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Li Y, Wang J, Chen X, Czajkowsky DM, Shao Z. Quantitative Super-Resolution Microscopy Reveals the Relationship between CENP-A Stoichiometry and Centromere Physical Size. Int J Mol Sci 2023; 24:15871. [PMID: 37958853 PMCID: PMC10649757 DOI: 10.3390/ijms242115871] [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: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Centromeric chromatin is thought to play a critical role in ensuring the faithful segregation of chromosomes during mitosis. However, our understanding of this role is presently limited by our poor understanding of the structure and composition of this unique chromatin. The nucleosomal variant, CENP-A, localizes to narrow regions within the centromere, where it plays a major role in centromeric function, effectively serving as a platform on which the kinetochore is assembled. Previous work found that, within a given cell, the number of microtubules within kinetochores is essentially unchanged between CENP-A-localized regions of different physical sizes. However, it is unknown if the amount of CENP-A is also unchanged between these regions of different sizes, which would reflect a strict structural correspondence between these two key characteristics of the centromere/kinetochore assembly. Here, we used super-resolution optical microscopy to image and quantify the amount of CENP-A and DNA within human centromere chromatin. We found that the amount of CENP-A within CENP-A domains of different physical sizes is indeed the same. Further, our measurements suggest that the ratio of CENP-A- to H3-containing nucleosomes within these domains is between 8:1 and 11:1. Thus, our results not only identify an unexpectedly strict relationship between CENP-A and microtubules stoichiometries but also that the CENP-A centromeric domain is almost exclusively composed of CENP-A nucleosomes.
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Affiliation(s)
- Yaqian Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
| | - Jiabin Wang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Daniel M. Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; (Y.L.); (Z.S.)
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Gelléri M, Chen SY, Hübner B, Neumann J, Kröger O, Sadlo F, Imhoff J, Hendzel MJ, Cremer M, Cremer T, Strickfaden H, Cremer C. True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin. Cell Rep 2023; 42:112567. [PMID: 37243597 DOI: 10.1016/j.celrep.2023.112567] [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: 06/27/2022] [Revised: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggest only modest compaction differences (∼2-10×) between the active nuclear compartment (ANC) and inactive nuclear compartment (INC). Here, we present maps of nuclear landscapes with true-to-scale DNA densities, ranging from <5 to >300 Mbp/μm3. Maps are generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial optical resolution and are supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription into nuclei of living cells demonstrates their localization and movements within the ANC and exclusion from the INC.
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Affiliation(s)
- Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Shih-Ya Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Jan Neumann
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Ole Kröger
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Filip Sadlo
- Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany
| | - Jorg Imhoff
- Neuroconsult GmbH, 69120 Heidelberg, Germany
| | - Michael J Hendzel
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilian University (LMU), 82152 Martinsried, Germany
| | - Hilmar Strickfaden
- Departments of Cell Biology and Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Max Planck Institute for Chemistry, 55128 Mainz, Germany; Interdisciplinary Center for Scientific Computing (IWR), University Heidelberg, 69120 Heidelberg, Germany; Kirchhoff Institute for Physics, University Heidelberg, 69120 Heidelberg, Germany.
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Ruben BS, Brahmachari S, Contessoto VG, Cheng RR, Oliveira Junior AB, Di Pierro M, Onuchic JN. Structural reorganization and relaxation dynamics of axially stressed chromosomes. Biophys J 2023; 122:1633-1645. [PMID: 36960531 PMCID: PMC10183323 DOI: 10.1016/j.bpj.2023.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/06/2023] [Accepted: 03/17/2023] [Indexed: 03/25/2023] Open
Abstract
Chromosomes endure mechanical stresses throughout the cell cycle; for example, resulting from the pulling of chromosomes by spindle fibers during mitosis or deformation of the nucleus during cell migration. The response to physical stress is closely related to chromosome structure and function. Micromechanical studies of mitotic chromosomes have revealed them to be remarkably extensible objects and informed early models of mitotic chromosome organization. We use a data-driven, coarse-grained polymer modeling approach to explore the relationship between the spatial organization of individual chromosomes and their emergent mechanical properties. In particular, we investigate the mechanical properties of our model chromosomes by axially stretching them. Simulated stretching led to a linear force-extension curve for small strain, with mitotic chromosomes behaving about 10-fold stiffer than interphase chromosomes. Studying their relaxation dynamics, we found that chromosomes are viscoelastic solids with a highly liquid-like, viscous behavior in interphase that becomes solid-like in mitosis. This emergent mechanical stiffness originates from lengthwise compaction, an effective potential capturing the activity of loop-extruding SMC complexes. Chromosomes denature under large strains via unraveling, which is characterized by opening of large-scale folding patterns. By quantifying the effect of mechanical perturbations on the chromosome's structural features, our model provides a nuanced understanding of in vivo mechanics of chromosomes.
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Affiliation(s)
- Benjamin S Ruben
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Biophysics PhD Program, Harvard University, Cambridge, Massachusetts.
| | | | | | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | | | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts; Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston, Texas
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Roh S, Lee T, Cheong DY, Kim Y, Oh S, Lee G. Direct observation of surface charge and stiffness of human metaphase chromosomes. NANOSCALE ADVANCES 2023; 5:368-377. [PMID: 36756276 PMCID: PMC9846444 DOI: 10.1039/d2na00620k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/17/2022] [Indexed: 06/18/2023]
Abstract
Metaphase chromosomes in which both polynucleotides and proteins are condensed with hierarchies are closely related to life phenomena such as cell division, cancer development, and cellular senescence. Nevertheless, their nature is rarely revealed, owing to their structural complexity and technical limitations in analytical methods. In this study, we used surface potential and nanomechanics mapping technology based on atomic force microscopy to measure the surface charge and intrinsic stiffness of metaphase chromosomes. We found that extra materials covering the chromosomes after the extraction process were positively charged. With the covering materials, the chromosomes were positively charged (ca. 44.9 ± 16.48 mV) and showed uniform stiffness (ca. 6.23 ± 1.98 MPa). In contrast, after getting rid of the extra materials through treatment with RNase and protease, the chromosomes were strongly negatively charged (ca. -197.4 ± 77.87 mV) and showed relatively non-uniform and augmented stiffness (ca. 36.87 ± 17.56 MPa). The results suggested undulating but compact coordination of condensed chromosomes. Additionally, excessive treatment with RNase and protease could destroy the chromosomal structure, providing an exceptional opportunity for multiscale stiffness mapping of polynucleotides, nucleosomes, chromatin fibers, and chromosomes in a single image. Our approach offers a new horizon in terms of an analytical technique for studying chromosome-related diseases.
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Affiliation(s)
- Seokbeom Roh
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Taeha Lee
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
| | - Yeonjin Kim
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
| | - Soohwan Oh
- College of Pharmacy, Korea University Sejong 30019 Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University Sejong 30019 Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University Sejong 30019 Korea
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