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Karami Y, Bignon E. Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad. Comput Struct Biotechnol J 2024; 23:1387-1396. [PMID: 38596314 PMCID: PMC11001638 DOI: 10.1016/j.csbj.2024.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Gene activity is tightly controlled by reversible chemical modifications called epigenetic marks, which are of various types and modulate gene accessibility without affecting the DNA sequence. Despite an increasing body of evidence demonstrating the role of oxidative-type modifications of histones in gene expression regulation, there remains a complete absence of structural data at the atomistic level to understand the molecular mechanisms behind their regulatory action. Owing to μs time-scale MD simulations and protein communication networks analysis, we describe the impact of histone H3 hyperoxidation (i.e., S-sulfonylation) on the nucleosome core particle dynamics. Our results reveal the atomic-scale details of the intrinsic structural networks within the canonical histone core and their perturbation by hyperoxidation of the histone H3 C110. We show that this modification involves local rearrangements of the communication networks and destabilizes the dyad, and that one modification is enough to induce a maximal structural signature. Our results suggest that cysteine hyperoxidation in the nucleosome core particle might favor its disassembly.
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Affiliation(s)
- Yasaman Karami
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France
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2
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Shi X, Fedulova AS, Kotova EY, Maluchenko NV, Armeev GA, Chen Q, Prasanna C, Sivkina AL, Feofanov AV, Kirpichnikov MP, Nordensköld L, Shaytan AK, Studitsky VM. Histone Tetrasome Dynamics Affects Chromatin Transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604164. [PMID: 39071396 PMCID: PMC11275759 DOI: 10.1101/2024.07.18.604164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
During various DNA-centered processes in the cell nucleus, the minimal structural units of chromatin organization, nucleosomes, are often transiently converted to hexasomes and tetrasomes missing one or both H2A/H2B histone dimers, respectively. However, the structural and functional properties of the subnucleosomes and their impact on biological processes in the nuclei are poorly understood. Here, using biochemical approaches, molecular dynamics simulations, single-particle Förster resonance energy transfer (spFRET) microscopy and NMR spectroscopy, we have shown that, surprisingly, removal of both dimers from a nucleosome results in much higher mobility of both histones and DNA in the tetrasome. Accordingly, DNase I footprinting shows that DNA-histone interactions in tetrasomes are greatly compromised, resulting in formation of a much lower barrier to transcribing RNA polymerase II than nucleosomes. The data suggest that tetrasomes are remarkably dynamic structures and their formation can strongly affect various biological processes.
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3
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Dulin D. An Introduction to Magnetic Tweezers. Methods Mol Biol 2024; 2694:375-401. [PMID: 37824014 DOI: 10.1007/978-1-0716-3377-9_18] [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] [Indexed: 10/13/2023]
Abstract
Magnetic tweezers are a single-molecule force and torque spectroscopy technique that enable the mechanical interrogation in vitro of biomolecules, such as nucleic acids and proteins. They use a magnetic field originating from either permanent magnets or electromagnets to attract a magnetic particle, thus stretching the tethering biomolecule. They nicely complement other force spectroscopy techniques such as optical tweezers and atomic force microscopy (AFM) as they operate as a very stable force clamp, enabling long-duration experiments over a very broad range of forces spanning from 10 fN to 1 nN, with 1-10 milliseconds time and sub-nanometer spatial resolution. Their simplicity, robustness, and versatility have made magnetic tweezers a key technique within the field of single-molecule biophysics, being broadly applied to study the mechanical properties of, e.g., nucleic acids, genome processing molecular motors, protein folding, and nucleoprotein filaments. Furthermore, magnetic tweezers allow for high-throughput single-molecule measurements by tracking hundreds of biomolecules simultaneously both in real-time and at high spatiotemporal resolution. Magnetic tweezers naturally combine with surface-based fluorescence spectroscopy techniques, such as total internal reflection fluorescence microscopy, enabling correlative fluorescence and force/torque spectroscopy on biomolecules. This chapter presents an introduction to magnetic tweezers including a description of the hardware, the theory behind force calibration, its spatiotemporal resolution, combining it with other techniques, and a (non-exhaustive) overview of biological applications.
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Affiliation(s)
- David Dulin
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.
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4
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A Horizontal Magnetic Tweezers for Studying Single DNA Molecules and DNA-Binding Proteins. Molecules 2021; 26:molecules26164781. [PMID: 34443369 PMCID: PMC8398817 DOI: 10.3390/molecules26164781] [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] [Received: 06/30/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
We report data from single molecule studies on the interaction between single DNA molecules and core histones using custom-designed horizontal magnetic tweezers. The DNA-core histone complexes were formed using λ-DNA tethers, core histones, and NAP1 and were exposed to forces ranging from ~2 pN to ~74 pN. During the assembly events, we observed the length of the DNA decrease in approximate integer multiples of ~50 nm, suggesting the binding of the histone octamers to the DNA tether. During the mechanically induced disassembly events, we observed disruption lengths in approximate integer multiples of ~50 nm, suggesting the unbinding of one or more octamers from the DNA tether. We also observed histone octamer unbinding events at forces as low as ~2 pN. Our horizontal magnetic tweezers yielded high-resolution, low-noise data on force-mediated DNA-core histone assembly and disassembly processes.
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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.
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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
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Winogradoff D, Li P, Joshi H, Quednau L, Maffeo C, Aksimentiev A. Chiral Systems Made from DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003113. [PMID: 33717850 PMCID: PMC7927625 DOI: 10.1002/advs.202003113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA's chirality, from plasmonics and spintronics to biosensing.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Pin‐Yi Li
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Himanshu Joshi
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Lauren Quednau
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Christopher Maffeo
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Aleksei Aksimentiev
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
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Dynamic networks observed in the nucleosome core particles couple the histone globular domains with DNA. Commun Biol 2020; 3:639. [PMID: 33128005 PMCID: PMC7599221 DOI: 10.1038/s42003-020-01369-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
The dynamics of eukaryotic nucleosomes are essential in gene activity and well regulated by various factors. Here, we elucidated the internal dynamics at multiple timescales for the human histones hH3 and hH4 in the Widom 601 nucleosome core particles (NCP), suggesting that four dynamic networks are formed by the residues exhibiting larger-scale μs-ms motions that extend from the NCP core to the histone tails and DNA. Furthermore, despite possessing highly conserved structural features, histones in the telomeric NCP exhibit enhanced μs-ms dynamics in the globular sites residing at the identified dynamic networks and in a neighboring region. In addition, higher mobility was observed for the N-terminal tails of hH3 and hH4 in the telomeric NCP. The results demonstrate the existence of dynamic networks in nucleosomes, through which the center of the core regions could interactively communicate with histone tails and DNA to potentially propagate epigenetic changes. Shi et al. use solid-state nuclear magnetic resonance spectroscopy to reveal the internal dynamics of human histones hH3 and hH4 in the Widom 601 and the telomeric nucleosome core particles. This work has implications for the propagation of epigenetic changes via the center of the nucleosome core communicating with histone tails and DNA.
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Kaczmarczyk A, Meng H, Ordu O, Noort JV, Dekker NH. Chromatin fibers stabilize nucleosomes under torsional stress. Nat Commun 2020; 11:126. [PMID: 31913285 PMCID: PMC6949304 DOI: 10.1038/s41467-019-13891-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/25/2019] [Indexed: 01/11/2023] Open
Abstract
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of 167 and 197. We find that both types of fibers fold into a left-handed superhelix that can be stabilized by positive torsion. We observe that the structural changes induced by twist were reversible, indicating that chromatin has a large degree of elasticity. Our direct measurements of torque confirmed the hypothesis of chromatin fibers as a twist buffer. Using a statistical mechanics-based torsional spring model, we extracted values of the chromatin twist modulus and the linking number per stacked nucleosome that were in good agreement with values measured here experimentally. Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by the higher-order structure of chromatin.
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Affiliation(s)
- Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
- Faculty of Medicine, Imperial College London, Du Cane Road, W12 0NN, London, United Kingdom
| | - He Meng
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands
| | - Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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9
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Ordu O, Lusser A, Dekker NH. DNA Sequence Is a Major Determinant of Tetrasome Dynamics. Biophys J 2019; 117:2217-2227. [PMID: 31521330 PMCID: PMC6895708 DOI: 10.1016/j.bpj.2019.07.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/13/2019] [Accepted: 07/30/2019] [Indexed: 10/26/2022] Open
Abstract
Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4)2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left- and right-handed conformations, which may prevent torque buildup in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a high-affinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono- and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono- and divalent salt concentrations counteracted this behavior. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites.
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Affiliation(s)
- Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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10
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Expression of UTX Indicates Poor Prognosis in Patients With Luminal Breast Cancer and is Associated With MMP-11 Expression. Appl Immunohistochem Mol Morphol 2019; 28:544-550. [DOI: 10.1097/pai.0000000000000795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Zhao H, Winogradoff D, Dalal Y, Papoian GA. The Oligomerization Landscape of Histones. Biophys J 2019; 116:1845-1855. [PMID: 31005236 DOI: 10.1016/j.bpj.2019.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/29/2022] Open
Abstract
In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investigate canonical histone assembly and that of the centromere-specific histone variant, centromere protein A (CENP-A), using molecular dynamics simulations. We quantitatively characterize their thermodynamical and dynamical features, showing that two H3/H4 dimers form a structurally floppy, weakly bound complex, the latter exhibiting large instability around the central interface manifested via a swiveling motion of two halves. This finding is consistent with the recently observed DNA handedness flipping of the tetrasome. In contrast, the variant CENP-A encodes distinctive stability to its tetramer with a rigid but twisted interface compared to the crystal structure, implying diverse structural possibilities of the histone variant. Interestingly, the observed tetramer dynamics alter significantly and appear to reach a new balance when H2A/H2B dimers are present. Furthermore, we found that the preferred structure for the (CENP-A/H4)2 tetramer is incongruent with the octameric structure, explaining many of the unusual dynamical behaviors of the CENP-A nucleosome. In all, these data reveal key mechanistic insights and structural details for the assembly of canonical and variant histone tetramers and octamers, providing theoretical quantifications and physical interpretations for longstanding and recent experimental observations. Based on these findings, we propose different chaperone-assisted binding and nucleosome assembly mechanisms for the canonical and CENP-A histone oligomers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Winogradoff
- Chemical Physics Program, Institute for Physical Science and Technology
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Garegin A Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Chemical Physics Program, Institute for Physical Science and Technology; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
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12
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Makarov DE, Schuler B. Preface: Special Topic on Single-Molecule Biophysics. J Chem Phys 2018; 148:123001. [PMID: 29604869 DOI: 10.1063/1.5028275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.
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Affiliation(s)
- Dmitrii E Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
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Zou T, Hashiya F, Wei Y, Yu Z, Pandian GN, Sugiyama H. Direct Observation of H3-H4 Octasome by High-Speed AFM. Chemistry 2018; 24:15998-16002. [DOI: 10.1002/chem.201804010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Tingting Zou
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Fumitaka Hashiya
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Yulei Wei
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Zutao Yu
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
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