaptonemal complex aligns homologous chromosome pairs and the pachytene checkpoint detects, selectively arrests, and in many organisms actively destroys gamete-producing cells with chromosomes that cannot adequately synapse; this creates a filter favoring transmission to the next generation of chromosomes that retain the parental organization, while selectively culling those with interrupted transcription units. This same meiotic checkpoint, reacting to accidental chromosomal reorganizations inflicted by error-prone break repair, can, as a side effect, provide a mechanism for the formation of new species in sympatry. It has been a long-standing puzzle how something as seemingly maladaptive as hybrid sterility between such new species can arise. I suggest that this paradox is resolved by understanding the adaptive importance of the pachytene checkpoint, as outlined above.
Collapse
|
25
|
Zakirov AN, Sosnovskaya S, Ryumina ED, Kharybina E, Strelkova OS, Zhironkina OA, Golyshev SA, Moiseenko A, Kireev II. Fiber-Like Organization as a Basic Principle for Euchromatin Higher-Order Structure. Front Cell Dev Biol 2022; 9:784440. [PMID: 35174159 PMCID: PMC8841976 DOI: 10.3389/fcell.2021.784440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
A detailed understanding of the principles of the structural organization of genetic material is of great importance for elucidating the mechanisms of differential regulation of genes in development. Modern ideas about the spatial organization of the genome are based on a microscopic analysis of chromatin structure and molecular data on DNA–DNA contact analysis using Chromatin conformation capture (3C) technology, ranging from the “polymer melt” model to a hierarchical folding concept. Heterogeneity of chromatin structure depending on its functional state and cell cycle progression brings another layer of complexity to the interpretation of structural data and requires selective labeling of various transcriptional states under nondestructive conditions. Here, we use a modified approach for replication timing-based metabolic labeling of transcriptionally active chromatin for ultrastructural analysis. The method allows pre-embedding labeling of optimally structurally preserved chromatin, thus making it compatible with various 3D-TEM techniques including electron tomography. By using variable pulse duration, we demonstrate that euchromatic genomic regions adopt a fiber-like higher-order structure of about 200 nm in diameter (chromonema), thus providing support for a hierarchical folding model of chromatin organization as well as the idea of transcription and replication occurring on a highly structured chromatin template.
Collapse
Affiliation(s)
- Amir N Zakirov
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Chair of Cell Biology and Histology, Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Sophie Sosnovskaya
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Chair of Cell Biology and Histology, Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina D Ryumina
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Kharybina
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Chair of Cell Biology and Histology, Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Olga S Strelkova
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Oxana A Zhironkina
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergei A Golyshev
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey Moiseenko
- Laboratory of Electron Microscopy, Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Igor I Kireev
- Department of Electron Microscopy, AN. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Chair of Cell Biology and Histology, Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
26
|
The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations. Methods Mol Biol 2022; 2301:235-258. [PMID: 34415539 DOI: 10.1007/978-1-0716-1390-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fluorescence in situ hybridization and chromosome conformation capture methods point to the same conclusion: that chromosomes appear to the external observer as compact structures with a highly nonrandom three-dimensional organization. In this work, we recapitulate the efforts made by us and other groups to rationalize this behavior in terms of the mathematical language and tools of polymer physics. After a brief introduction dedicated to some crucial experiments dissecting the structure of interphase chromosomes, we discuss at a nonspecialistic level some fundamental aspects of theoretical and numerical polymer physics. Then, we inglobe biological and polymer aspects into a polymer model for interphase chromosomes which moves from the observation that mutual topological constraints, such as those typically present between polymer chains in ordinary melts, induce slow chain dynamics and "constraint" chromosomes to resemble double-folded randomly branched polymer conformations. By explicitly turning these ideas into a multi-scale numerical algorithm which is described here in full details, we can design accurate model polymer conformations for interphase chromosomes and offer them for systematic comparison to experiments. The review is concluded by discussing the limitations of our approach and pointing to promising perspectives for future work.
Collapse
|
27
|
Leonova OG, Potekhin AA, Nekrasova IV, Karajan BP, Syomin BV, Prassolov VS, Popenko VI. Packaging of Subchromosomal-Size DNA Molecules in Chromatin Bodies in the Ciliate Macronucleus. Mol Biol 2021. [DOI: 10.1134/s0026893321050083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
28
|
Iashina EG, Varfolomeeva EY, Pantina RA, Bairamukov VY, Kovalev RA, Fedorova ND, Pipich V, Radulescu A, Grigoriev SV. Bifractal structure of chromatin in rat lymphocyte nuclei. Phys Rev E 2021; 104:064409. [PMID: 35030913 DOI: 10.1103/physreve.104.064409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/29/2021] [Indexed: 11/07/2022]
Abstract
The small-angle neutron scattering (SANS) on the rat lymphocyte nuclei demonstrates the bifractal nature of the chromatin structural organization. The scattering intensity from rat lymphocyte nuclei is described by power law Q^{-D} with fractal dimension approximately 2.3 on smaller scales and 3 on larger scales. The crossover between two fractal structures is detected at momentum transfer near 10^{-1}nm^{-1}. The use of contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals clear similarity in the structural organizations of nucleic acids (NA) and proteins. Both chromatin components show bifractal behavior with logarithmic fractal structure on the large scale and volume fractal with slightly smaller than 2.5 structure on the small scale. Scattering intensities from chromatin, protein component, and NA component demonstrate an extremely extensive range of logarithmic fractal behavior (from 10^{-3} to approximately 10^{-1}nm^{-1}). We compare the fractal arrangement of rat lymphocyte nuclei with that of chicken erythrocytes and the immortal HeLa cell line. We conclude that the bifractal nature of the chromatin arrangement is inherent in the nuclei of all these cells. The details of the fractal arrangement-its range and correlation/interaction between nuclear acids and proteins are specific for different cells and is related to their functionality.
Collapse
Affiliation(s)
- E G Iashina
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia.,Saint-Petersburg State University (SPSU), Ulyanovskaya str. 1, 198504, Saint-Petersburg, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - V Yu Bairamukov
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - R A Kovalev
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - N D Fedorova
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - V Pipich
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, D-85748 Garching, Germany
| | - A Radulescu
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, D-85748 Garching, Germany
| | - S V Grigoriev
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia.,Saint-Petersburg State University (SPSU), Ulyanovskaya str. 1, 198504, Saint-Petersburg, Russia
| |
Collapse
|
29
|
Grigoriev SV, Iashina EG, Wu B, Pipich V, Lang C, Radulescu A, Bairamukov VY, Filatov MV, Pantina RA, Varfolomeeva EY. Observation of nucleic acid and protein correlation in chromatin of HeLa nuclei using small-angle neutron scattering with D_{2}O-H_{2}O contrast variation. Phys Rev E 2021; 104:044404. [PMID: 34781557 DOI: 10.1103/physreve.104.044404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023]
Abstract
The small-angle neutron scattering (SANS) on HeLa nuclei demonstrates the bifractal nature of the chromatin structural organization. The border line between two fractal structures is detected as a crossover point at Q_{c}≈4×10^{-2}nm^{-1} in the momentum transfer dependence Q^{-D}. The use of contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals clear similarity in the large scale structural organizations of nucleic acids (NA) and proteins. Both NA and protein structures have a mass fractal arrangement with the fractal dimension of D≈2.5 at scales smaller than 150 nm down to 20 nm. Both NA and proteins show a logarithmic fractal behavior with D≈3 at scales larger than 150 nm up to 6000 nm. The combined analysis of the SANS and atomic force microscopy data allows one to conclude that chromatin and its constitutes (DNA and proteins) are characterized as soft, densely packed, logarithmic fractals on the large scale and as rigid, loosely packed, mass fractals on the smaller scale. The comparison of the partial cross sections from NA and proteins with one from chromatin as a whole demonstrates spatial correlation of two chromatin's components in the range up to 900 nm. Thus chromatin in HeLa nuclei is built as the unified structure of the NA and proteins entwined through each other. Correlation between two components is lost upon scale increases toward 6000 nm. The structural features at the large scale, probably, provide nuclei with the flexibility and chromatin-free space to build supercorrelations on the distance of 10^{3} nm resembling cycle cell activity, such as an appearance of nucleoli and a DNA replication.
Collapse
Affiliation(s)
- S V Grigoriev
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia.,Saint-Petersburg State University, Ulyanovskaya 1, Saint-Petersburg 198504, Russia
| | - E G Iashina
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia.,Saint-Petersburg State University, Ulyanovskaya 1, Saint-Petersburg 198504, Russia
| | - B Wu
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - V Pipich
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - Ch Lang
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - A Radulescu
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - V Yu Bairamukov
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - M V Filatov
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| |
Collapse
|
30
|
Stochastic chromatin packing of 3D mitotic chromosomes revealed by coherent X-rays. Proc Natl Acad Sci U S A 2021; 118:2109921118. [PMID: 34750262 DOI: 10.1073/pnas.2109921118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
DNA molecules are atomic-scale information storage molecules that promote reliable information transfer via fault-free repetitions of replications and transcriptions. Remarkable accuracy of compacting a few-meters-long DNA into a micrometer-scale object, and the reverse, makes the chromosome one of the most intriguing structures from both physical and biological viewpoints. However, its three-dimensional (3D) structure remains elusive with challenges in observing native structures of specimens at tens-of-nanometers resolution. Here, using cryogenic coherent X-ray diffraction imaging, we succeeded in obtaining nanoscale 3D structures of metaphase chromosomes that exhibited a random distribution of electron density without characteristics of high-order folding structures. Scaling analysis of the chromosomes, compared with a model structure having the same density profile as the experimental results, has discovered the fractal nature of density distributions. Quantitative 3D density maps, corroborated by molecular dynamics simulations, reveal that internal structures of chromosomes conform to diffusion-limited aggregation behavior, which indicates that 3D chromatin packing occurs via stochastic processes.
Collapse
|
31
|
Arimura Y, Shih RM, Froom R, Funabiki H. Structural features of nucleosomes in interphase and metaphase chromosomes. Mol Cell 2021; 81:4377-4397.e12. [PMID: 34478647 PMCID: PMC8571072 DOI: 10.1016/j.molcel.2021.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022]
Abstract
Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.
Collapse
Affiliation(s)
- Yasuhiro Arimura
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Rochelle M Shih
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
32
|
Beel AJ, Azubel M, Matteï PJ, Kornberg RD. Structure of mitotic chromosomes. Mol Cell 2021; 81:4369-4376.e3. [PMID: 34520722 DOI: 10.1016/j.molcel.2021.08.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/28/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022]
Abstract
Chromatin fibers must fold or coil in the process of chromosome condensation. Patterns of coiling have been demonstrated for reconstituted chromatin, but the actual trajectories of fibers in condensed states of chromosomes could not be visualized because of the high density of the material. We have exploited partial decondensation of mitotic chromosomes to reveal their internal structure at sub-nucleosomal resolution by cryo-electron tomography, without the use of stains, fixatives, milling, or sectioning. DNA gyres around nucleosomes were visible, allowing the nucleosomes to be identified and their orientations to be determined. Linker DNA regions were traced, revealing the trajectories of the chromatin fibers. The trajectories were irregular, with almost no evidence of coiling and no short- or long-range order of the chromosomal material. The 146-bp core particle, long known as a product of nuclease digestion, is identified as the native state of the nucleosome, with no regular spacing along the chromatin fibers.
Collapse
Affiliation(s)
- Andrew J Beel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Maia Azubel
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
| | - Pierre-Jean Matteï
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
33
|
Hansen JC, Maeshima K, Hendzel MJ. The solid and liquid states of chromatin. Epigenetics Chromatin 2021; 14:50. [PMID: 34717733 PMCID: PMC8557566 DOI: 10.1186/s13072-021-00424-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chromatin aggregation studies, discuss the evidence that chromatin aggregation intrinsically is a physiologically relevant liquid-solid phase separation (LSPS) process driven by chromatin self-interaction, and highlight the recent findings that under specific solution conditions chromatin can undergo liquid-liquid phase separation (LLPS) rather than LSPS. In the next section of the review, we discuss how certain chromatin-associated proteins undergo LLPS in vitro and in vivo. Some chromatin-binding proteins undergo LLPS in purified form in near-physiological ionic strength buffers while others will do so only in the presence of DNA, nucleosomes, or chromatin. The final section of the review evaluates the solid and liquid states of chromatin in the nucleus. While chromatin behaves as an immobile solid on the mesoscale, nucleosomes are mobile on the nanoscale. We discuss how this dual nature of chromatin, which fits well the concept of viscoelasticity, contributes to genome structure, emphasizing the dominant role of chromatin self-interaction.
Collapse
Affiliation(s)
- Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
34
|
Abstract
Condensation and faithful separation of the genome are crucial for the cellular life cycle. During chromosome segregation, mechanical forces generated by the mitotic spindle pull apart the sister chromatids. The mechanical nature of this process has motivated a lot of research interest into the mechanical properties of mitotic chromosomes. Although their fundamental mechanical characteristics are known, it still remains unclear how these characteristics emerge from the structure of the mitotic chromosome. Recent advances in genomics, computational and super-resolution microscopy techniques have greatly promoted our understanding of the chromosomal structure and have motivated us to review the mechanical characteristics of chromosomes in light of the current structural insights. In this review, we will first introduce the current understanding of the chromosomal structure, before reviewing characteristic mechanical properties such as the Young's modulus and the bending modulus of mitotic chromosomes. Then we will address the approaches used to relate mechanical properties to the structure of chromosomes and we will also discuss how mechanical characterization can aid in elucidating their structure. Finally, future challenges, recent developments and emergent questions in this research field will be discussed.
Collapse
|
35
|
Itoh Y, Woods EJ, Minami K, Maeshima K, Collepardo-Guevara R. Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling? Curr Opin Struct Biol 2021; 71:123-135. [PMID: 34303931 DOI: 10.1016/j.sbi.2021.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
Chromatin in eukaryotic cells is a negatively charged long polymer consisting of DNA, histones, and various associated proteins. With its highly charged and heterogeneous nature, chromatin structure varies greatly depending on various factors (e.g. chemical modifications and protein enrichment) and the surrounding environment (e.g. cations): from a 10-nm fiber, a folded 30-nm fiber, to chromatin condensates/droplets. Recent advanced imaging has observed that chromatin exhibits a dynamic liquid-like behavior and undergoes structural variations within the cell. Current computational modeling has made it possible to reconstruct the liquid-like chromatin in the cell by dealing with a number of nucleosomes on multiscale levels and has become a powerful technique to inspect the molecular mechanisms giving rise to the observed behavior, which imaging methods cannot do on their own. Based on new findings from both imaging and modeling studies, we discuss the dynamic aspect of chromatin in living cells and its functional relevance.
Collapse
Affiliation(s)
- Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK; Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
| |
Collapse
|
36
|
Daban JR. Soft-matter properties of multilayer chromosomes. Phys Biol 2021; 18. [PMID: 34126606 DOI: 10.1088/1478-3975/ac0aff] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 06/14/2021] [Indexed: 12/17/2022]
Abstract
This perspective aims to identify the relationships between the structural and dynamic properties of chromosomes and the fundamental properties of soft-matter systems. Chromatin is condensed into metaphase chromosomes during mitosis. The resulting structures are elongated cylinders having micrometer-scale dimensions. Our previous studies, using transmission electron microscopy, atomic force microscopy, and cryo-electron tomography, suggested that metaphase chromosomes have a multilayered structure, in which each individual layer has the width corresponding to a mononucleosome sheet. The self-assembly of multilayer chromatin plates from small chromatin fragments suggests that metaphase chromosomes are self-organized hydrogels (in which a single DNA molecule crosslinks the whole structure) with an internal liquid-crystal order produced by the stacking of chromatin layers along the chromosome axis. This organization of chromatin was unexpected, but the spontaneous assembly of large structures has been studied in different soft-matter systems and, according to these studies, the self-organization of chromosomes could be justified by the interplay between weak interactions of repetitive nucleosome building blocks and thermal fluctuations. The low energy of interaction between relatively large building blocks also justifies the easy deformation and structural fluctuations of soft-matter structures and the changes of phase caused by diverse external factors. Consistent with these properties of soft matter, different experimental results show that metaphase chromosomes are easily deformable. Furthermore, at the end of mitosis, condensed chromosomes undergo a phase transition into a more fluid structure, which can be correlated to the decrease in the Mg2+concentration and to the dissociation of condensins from chromosomes. Presumably, the unstacking of layers and chromatin fluctuations driven by thermal energy facilitate gene expression during interphase.
Collapse
Affiliation(s)
- Joan-Ramon Daban
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
| |
Collapse
|
37
|
Lin X, Qi Y, Latham AP, Zhang B. Multiscale modeling of genome organization with maximum entropy optimization. J Chem Phys 2021; 155:010901. [PMID: 34241389 PMCID: PMC8253599 DOI: 10.1063/5.0044150] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional (3D) organization of the human genome plays an essential role in all DNA-templated processes, including gene transcription, gene regulation, and DNA replication. Computational modeling can be an effective way of building high-resolution genome structures and improving our understanding of these molecular processes. However, it faces significant challenges as the human genome consists of over 6 × 109 base pairs, a system size that exceeds the capacity of traditional modeling approaches. In this perspective, we review the progress that has been made in modeling the human genome. Coarse-grained models parameterized to reproduce experimental data via the maximum entropy optimization algorithm serve as effective means to study genome organization at various length scales. They have provided insight into the principles of whole-genome organization and enabled de novo predictions of chromosome structures from epigenetic modifications. Applications of these models at a near-atomistic resolution further revealed physicochemical interactions that drive the phase separation of disordered proteins and dictate chromatin stability in situ. We conclude with an outlook on the opportunities and challenges in studying chromosome dynamics.
Collapse
Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
38
|
Alvarado W, Moller J, Ferguson AL, de Pablo JJ. Tetranucleosome Interactions Drive Chromatin Folding. ACS CENTRAL SCIENCE 2021; 7:1019-1027. [PMID: 34235262 PMCID: PMC8227587 DOI: 10.1021/acscentsci.1c00085] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Indexed: 06/10/2023]
Abstract
The multiscale organizational structure of chromatin in eukaryotic cells is instrumental to DNA transcription, replication, and repair. At mesoscopic length scales, nucleosomes pack in a manner that serves to regulate gene expression through condensation and expansion of the genome. The particular structures that arise and their respective thermodynamic stabilities, however, have yet to be fully resolved. In this study, we combine molecular modeling using the 1CPN mesoscale model of chromatin with nonlinear manifold learning to identify and characterize the structure and free energy of metastable states of short chromatin segments comprising between 4- and 16-nucleosomes. Our results reveal the formation of two previously characterized tetranucleosomal conformations, the "α-tetrahedron" and the "β-rhombus", which have been suggested to play an important role in the accessibility of DNA and, respectively, induce local chromatin compaction or elongation. The spontaneous formation of these motifs is potentially responsible for the slow nucleosome dynamics observed in experimental studies. Increases of the nucleosome repeat length are accompanied by more pronounced structural irregularity and flexibility and, ultimately, a dynamic liquid-like behavior that allows for frequent structural reorganization. Our findings indicate that tetranucleosome motifs are intrinsically stable structural states, driven by local internucleosomal interactions, and support a mechanistic picture of chromatin packing, dynamics, and accessibility that is strongly influenced by emergent local mesoscale structure.
Collapse
Affiliation(s)
- Walter Alvarado
- Biophysical
Sciences, University of Chicago, Chicago, Illinois 60637 United States
| | - Joshua Moller
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637 United States
| | - Andrew L. Ferguson
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637 United States
| | - Juan J. de Pablo
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637 United States
| |
Collapse
|
39
|
Interphase epichromatin: last refuge for the 30-nm chromatin fiber? Chromosoma 2021; 130:91-102. [PMID: 34091761 DOI: 10.1007/s00412-021-00759-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/30/2021] [Accepted: 05/16/2021] [Indexed: 01/08/2023]
Abstract
"Interphase epichromatin" describes the surface of chromatin located adjacent to the interphase nuclear envelope. It was discovered in 2011 using a bivalent anti-nucleosome antibody (mAb PL2-6), now known to be directed against the nucleosome acidic patch. The molecular structure of interphase epichromatin is unknown, but is thought to be heterochromatic with a high density of "exposed" acidic patches. In the 1960s, transmission electron microscopy of fixed, dehydrated, sectioned, and stained inactive chromatin revealed "unit threads," frequently organized into parallel arrays at the nuclear envelope, which were interpreted as regular helices with ~ 30-nm center-to-center distance. Also observed in certain cell types, the nuclear envelope forms a "sandwich" around a layer of closely packed unit threads (ELCS, envelope-limited chromatin sheets). Discovery of the nucleosome in 1974 led to revised helical models of chromatin. But these models became very controversial and the existence of in situ 30-nm chromatin fibers has been challenged. Development of cryo-electron microscopy (Cryo-EM) gave hope that in situ chromatin fibers, devoid of artifacts, could be structurally defined. Combining a contrast-enhancing phase plate and cryo-electron tomography (Cryo-ET), it is now possible to visualize chromatin in a "close-to-native" situation. ELCS are particularly interesting to study by Cryo-ET. The chromatin sheet appears to have two layers of ~ 30-nm chromatin fibers arranged in a criss-crossed pattern. The chromatin in ELCS is continuous with adjacent interphase epichromatin. It appears that hydrated ~ 30-nm chromatin fibers are quite rare in most cells, possibly confined to interphase epichromatin at the nuclear envelope.
Collapse
|
40
|
Rakshit T, Melters DP, Dimitriadis EK, Dalal Y. Mechanical properties of nucleoprotein complexes determined by nanoindentation spectroscopy. Nucleus 2021; 11:264-282. [PMID: 32954931 PMCID: PMC7529419 DOI: 10.1080/19491034.2020.1816053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The interplay between transcription factors, chromatin remodelers, 3-D organization, and mechanical properties of the chromatin fiber controls genome function in eukaryotes. Besides the canonical histones which fold the bulk of the chromatin into nucleosomes, histone variants create distinctive chromatin domains that are thought to regulate transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether histone variants translate distinctive biochemical or biophysical properties to their associated chromatin structures, and whether these properties impact chromatin dynamics as the genome undergoes a multitude of transactions, is an important question in biology. Here, we describe single-molecule nanoindentation tools that we developed specifically to determine the mechanical properties of histone variant nucleosomes and their complexes. These methods join an array of cutting-edge new methods that further our quantitative understanding of the response of chromatin to intrinsic and extrinsic forces which act upon it during biological transactions in the nucleus.
Collapse
Affiliation(s)
- Tatini Rakshit
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA.,Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Salt Lake, India
| | - Daniël P Melters
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
| |
Collapse
|
41
|
Abstract
In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome-nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. In this review, we provide a summary of recent progress on the structure of chromatin fibers in vitro and in the nucleus, highlight studies on the dynamic regulation of chromatin fibers, and discuss their related biological functions and abnormal organization in diseases.
Collapse
Affiliation(s)
- Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China; .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Wei Li
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; .,Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; .,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
42
|
Abstract
Genomic information is encoded on long strands of DNA, which are folded into chromatin and stored in a tiny nucleus. Nuclear chromatin is a negatively charged polymer composed of DNA, histones, and various nonhistone proteins. Because of its highly charged nature, chromatin structure varies greatly depending on the surrounding environment (e.g., cations, molecular crowding, etc.). New technologies to capture chromatin in living cells have been developed over the past 10 years. Our view on chromatin organization has drastically shifted from a regular and static one to a more variable and dynamic one. Chromatin forms numerous compact dynamic domains that act as functional units of the genome in higher eukaryotic cells and locally appear liquid-like. By changing DNA accessibility, these domains can govern various functions. Based on new evidences from versatile genomics and advanced imaging studies, we discuss the physical nature of chromatin in the crowded nuclear environment and how it is regulated.
Collapse
Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
43
|
Phengchat R, Malac M, Hayashida M. Chromosome inner structure investigation by electron tomography and electron diffraction in a transmission electron microscope. Chromosome Res 2021; 29:63-80. [PMID: 33733375 DOI: 10.1007/s10577-021-09661-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/19/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
Our understanding of the inner structure of metaphase chromosomes remains inconclusive despite intensive studies using multiple imaging techniques. Transmission electron microscopy has been extensively used to visualize chromosome ultrastructure. This review summarizes recent results obtained using two transmission electron microscopy-based techniques: electron tomography and electron diffraction. Electron tomography allows advanced three-dimensional imaging of chromosomes, while electron diffraction detects the presence of periodic structures within chromosomes. The combination of these two techniques provides results contributing to the understanding of local structural organization of chromatin fibers within chromosomes.
Collapse
Affiliation(s)
- Rinyaporn Phengchat
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, 657-8501, Japan.
| | - Marek Malac
- Nanotechnology Research Centre, National Research of Council, 11421 Saskatchewan Drive, T6G 2 M9, Edmonton, Alberta, Canada.,Department of Physics, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Misa Hayashida
- Nanotechnology Research Centre, National Research of Council, 11421 Saskatchewan Drive, T6G 2 M9, Edmonton, Alberta, Canada
| |
Collapse
|
44
|
Botchway SW, Farooq S, Sajid A, Robinson IK, Yusuf M. Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure. Chromosome Res 2021; 29:19-36. [PMID: 33686484 DOI: 10.1007/s10577-021-09654-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/07/2023]
Abstract
The organization of chromatin into higher-order structures and its condensation process represent one of the key challenges in structural biology. This is important for elucidating several disease states. To address this long-standing problem, development of advanced imaging methods has played an essential role in providing understanding into mitotic chromosome structure and compaction. Amongst these are two fast evolving fluorescence imaging technologies, specifically fluorescence lifetime imaging (FLIM) and super-resolution microscopy (SRM). FLIM in particular has been lacking in the application of chromosome research while SRM has been successfully applied although not widely. Both these techniques are capable of providing fluorescence imaging with nanometer information. SRM or "nanoscopy" is capable of generating images of DNA with less than 50 nm resolution while FLIM when coupled with energy transfer may provide less than 20 nm information. Here, we discuss the advantages and limitations of both methods followed by their contribution to mitotic chromosome studies. Furthermore, we highlight the future prospects of how advancements in new technologies can contribute in the field of chromosome science.
Collapse
Affiliation(s)
- S W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, UK
| | - S Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - A Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - I K Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Brookhaven National Lab, Upton, NY, 11973, USA
| | - M Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan. .,London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
| |
Collapse
|
45
|
Woods DC, Rodríguez-Ropero F, Wereszczynski J. The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array. J Mol Biol 2021; 433:166902. [PMID: 33667509 DOI: 10.1016/j.jmb.2021.166902] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 02/08/2023]
Abstract
Linker histones bind to nucleosomes and modify chromatin structure and dynamics as a means of epigenetic regulation. Biophysical studies have shown that chromatin fibers can adopt a plethora of conformations with varying levels of compaction. Linker histone condensation, and its specific binding disposition, has been associated with directly tuning this ensemble of states. However, the atomistic dynamics and quantification of this mechanism remains poorly understood. Here, we present molecular dynamics simulations of octa-nucleosome arrays, based on a cryo-EM structure of the 30-nm chromatin fiber, with and without the globular domains of the H1 linker histone to determine how they influence fiber structures and dynamics. Results show that when bound, linker histones inhibit DNA flexibility and stabilize repeating tetra-nucleosomal units, giving rise to increased chromatin compaction. Furthermore, upon the removal of H1, there is a significant destabilization of this compact structure as the fiber adopts less strained and untwisted states. Interestingly, linker DNA sampling in the octa-nucleosome is exaggerated compared to its mono-nucleosome counterparts, suggesting that chromatin architecture plays a significant role in DNA strain even in the absence of linker histones. Moreover, H1-bound states are shown to have increased stiffness within tetra-nucleosomes, but not between them. This increased stiffness leads to stronger long-range correlations within the fiber, which may result in the propagation of epigenetic signals over longer spatial ranges. These simulations highlight the effects of linker histone binding on the internal dynamics and global structure of poly-nucleosome arrays, while providing physical insight into a mechanism of chromatin compaction.
Collapse
Affiliation(s)
- Dustin C Woods
- Department of Chemistry and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States
| | - Francisco Rodríguez-Ropero
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States.
| |
Collapse
|
46
|
Imaging the inner structure of chromosomes: contribution of focused ion beam/scanning electron microscopy to chromosome research. Chromosome Res 2021; 29:51-62. [PMID: 33587224 DOI: 10.1007/s10577-021-09650-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 10/22/2022]
Abstract
Visualization of the chromosome ultrastructure has revealed new insights into its structural and functional properties. The use of new methods for revealing not only the surface but also the inner structure of the chromosome has been emerged. Some methods have long been used, such as conventional transmission electron microscopy (TEM). Although it has indispensably contributed to the revelation of the ultrastructure of the various biological samples, including chromosomes, some challenges have also been encountered, such as laborious sample preparation, limited view areas, and loss of information on some parts due to ultramicrotome sectioning. Therefore, a more advanced method is needed. Scanning electron microscopy (SEM) is also advantageous in the surface visualization of chromosome samples. However, it is limited by accessibility to gain the inner structure information. Focused ion beam/scanning electron microscopy (FIB/SEM) provides a way to investigate the inner structure of the samples in a direct slice-and-view manner to observe the ultrastructure of the inner part of the sample continuously and further construct a three-dimensional image. This method has long been used in the material science field, and recently, it has also been applied to biological research, such as in showing the inner structure of chromosomes. This review article presents the contributions of this new method to chromosome research and its recent developments in the inner structure of chromosome and discusses its current and potential applications to the high-resolution imaging of chromosomes.
Collapse
|
47
|
Nucleosome Positioning and Spacing: From Mechanism to Function. J Mol Biol 2021; 433:166847. [PMID: 33539878 DOI: 10.1016/j.jmb.2021.166847] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023]
Abstract
Eukaryotes associate their genomes with histone proteins, forming nucleosome particles. Nucleosomes regulate and protect the genetic information. They often assemble into evenly spaced arrays of nucleosomes. These regular nucleosome arrays cover significant portions of the genome, in particular over genes. The presence of these evenly spaced nucleosome arrays is highly conserved throughout the entire eukaryotic domain. Here, we review the mechanisms behind the establishment of this primary structure of chromatin with special emphasis on the biogenesis of evenly spaced nucleosome arrays. We highlight the roles that transcription, nucleosome remodelers, DNA sequence, and histone density play towards the formation of evenly spaced nucleosome arrays and summarize our current understanding of their cellular functions. We end with key unanswered questions that remain to be explored to obtain an in-depth understanding of the biogenesis and function of the nucleosome landscape.
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
Enukashvily NI, Dobrynin MA, Chubar AV. RNA-seeded membraneless bodies: Role of tandemly repeated RNA. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 126:151-193. [PMID: 34090614 DOI: 10.1016/bs.apcsb.2020.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Membraneless organelles (bodies, granules, etc.) are spatially distinct sub-nuclear and cytoplasmic foci involved in all the processes in a living cell, such as development, cell death, carcinogenesis, proliferation, and differentiation. Today the list of the membraneless organelles includes a wide spectrum of intranuclear and cytoplasmic bodies. Proteins with intrinsically disordered regions are the key players in the membraneless body assembly. However, recent data assume an important role of RNA molecules in the process of the liquid-liquid phase separation. High-level expression of RNA above a critical concentration threshold is mandatory to nucleate interactions with specific proteins and for seeding membraneless organelles. RNA components are considered by many authors as the principal determinants of organelle identity. Tandemly repeated (TR) DNA of big satellites (a TR family that includes centromeric and pericentromeric DNA sequences) was believed to be transcriptionally silent for a long period. Now we know about the TR transcription upregulation during gameto- and embryogenesis, carcinogenesis, stress response. In the review, we summarize the recent data about the involvement of TR RNA in the formation of nuclear membraneless granules, bodies, etc., with different functions being in some cases an initiator of the structures assembly. These RNP structures sequestrate and inactivate different proteins and transcripts. The TR induced sequestration is one of the key principles of nuclear architecture and genome functioning. Studying the role of the TR-based membraneless organelles in stress and disease will bring some new ideas for translational medicine.
Collapse
Affiliation(s)
- Natella I Enukashvily
- Institute of Cytology RAS, St. Petersburg, Russia; North-Western Medical State University named after I.I. Mechnikov, St. Petersburg, Russia.
| | | | | |
Collapse
|
50
|
Li Y, Eshein A, Virk RKA, Eid A, Wu W, Frederick J, VanDerway D, Gladstein S, Huang K, Shim AR, Anthony NM, Bauer GM, Zhou X, Agrawal V, Pujadas EM, Jain S, Esteve G, Chandler JE, Nguyen TQ, Bleher R, de Pablo JJ, Szleifer I, Dravid VP, Almassalha LM, Backman V. Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function. SCIENCE ADVANCES 2021; 7:eabe4310. [PMID: 33523864 PMCID: PMC7775763 DOI: 10.1126/sciadv.abe4310] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
Abstract
Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.
Collapse
Affiliation(s)
- Yue Li
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Adam Eshein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Ranya K A Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Aya Eid
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Wenli Wu
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - David VanDerway
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Scott Gladstein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Anne R Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Nicholas M Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Greta M Bauer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Xiang Zhou
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Emily M Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - George Esteve
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - John E Chandler
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - The-Quyen Nguyen
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Reiner Bleher
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
| |
Collapse
|