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Mora KE, Mlawer SJ, Loiselle AE, Buckley MR. The Micromechanical Environment of the Impinged Achilles Tendon. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401015. [PMID: 38966889 DOI: 10.1002/smll.202401015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Indexed: 07/06/2024]
Abstract
Although tendon predominantly experiences longitudinal tensile forces, transverse forces due to impingement from bone are implicated in both physiological and pathophysiological processes. However, prior studies have not characterized the micromechanical strain environment in the context of tendon impingement. To address this knowledge gap, mouse hindlimb explants are imaged on a multiphoton microscope, and image stacks of the same population of tendon cells are obtained in the Achilles tendon before and after dorsiflexion-induced impingement by the heel bone. Based on the acquired images, multiaxial strains are measured at the extracellular matrix (ECM), pericellular matrix (PCM), and cell scales. Impingement generated substantial transverse compression at the matrix-scale, which led to longitudinal stretching of cells, increased cell aspect ratio, and enormous volumetric compression of the PCM. These experimental results are corroborated by a finite element model, which further demonstrated that impingement produces high cell surface stresses and strains that greatly exceed those brought about by longitudinal tension. Moreover, in both experiments and simulations, impingement-generated microscale stresses and strains are highly dependent on initial cell-cell gap spacing. Identifying factors that influence the microscale strain environment generated by impingement could contribute to a more mechanistic understanding of impingement-induced tendinopathies.
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Affiliation(s)
- Keshia E Mora
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
- Center for Musculoskeletal Research, Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, NY, 14642, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel J Mlawer
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Alayna E Loiselle
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
- Center for Musculoskeletal Research, Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Mark R Buckley
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627, USA
- Center for Musculoskeletal Research, Department of Orthopaedics and Rehabilitation, University of Rochester Medical Center, Rochester, NY, 14642, USA
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2
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Buisson J, Zhang X, Zambelli T, Lavalle P, Vautier D, Rabineau M. Reverse Mechanotransduction: Driving Chromatin Compaction to Decompaction Increases Cell Adhesion Strength and Contractility. NANO LETTERS 2024; 24:4279-4290. [PMID: 38546049 DOI: 10.1021/acs.nanolett.4c00732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Mechanical extracellular signals elicit chromatin remodeling via the mechanotransduction pathway, thus determining cellular function. However, the reverse pathway is an open question: does chromatin remodeling shape cells, regulating their adhesion strength? With fluidic force microscopy, we can directly measure the adhesion strength of epithelial cells by driving chromatin compaction to decompaction with chromatin remodelers. We observe that chromatin compaction, induced by performing histone acetyltransferase inhibition or ATP depletion, leads to a reduction in nuclear volume, disrupting actin cytoskeleton and focal adhesion assembly, and ultimately decreases in cell adhesion strength and traction force. Conversely, when chromatin decompaction is drived by removing the remodelers, cells recover their original shape, adhesion strength, and traction force. During chromatin decompaction, cells use depolymerized proteins to restore focal adhesion assemblies rather than neo-synthesized cytoskeletal proteins. We conclude that chromatin remodeling shapes cells, regulating adhesion strength through a reverse mechanotransduction pathway from the nucleus to the cell surface involving RhoA activation.
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Affiliation(s)
- Julie Buisson
- Inserm UMR_S 1121, CNRS EMR 7003, Université de Strasbourg, Biomaterials and Bioengineering, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg F-67000, France
| | - Xinyu Zhang
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich 8092, Switzerland
| | - Tomaso Zambelli
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich 8092, Switzerland
| | - Philippe Lavalle
- Inserm UMR_S 1121, CNRS EMR 7003, Université de Strasbourg, Biomaterials and Bioengineering, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg F-67000, France
- SPARTHA Medical SAS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg F-67000, France
| | - Dominique Vautier
- Inserm UMR_S 1121, CNRS EMR 7003, Université de Strasbourg, Biomaterials and Bioengineering, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg F-67000, France
| | - Morgane Rabineau
- Inserm UMR_S 1121, CNRS EMR 7003, Université de Strasbourg, Biomaterials and Bioengineering, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg F-67000, France
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3
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Spegg V, Altmeyer M. Genome maintenance meets mechanobiology. Chromosoma 2024; 133:15-36. [PMID: 37581649 PMCID: PMC10904543 DOI: 10.1007/s00412-023-00807-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023]
Abstract
Genome stability is key for healthy cells in healthy organisms, and deregulated maintenance of genome integrity is a hallmark of aging and of age-associated diseases including cancer and neurodegeneration. To maintain a stable genome, genome surveillance and repair pathways are closely intertwined with cell cycle regulation and with DNA transactions that occur during transcription and DNA replication. Coordination of these processes across different time and length scales involves dynamic changes of chromatin topology, clustering of fragile genomic regions and repair factors into nuclear repair centers, mobilization of the nuclear cytoskeleton, and activation of cell cycle checkpoints. Here, we provide a general overview of cell cycle regulation and of the processes involved in genome duplication in human cells, followed by an introduction to replication stress and to the cellular responses elicited by perturbed DNA synthesis. We discuss fragile genomic regions that experience high levels of replication stress, with a particular focus on telomere fragility caused by replication stress at the ends of linear chromosomes. Using alternative lengthening of telomeres (ALT) in cancer cells and ALT-associated PML bodies (APBs) as examples of replication stress-associated clustered DNA damage, we discuss compartmentalization of DNA repair reactions and the role of protein properties implicated in phase separation. Finally, we highlight emerging connections between DNA repair and mechanobiology and discuss how biomolecular condensates, components of the nuclear cytoskeleton, and interfaces between membrane-bound organelles and membraneless macromolecular condensates may cooperate to coordinate genome maintenance in space and time.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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4
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Vasquez PA, Walker B, Bloom K, Kolbin D, Caughman N, Freeman R, Lysy M, Hult C, Newhall KA, Papanikolas M, Edelmaier C, Forest MG. The power of weak, transient interactions across biology: A paradigm of emergent behavior. PHYSICA D. NONLINEAR PHENOMENA 2023; 454:133866. [PMID: 38274029 PMCID: PMC10806540 DOI: 10.1016/j.physd.2023.133866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
A growing list of diverse biological systems and their equally diverse functionalities provides realizations of a paradigm of emergent behavior. In each of these biological systems, pervasive ensembles of weak, short-lived, spatially local interactions act autonomously to convey functionalities at larger spatial and temporal scales. In this article, a range of diverse systems and functionalities are presented in a cursory manner with literature citations for further details. Then two systems and their properties are discussed in more detail: yeast chromosome biology and human respiratory mucus.
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Affiliation(s)
- Paula A. Vasquez
- Department of Mathematics, University of South Carolina, United States of America
| | - Ben Walker
- Department of Mathematics, University of California at Irvine, United States of America
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Neall Caughman
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Martin Lysy
- Department of Statistics and Actuarial Science, University of Waterloo, Canada
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, United States of America
| | - Katherine A. Newhall
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Christopher Edelmaier
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
- Center for Computational Biology, Flatiron Institute, United States of America
| | - M. Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
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5
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Scott AK, Rafuse M, Neu CP. Mechanically induced alterations in chromatin architecture guide the balance between cell plasticity and mechanical memory. Front Cell Dev Biol 2023; 11:1084759. [PMID: 37143893 PMCID: PMC10151697 DOI: 10.3389/fcell.2023.1084759] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 04/07/2023] [Indexed: 05/06/2023] Open
Abstract
Phenotypic plasticity, or adaptability, of a cell determines its ability to survive and function within changing cellular environments. Changes in the mechanical environment, ranging from stiffness of the extracellular matrix (ECM) to physical stress such as tension, compression, and shear, are critical environmental cues that influence phenotypic plasticity and stability. Furthermore, an exposure to a prior mechanical signal has been demonstrated to play a fundamental role in modulating phenotypic changes that persist even after the mechanical stimulus is removed, creating stable mechanical memories. In this mini review, our objective is to highlight how the mechanical environment alters both phenotypic plasticity and stable memories through changes in chromatin architecture, mainly focusing on examples in cardiac tissue. We first explore how cell phenotypic plasticity is modulated in response to changes in the mechanical environment, and then connect the changes in phenotypic plasticity to changes in chromatin architecture that reflect short-term and long-term memories. Finally, we discuss how elucidating the mechanisms behind mechanically induced chromatin architecture that lead to cell adaptations and retention of stable mechanical memories could uncover treatment methods to prevent mal-adaptive permanent disease states.
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Affiliation(s)
- Adrienne K. Scott
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Michael Rafuse
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Corey P. Neu
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, Boulder, CO, United States
- Biomedical Engineering Program, University of Colorado Boulder, Boulder, CO, United States
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States
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6
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Danielsson BE, Tieu KV, Spagnol ST, Vu KK, Cabe JI, Raisch TB, Dahl KN, Conway DE. Chromatin condensation regulates endothelial cell adaptation to shear stress. Mol Biol Cell 2022; 33:ar101. [PMID: 35895088 DOI: 10.1091/mbc.e22-02-0064] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Vascular endothelial cells (ECs) have been shown to be mechanoresponsive to the forces of blood flow, including fluid shear stress (FSS), the frictional force of blood on the vessel wall. Recent reports have shown that FSS induces epigenetic changes in chromatin. Epigenetic changes, such as methylation and acetylation of histones, not only affect gene expression but also affect chromatin condensation, which can alter nuclear stiffness. Thus, we hypothesized that changes in chromatin condensation may be an important component for how ECs adapt to FSS. Using both in vitro and in vivo models of EC adaptation to FSS, we observed an increase in histone acetylation and a decrease in histone methylation in ECs adapted to flow as compared with static. Using small molecule drugs, as well as vascular endothelial growth factor, to change chromatin condensation, we show that decreasing chromatin condensation enables cells to more quickly align to FSS, whereas increasing chromatin condensation inhibited alignment. Additionally, we show data that changes in chromatin condensation can also prevent or increase DNA damage, as measured by phosphorylation of γH2AX. Taken together, these results indicate that chromatin condensation, and potentially by extension nuclear stiffness, is an important aspect of EC adaptation to FSS.
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Affiliation(s)
- Brooke E Danielsson
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Katie V Tieu
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Stephen T Spagnol
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Kira K Vu
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Jolene I Cabe
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Tristan B Raisch
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Kris Noel Dahl
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213.,Forensics Department, Thornton Tomasetti, New York City, NY 10271
| | - Daniel E Conway
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia 23284.,Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210.,Center for Cancer Engineering, and Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
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7
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Seelbinder B, Ghosh S, Schneider SE, Scott AK, Berman AG, Goergen CJ, Margulies KB, Bedi K, Casas E, Swearingen AR, Brumbaugh J, Calve S, Neu CP. Nuclear deformation guides chromatin reorganization in cardiac development and disease. Nat Biomed Eng 2021; 5:1500-1516. [PMID: 34857921 PMCID: PMC9300284 DOI: 10.1038/s41551-021-00823-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/20/2021] [Indexed: 01/31/2023]
Abstract
In cardiovascular tissues, changes in the mechanical properties of the extracellular matrix are associated with cellular de-differentiation and with subsequent functional declines. However, the underlying mechanoreceptive mechanisms are largely unclear. Here, by generating high-resolution, full-field strain maps of cardiomyocyte nuclei during contraction in vitro, complemented with evidence from tissues from patients with cardiomyopathy and from mice with reduced cardiac performance, we show that cardiomyocytes establish a distinct nuclear organization during maturation, characterized by the reorganization of H3K9me3-marked chromatin towards the nuclear border. Specifically, we show that intranuclear tension is spatially correlated with H3K9me3-marked chromatin, that reductions in nuclear deformation (through environmental stiffening or through the disruption of complexes of the linker of nucleoskeleton and cytoskeleton) abrogate chromatin reorganization and lead to the dissociation of H3K9me3-marked chromatin from the nuclear periphery, and that the suppression of H3K9 methylation induces chromatin reorganization and reduces the expression of cardiac developmental genes. Overall, our findings indicate that, by integrating environmental mechanical cues, the nuclei of cardiomyocytes guide and stabilize the fate of cells through the reorganization of epigenetically marked chromatin.
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Affiliation(s)
- Benjamin Seelbinder
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Soham Ghosh
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | | | - Adrienne K. Scott
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO)
| | - Alycia G. Berman
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Craig J. Goergen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | | | - Kenneth Bedi
- Cardiovascular Institute, University of Pennsylvania, Philadelphia (PA)
| | - Eduard Casas
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Alison R. Swearingen
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Justin Brumbaugh
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder (CO)
| | - Sarah Calve
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Weldon School of Biomedical Engineering, Purdue University, West Lafayette (IN)
| | - Corey P. Neu
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder (CO),Corresponding Author
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8
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Orchestration of Force Generation and Nuclear Collapse in Apoptotic Cells. Int J Mol Sci 2021; 22:ijms221910257. [PMID: 34638598 PMCID: PMC8508646 DOI: 10.3390/ijms221910257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/03/2021] [Accepted: 09/20/2021] [Indexed: 12/26/2022] Open
Abstract
Apoptosis, or programmed cell death, is a form of cell suicide that is extremely important for ridding the body of cells that are no longer required, to protect the body against hazardous cells, such as cancerous ones, and to promote tissue morphogenesis during animal development. Upon reception of a death stimulus, the doomed cell activates biochemical pathways that eventually converge on the activation of dedicated enzymes, caspases. Numerous pieces of information on the biochemical control of the process have been gathered, from the successive events of caspase activation to the identification of their targets, such as lamins, which constitute the nuclear skeleton. Yet, evidence from multiple systems now shows that apoptosis is also a mechanical process, which may even ultimately impinge on the morphogenesis of the surrounding tissues. This mechanical role relies on dramatic actomyosin cytoskeleton remodelling, and on its coupling with the nucleus before nucleus fragmentation. Here, we provide an overview of apoptosis before describing how apoptotic forces could combine with selective caspase-dependent proteolysis to orchestrate nucleus destruction.
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9
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Lavrenyuk K, Conway D, Dahl KN. Imaging methods in mechanosensing: a historical perspective and visions for the future. Mol Biol Cell 2021; 32:842-854. [PMID: 33788578 PMCID: PMC8108522 DOI: 10.1091/mbc.e20-10-0671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Over the past three decades, as mechanobiology has become a distinct area of study, researchers have developed novel imaging tools to discover the pathways of biomechanical signaling. Early work with substrate engineering and particle tracking demonstrated the importance of cell–extracellular matrix interactions on the cell cycle as well as the mechanical flux of the intracellular environment. Most recently, tension sensor approaches allowed directly measuring tension in cell–cell and cell–substrate interactions. We retrospectively analyze how these various optical techniques progressed the field and suggest our vision forward for a unified theory of cell mechanics, mapping cellular mechanosensing, and novel biomedical applications for mechanobiology.
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Affiliation(s)
- Kirill Lavrenyuk
- Carnegie Mellon University, College of Engineering, Pittsburgh, PA 15213
| | - Daniel Conway
- Virginia Commonwealth University, College of Engineering, Richmond, VA 23284
| | - Kris Noel Dahl
- Carnegie Mellon University, College of Engineering, Pittsburgh, PA 15213
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10
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Multiple particle tracking analysis in isolated nuclei reveals the mechanical phenotype of leukemia cells. Sci Rep 2020; 10:6707. [PMID: 32317728 PMCID: PMC7174401 DOI: 10.1038/s41598-020-63682-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 04/02/2020] [Indexed: 12/14/2022] Open
Abstract
The nucleus is fundamentally composed by lamina and nuclear membranes that enclose the chromatin, nucleoskeletal components and suspending nucleoplasm. The functional connections of this network integrate external stimuli into cell signals, including physical forces to mechanical responses of the nucleus. Canonically, the morphological characteristics of the nucleus, as shape and size, have served for pathologists to stratify and diagnose cancer patients; however, novel biophysical techniques must exploit physical parameters to improve cancer diagnosis. By using multiple particle tracking (MPT) technique on chromatin granules, we designed a SURF (Speeded Up Robust Features)-based algorithm to study the mechanical properties of isolated nuclei and in living cells. We have determined the apparent shear stiffness, viscosity and optical density of the nucleus, and how the chromatin structure influences on these biophysical values. Moreover, we used our MPT-SURF analysis to study the apparent mechanical properties of isolated nuclei from patients of acute lymphoblastic leukemia. We found that leukemia cells exhibited mechanical differences compared to normal lymphocytes. Interestingly, isolated nuclei from high-risk leukemia cells showed increased viscosity than their counterparts from normal lymphocytes, whilst nuclei from relapsed-patient's cells presented higher density than those from normal lymphocytes or standard- and high-risk leukemia cells. Taken together, here we presented how MPT-SURF analysis of nuclear chromatin granules defines nuclear mechanical phenotypic features, which might be clinically relevant.
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11
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Job Opening for Nucleosome Mechanic: Flexibility Required. Cells 2020; 9:cells9030580. [PMID: 32121488 PMCID: PMC7140402 DOI: 10.3390/cells9030580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/21/2022] Open
Abstract
The nucleus has been studied for well over 100 years, and chromatin has been the intense focus of experiments for decades. In this review, we focus on an understudied aspect of chromatin biology, namely the chromatin fiber polymer’s mechanical properties. In recent years, innovative work deploying interdisciplinary approaches including computational modeling, in vitro manipulations of purified and native chromatin have resulted in deep mechanistic insights into how the mechanics of chromatin might contribute to its function. The picture that emerges is one of a nucleus that is shaped as much by external forces pressing down upon it, as internal forces pushing outwards from the chromatin. These properties may have evolved to afford the cell a dynamic and reversible force-induced communication highway which allows rapid coordination between external cues and internal genomic function.
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12
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Abstract
We review the current understanding of the mechanics of DNA and DNA-protein complexes, from scales of base pairs up to whole chromosomes. Mechanics of the double helix as revealed by single-molecule experiments will be described, with an emphasis on the role of polymer statistical mechanics. We will then discuss how topological constraints- entanglement and supercoiling-impact physical and mechanical responses. Models for protein-DNA interactions, including effects on polymer properties of DNA of DNA-bending proteins will be described, relevant to behavior of protein-DNA complexes in vivo. We also discuss control of DNA entanglement topology by DNA-lengthwise-compaction machinery acting in concert with topoisomerases. Finally, the chapter will conclude with a discussion of relevance of several aspects of physical properties of DNA and chromatin to oncology.
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13
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Quantifying site-specific chromatin mechanics and DNA damage response. Sci Rep 2018; 8:18084. [PMID: 30591710 PMCID: PMC6308236 DOI: 10.1038/s41598-018-36343-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 11/14/2018] [Indexed: 01/06/2023] Open
Abstract
DNA double-strand breaks pose a direct threat to genomic stability. Studies of DNA damage and chromatin dynamics have yielded opposing results that support either increased or decreased chromatin motion after damage. In this study, we independently measure the dynamics of transcriptionally active or repressed chromatin regions using particle tracking microrheology. We find that the baseline motion of transcriptionally repressed regions of chromatin are significantly less mobile than transcriptionally active chromatin, which is statistically similar to the bulk motion of chromatin within the nucleus. Site specific DNA damage using KillerRed tags induced in loci within repressed chromatin causes an increased motion, while loci within transcriptionally active regions remains unchanged at similar time scales. We also observe a time-dependent response associated with a further increase in chromatin decondensation. Global induction of damage with bleocin displays similar trends of chromatin decondensation and increased mobility only at 53BP1-labeled damage sites but not at non-damaged sites, indicating that chromatin dynamics are tightly regulated locally after damage. These results shed light on the evolution of the local and global DNA damage response associated with chromatin remodeling and dynamics, with direct implications for their role in repair.
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14
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Emerging views of the nucleus as a cellular mechanosensor. Nat Cell Biol 2018; 20:373-381. [PMID: 29467443 DOI: 10.1038/s41556-018-0038-y] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
The ability of cells to respond to mechanical forces is critical for numerous biological processes. Emerging evidence indicates that external mechanical forces trigger changes in nuclear envelope structure and composition, chromatin organization and gene expression. However, it remains unclear if these processes originate in the nucleus or are downstream of cytoplasmic signals. Here we discuss recent findings that support a direct role of the nucleus in cellular mechanosensing and highlight novel tools to study nuclear mechanotransduction.
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15
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Liu L, Luo Q, Sun J, Ju Y, Morita Y, Song G. Chromatin organization regulated by EZH2-mediated H3K27me3 is required for OPN-induced migration of bone marrow-derived mesenchymal stem cells. Int J Biochem Cell Biol 2018; 96:29-39. [PMID: 29337251 DOI: 10.1016/j.biocel.2018.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/22/2017] [Accepted: 01/09/2018] [Indexed: 11/27/2022]
Abstract
Osteopontin (OPN) is a chemokine-like extracellular matrix-associated protein involved in the migration of bone marrow-derived mesenchymal stem cells (BMSCs). An increasing number of studies have found that chromatin organization may affect cellular migration. However, whether OPN regulates chromatin organization is not understood, nor are the underlying molecular mechanisms. In this study, we investigated the link between chromatin organization and BMSC migration and demonstrated that OPN-mediated BMSC migration leads to elevated levels of heterochromatin marker histone H3 lysine 27 trimethylation (H3K27me3) through the methyltransferase EZH2. The expression of EZH2 reorganizes the chromatin structure of BMSCs. Pharmacological inhibition or depletion of EZH2 blocks BMSC migration. Moreover, using an atomic force microscope (AFM), we found that chromatin decondensation alters the mechanical properties of the nucleus. In addition, inhibition of extracellular signal-regulated kinase 1/2 (ERK1/2) signals represses OPN-promoted chromatin condensation and cell migration. Thus, our results identify a mechanism by which ERK1/2 signalling drives specific chromatin modifications in BMSCs, which alters chromatin organization and thereby enables OPN-mediated BMSC migration.
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Affiliation(s)
- Lingling Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, People's Republic of China; School of Medical Laboratory Science, Chengdu Medical College, Chengdu 610500, People's Republic of China.
| | - Qing Luo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, People's Republic of China.
| | - Jinghui Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, People's Republic of China; School of Medical Laboratory Science, Chengdu Medical College, Chengdu 610500, People's Republic of China.
| | - Yang Ju
- Department of Mechanical Science and Engineering, Nagoya University, Nagoya 464-8603, Japan.
| | - Yasuyuki Morita
- Department of Mechanical Science and Engineering, Nagoya University, Nagoya 464-8603, Japan.
| | - Guanbin Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, People's Republic of China.
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16
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Abstract
Biological cells sample their surrounding microenvironments using nanoscale force sensors on the cell surfaces. These surface-based force and stress sensors generate physical and chemical responses inside the cell. The inherently well-connected cytoskeleton and its physical contacts with the force elements on the nuclear membrane lead these physicochemical responses to cascade all the way inside the cell nucleus, physically altering the nuclear state. These physical alterations of the cell nucleus, through yet-unknown complex steps elicit physical and functional response from the chromatin in the form of altered gene expression profiles. This mechanism of force/stress sensing by the cell and then its nuclear response has been shown to play a vital role in maintaining robust cellular homeostasis, controlling gene expression profiles during developmental phases as well as cell differentiation. Over the last few years, there has been appreciable progress toward identification of the molecular players responsible for force sensing. However, the actual sensing mechanism of cell surface bound force sensors and more importantly cascading of the signals, both physical (via cytosolic force sensing elements such as microtubule and actin framework) and chemical (cascade of biochemical signaling from cell surface to nuclear surface and further to the chromatin), inside the cell is poorly understood. In this chapter, we present a review of the currently known molecular players in cellular as well as nuclear force sensing repertoire and their possible mechanistic aspects. We also introduce various biophysical concepts that are used to describe the force/stress sensing and response of a cell. We hope this will help asking clearer questions and designing pointed experiments for better understanding of the force-dependent design principles of the cell surface, nuclear surface, and gene expression.
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Affiliation(s)
- Bidisha Sinha
- Indian Institute of Science Education and Research Kolkata, Mohanpur, WB, India
| | - Arikta Biswas
- Indian Institute of Science Education and Research Kolkata, Mohanpur, WB, India
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17
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Hasturk O, Sivas A, Karasozen B, Demirci U, Hasirci N, Hasirci V. Quantification of Type, Timing, and Extent of Cell Body and Nucleus Deformations Caused by the Dimensions and Hydrophilicity of Square Prism Micropillars. Adv Healthc Mater 2016; 5:2972-2982. [PMID: 27925459 DOI: 10.1002/adhm.201600857] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/21/2016] [Indexed: 01/30/2023]
Abstract
Novel digital analysis strategies are developed for the quantification of changes in the cytoskeletal and nuclear morphologies of mesenchymal stem cells cultured on micropillars. Severe deformations of nucleus and distinct conformational changes of cell body ranging from extensive elongation to branching are visualized and quantified. These deformations are caused mainly by the dimensions and hydrophilicity of the micropillars.
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Affiliation(s)
- Onur Hasturk
- Graduate Department of Biotechnology; Middle East Technical University (METU); Ankara 06800 Turkey
- BIOMATEN; Center of Excellence in Biomaterials and Tissue Engineering; Middle East Technical University (METU); Ankara 06800 Turkey
| | - Abdullah Sivas
- Institute of Applied Mathematics; Middle East Technical University (METU); Ankara 06800 Turkey
| | - Bulent Karasozen
- Institute of Applied Mathematics; Middle East Technical University (METU); Ankara 06800 Turkey
| | - Utkan Demirci
- Bio-Acoustic-MEMs in Medicine (BAMM) Laboratory; Stanford School of Medicine; Palo Alto CA 94394 USA
| | - Nesrin Hasirci
- Graduate Department of Biotechnology; Middle East Technical University (METU); Ankara 06800 Turkey
- BIOMATEN; Center of Excellence in Biomaterials and Tissue Engineering; Middle East Technical University (METU); Ankara 06800 Turkey
- Department of Chemistry; Middle East Technical University (METU); Ankara 06800 Turkey
| | - Vasif Hasirci
- Graduate Department of Biotechnology; Middle East Technical University (METU); Ankara 06800 Turkey
- BIOMATEN; Center of Excellence in Biomaterials and Tissue Engineering; Middle East Technical University (METU); Ankara 06800 Turkey
- Department of Biological Sciences; Middle East Technical University (METU); Ankara 06800 Turkey
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