1
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Attar AG, Paturej J, Banigan EJ, Erbaş A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. Nucleus 2024; 15:2351957. [PMID: 38753956 DOI: 10.1080/19491034.2024.2351957] [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: 01/30/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a "wetting"-like interaction. In contrast, fluctuations are insensitive to heterochromatin's internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.
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Affiliation(s)
- Ali Goktug Attar
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
| | | | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
- Institute of Physics, University of Silesia, Chorzów, Poland
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2
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression. Proc Natl Acad Sci U S A 2024; 121:e2401494121. [PMID: 38753513 PMCID: PMC11127048 DOI: 10.1073/pnas.2401494121] [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: 01/26/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross-over between two and four at contour lengths on the order of 30 kilo-base pairs. The anomalously high fractal dimension [Formula: see text] is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ([Formula: see text]) longer than tens of minutes to be proportional to [Formula: see text]. We validate our results with hybrid molecular dynamics-Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, NC27708
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, NC27708
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
- Department of Physics, Duke University, Durham, NC27708
- Department of Chemistry, Duke University, Durham, NC27708
- World Premier International Research Center Initiative–Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
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3
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Wu ZP, Bloom KS, Forest MG, Cao XZ. Transient crosslinking controls the condensate formation pathway within chromatin networks. Phys Rev E 2024; 109:L042401. [PMID: 38755828 PMCID: PMC11137846 DOI: 10.1103/physreve.109.l042401] [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: 09/10/2023] [Accepted: 02/26/2024] [Indexed: 05/18/2024]
Abstract
The network structure of densely packed chromatin within the nucleus of eukaryotic cells acts in concert with nonequilibrium processes. Using statistical physics simulations, we explore the control provided by transient crosslinking of the chromatin network by structural-maintenance-of-chromosome (SMC) proteins over (i) the physical properties of the chromatin network and (ii) condensate formation of embedded molecular species. We find that the density and lifetime of transient SMC crosslinks regulate structural relaxation modes and tune the sol-vs-gel state of the chromatin network, which imparts control over the kinetic pathway to condensate formation. Specifically, lower density, shorter-lived crosslinks induce sollike networks and a droplet-fusion pathway, whereas higher density, longer-lived crosslinks induce gellike networks and an Ostwald-ripening pathway.
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Affiliation(s)
- Zong-Pei Wu
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - M. Gregory Forest
- Departments of Mathematics, Applied Physical Sciences and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xue-Zheng Cao
- Department of Physics at Xiamen University, Xiamen 361005, P.R. China
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4
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Neill P, Crist N, McGorty R, Robertson-Anderson R. Enzymatic cleaving of entangled DNA rings drives scale-dependent rheological trajectories. SOFT MATTER 2024; 20:2750-2766. [PMID: 38440846 DOI: 10.1039/d3sm01641b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA, which naturally occurs in linear, ring, and supercoiled topologies, frequently undergoes enzyme-driven topological conversion and fragmentation in vivo, enabling it to perform a variety of functions within the cell. In vitro, highly concentrated DNA polymers form entanglements that yield viscoelastic properties dependent on the topologies and lengths of the DNA. Enzyme-driven alterations of DNA size and shape therefore offer a means of designing active materials with programmable viscoelastic properties. Here, we incorporate multi-site restriction endonucleases into dense DNA solutions to linearize and fragment circular DNA molecules. We pair optical tweezers microrheology with differential dynamic microscopy and single-molecule tracking to measure the linear and nonlinear viscoelastic response and transport properties of entangled DNA solutions over a wide range of spatiotemporal scales throughout the course of enzymatic digestion. We show that, at short timescales, relative to the relaxation timescales of the polymers, digestion of these 'topologically-active' fluids initially causes an increase in elasticity and relaxation times followed by a gradual decrease. Conversely, for long timescales, linear viscoelastic moduli exhibit signatures of increasing elasticity. DNA diffusion, likewise, becomes increasingly slowed, in direct opposition to the short-time behavior. We hypothesize that this scale-dependent rheology arises from the population of small DNA fragments, which increases as digestion proceeds, driving self-association of larger fragments via depletion interactions, giving rise to slow relaxation modes of clusters of entangled chains, interspersed among shorter unentangled fragments. While these slow modes likely dominate at long times, they are presumably frozen out in the short-time limit, which instead probes the faster relaxation modes of the unentangled population.
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Affiliation(s)
- Philip Neill
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Natalie Crist
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Ryan McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
| | - Rae Robertson-Anderson
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92104, USA.
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5
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Shin S, Shi G, Cho HW, Thirumalai D. Transcription-induced active forces suppress chromatin motion. Proc Natl Acad Sci U S A 2024; 121:e2307309121. [PMID: 38489381 PMCID: PMC10963020 DOI: 10.1073/pnas.2307309121] [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: 05/02/2023] [Accepted: 02/06/2024] [Indexed: 03/17/2024] Open
Abstract
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of chromatin. Some experiments have shown that the motility of individual loci in human interphase chromosome decreases during transcription and increases upon inhibiting transcription. This is a counterintuitive finding because it is thought that the active mechanical force (F) on the order of ten piconewtons, generated by RNA polymerase II (RNAPII) that is presumably transmitted to the gene-rich region of the chromatin, would render it more open, thus enhancing the mobility. We developed a minimal active copolymer model for interphase chromosomes to investigate how F affects the dynamical properties of chromatin. The movements of the loci in the gene-rich region are suppressed in an intermediate range of F and are enhanced at small F values, which has also been observed in experiments. In the intermediate F, the bond length between consecutive loci increases, becoming commensurate with the distance at the minimum of the attractive interaction between nonbonded loci. This results in a transient disorder-to-order transition, leading to a decreased mobility during transcription. Strikingly, the F-dependent change in the locus dynamics preserves the organization of the chromosome at [Formula: see text]. Transient ordering of the loci, which is not found in the polymers with random epigenetic profiles, in the gene-rich region might be a plausible mechanism for nucleating a dynamic network involving transcription factors, RNAPII, and chromatin.
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Affiliation(s)
- Sucheol Shin
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
| | - Guang Shi
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Materials Science, University of Illinois, Urbana, IL61801
| | - Hyun Woo Cho
- Department of Fine Chemistry and Center for Functional Biomaterials, Seoul National University of Science and Technology, Seoul01811, Republic of Korea
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Physics, The University of Texas at Austin, Austin, TX78712
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6
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Miranda JP, Locatelli E, Valeriani C. Self-Organized States from Solutions of Active Ring Polymers in Bulk and under Confinement. J Chem Theory Comput 2024; 20:1636-1645. [PMID: 38153343 DOI: 10.1021/acs.jctc.3c00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In the present work, we study, by means of numerical simulations, the structural and dynamical behavior of a suspension of active ring polymers in bulk and under lateral confinement. At high activity, when changing the distance between the confining planes and the polymers' density, we identify the emergence of a self-organized dynamical state, characterized by the coexistence of slowly diffusing clusters of rotating disks and faster rings moving in between them. We further assess that self-organization is robust in a range of polymer sizes, and we identify a critical value of the activity, necessary to trigger cluster formation. This system has distinctive features resembling at the same time polymers, liquid crystals, and active systems, where the interplay between activity, topology, and confinement leads to a spontaneous segregation in an initially one-component solution.
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Affiliation(s)
- Juan Pablo Miranda
- Dep. Est. de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain
- GISC - Grupo Interdisciplinar de Sistemas Complejos, 28040 Madrid, Spain
| | - Emanuele Locatelli
- Department of Physics and Astronomy, University of Padova, 35131 Padova, Italy
- INFN, Sezione di Padova, via Marzolo 8, I-35131 Padova, Italy
| | - Chantal Valeriani
- Dep. Est. de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain
- GISC - Grupo Interdisciplinar de Sistemas Complejos, 28040 Madrid, Spain
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7
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Bunner S, Prince K, Srikrishna K, Pujadas EM, McCarthy AA, Kuklinski A, Jackson O, Pellegrino P, Jagtap S, Eweka I, Lawlor C, Eastin E, Yas G, Aiello J, LaPointe N, von Blucher IS, Hardy J, Chen J, Backman V, Janssen A, Packard M, Dorfman K, Almassalha L, Bahiru MS, Stephens AD. DNA density is a better indicator of a nuclear bleb than lamin B loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579152. [PMID: 38370828 PMCID: PMC10871186 DOI: 10.1101/2024.02.06.579152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Nuclear blebs are herniations of the nucleus that occur in diseased nuclei that cause nuclear rupture leading to cellular dysfunction. Chromatin and lamins are two of the major structural components of the nucleus that maintain its shape and function, but their relative roles in nuclear blebbing remain elusive. Lamin B is reported to be lost in blebs by qualitative data while quantitative studies reveal a spectrum of lamin B levels in nuclear blebs dependent on perturbation and cell type. Chromatin has been reported to be decreased or de-compacted in nuclear blebs, but again the data are not conclusive. To determine the composition of nuclear blebs, we compared the immunofluorescence intensity of lamin B and DNA in the main nucleus body and nuclear bleb across cell types and perturbations. Lamin B nuclear bleb levels varied drastically across MEF wild type and chromatin or lamins perturbations, HCT116 lamin B1-GFP imaging, and human disease model cells of progeria and prostate cancer. However, DNA concentration was consistently decreased to about half that of the main nucleus body across all measured conditions. Using Partial Wave Spectroscopic (PWS) microscopy to measure chromatin density in the nuclear bleb vs body we find similar results that DNA is consistently less dense in nuclear blebs. Thus, our data spanning many different cell types and perturbations supports that decreased DNA is a better marker of a nuclear bleb than lamin B levels that vary widely.
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Affiliation(s)
- Samantha Bunner
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Kelsey Prince
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Karan Srikrishna
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Emily Marie Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | | | - Anna Kuklinski
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Olivia Jackson
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Pedro Pellegrino
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Shrushti Jagtap
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Imuetiyan Eweka
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Colman Lawlor
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Emma Eastin
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Griffin Yas
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Julianna Aiello
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Nathan LaPointe
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | | | - Jillian Hardy
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Jason Chen
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Anne Janssen
- School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Mary Packard
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Katherine Dorfman
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
| | - Luay Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Michael Seifu Bahiru
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
- Program in Neuroscience and Behavior, University of Massachusetts, Amherst, MA 01003, USA
| | - A. D. Stephens
- Biology department, University of Massachusetts Amherst, Amherst, MA. 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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8
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Attar AG, Paturej J, Banigan EJ, Erbas A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.16.571697. [PMID: 38168411 PMCID: PMC10760070 DOI: 10.1101/2023.12.16.571697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Abnormalities in the shapes of mammalian cell nuclei are hallmarks of a variety of diseases, including progeria, muscular dystrophy, and various cancers. Experiments have shown that there is a causal relationship between chromatin organization and nuclear morphology. Decreases in heterochromatin levels, perturbations to heterochromatin organization, and increases in euchromatin levels all lead to misshapen nuclei, which exhibit deformations, such as nuclear blebs and nuclear ruptures. However, the polymer physical mechanisms of how chromatin governs nuclear shape and integrity are poorly understood. To investigate how heterochromatin and euchromatin, which are thought to microphase separate in vivo , govern nuclear morphology, we implemented a composite coarse-grained polymer and elastic shell model. By varying chromatin volume fraction (density), heterochromatin levels and structure, and heterochromatin-lamina interactions, we show how the spatial organization of chromatin polymer phases within the nucleus could perturb nuclear shape in some scenarios. Increasing the volume fraction of chromatin in the cell nucleus stabilizes the nuclear lamina against large fluctuations. However, surprisingly, we find that increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations in our simulations by a "wetting"-like interaction. In contrast, shape fluctuations are largely insensitive to the internal structure of the heterochromatin, such as the presence or absence of chromatin-chromatin crosslinks. Therefore, our simulations suggest that heterochromatin accumulation at the nuclear periphery could perturb nuclear morphology in a nucleus or nuclear region that is sufficiently soft, while stabilization of the nucleus via heterochromatin likely occurs through mechanisms other than chromatin microphase organization.
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9
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: compaction, segregation, and entanglement suppression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576729. [PMID: 38328091 PMCID: PMC10849557 DOI: 10.1101/2024.01.22.576729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross over between two and four at contour lengths on the order of 30 kilo-base pairs (kbp). The anomalously high fractal dimension D = 4 is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ( Δ t ) longer than tens of minutes to be proportional to Δ t 1 / 3 . We validate our results with hybrid molecular dynamics - Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, United States
- Department of Physics, Duke University, Durham, North Carolina, 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina, 27708, United States
- World Premier International Research Center Initiative — Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, 001-0021, Japan
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10
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Berg IK, Currey ML, Gupta S, Berrada Y, Nguyen BV, Pho M, Patteson AE, Schwarz JM, Banigan EJ, Stephens AD. Transcription inhibition suppresses nuclear blebbing and rupture independently of nuclear rigidity. J Cell Sci 2023; 136:jcs261547. [PMID: 37756607 PMCID: PMC10660790 DOI: 10.1242/jcs.261547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Chromatin plays an essential role in the nuclear mechanical response and determining nuclear shape, which maintain nuclear compartmentalization and function. However, major genomic functions, such as transcription activity, might also impact cell nuclear shape via blebbing and rupture through their effects on chromatin structure and dynamics. To test this idea, we inhibited transcription with several RNA polymerase II inhibitors in wild-type cells and perturbed cells that presented increased nuclear blebbing. Transcription inhibition suppressed nuclear blebbing for several cell types, nuclear perturbations and transcription inhibitors. Furthermore, transcription inhibition suppressed nuclear bleb formation, bleb stabilization and bleb-based nuclear ruptures. Interestingly, transcription inhibition did not alter the histone H3 lysine 9 (H3K9) modification state, nuclear rigidity, and actin compression and contraction, which typically control nuclear blebbing. Polymer simulations suggested that RNA polymerase II motor activity within chromatin could drive chromatin motions that deform the nuclear periphery. Our data provide evidence that transcription inhibition suppresses nuclear blebbing and rupture, in a manner separate and distinct from chromatin rigidity.
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Affiliation(s)
- Isabel K. Berg
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Marilena L. Currey
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sarthak Gupta
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - Yasmin Berrada
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Bao V. Nguyen
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Mai Pho
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Alison E. Patteson
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - J. M. Schwarz
- Department of Physics and BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
- Indian Creek Farm, Ithaca, NY 14850, USA
| | - Edward J. Banigan
- Institute of Medical Engineering & Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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11
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Liu JX, Haataja MP, Košmrlj A, Datta SS, Arnold CB, Priestley RD. Liquid-liquid phase separation within fibrillar networks. Nat Commun 2023; 14:6085. [PMID: 37770446 PMCID: PMC10539382 DOI: 10.1038/s41467-023-41528-8] [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: 02/14/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Complex fibrillar networks mediate liquid-liquid phase separation of biomolecular condensates within the cell. Mechanical interactions between these condensates and the surrounding networks are increasingly implicated in the physiology of the condensates and yet, the physical principles underlying phase separation within intracellular media remain poorly understood. Here, we elucidate the dynamics and mechanics of liquid-liquid phase separation within fibrillar networks by condensing oil droplets within biopolymer gels. We find that condensates constrained within the network pore space grow in abrupt temporal bursts. The subsequent restructuring of condensates and concomitant network deformation is contingent on the fracture of network fibrils, which is determined by a competition between condensate capillarity and network strength. As a synthetic analog to intracellular phase separation, these results further our understanding of the mechanical interactions between biomolecular condensates and fibrillar networks in the cell.
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Affiliation(s)
- Jason X Liu
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Craig B Arnold
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Rodney D Priestley
- Princeton Materials Institute, Princeton University, Princeton, NJ, 08544, USA.
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
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12
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Chaki S, Theeyancheri L, Chakrabarti R. A polymer chain with dipolar active forces in connection to spatial organization of chromatin. SOFT MATTER 2023; 19:1348-1355. [PMID: 36723034 DOI: 10.1039/d2sm01170k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A living cell is an active environment where the organization and dynamics of chromatin are affected by different forms of activity. Optical experiments report that loci show subdiffusive dynamics and the chromatin fiber is seen to be coherent over micrometer-scale regions. Using a bead-spring polymer chain with dipolar active forces, we study how the subdiffusive motion of the loci generate large-scale coherent motion of the chromatin. We show that in the presence of extensile (contractile) activity, the dynamics of the loci grows faster (slower) and the spatial correlation length increases (decreases) compared to the case with no dipolar forces. Hence, both the dipolar active forces modify the elasticity of the chain. Interestingly in our model, the dynamics and organization of such dipolar active chains largely differ from the passive chain with renormalized elasticity.
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Affiliation(s)
- Subhasish Chaki
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois, 61801, USA.
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Ligesh Theeyancheri
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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13
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Jiang Z, Qi Y, Kamat K, Zhang B. Phase Separation and Correlated Motions in Motorized Genome. J Phys Chem B 2022; 126:5619-5628. [PMID: 35858189 PMCID: PMC9899348 DOI: 10.1021/acs.jpcb.2c03238] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human genome is arranged in the cell nucleus nonrandomly, and phase separation has been proposed as an important driving force for genome organization. However, the cell nucleus is an active system, and the contribution of nonequilibrium activities to phase separation and genome structure and dynamics remains to be explored. We simulated the genome using an energy function parametrized with chromosome conformation capture (Hi-C) data with the presence of active, nondirectional forces that break the detailed balance. We found that active forces that may arise from transcription and chromatin remodeling can dramatically impact the spatial localization of heterochromatin. When applied to euchromatin, active forces can drive heterochromatin to the nuclear envelope and compete with passive interactions among heterochromatin that tend to pull them in opposite directions. Furthermore, active forces induce long-range spatial correlations among genomic loci beyond single chromosome territories. We further showed that the impact of active forces could be understood from the effective temperature defined as the fluctuation-dissipation ratio. Our study suggests that nonequilibrium activities can significantly impact genome structure and dynamics, producing unexpected collective phenomena.
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Affiliation(s)
- Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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14
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Chubak I, Pachong SM, Kremer K, Likos CN, Smrek J. Active Topological Glass Confined within a Spherical Cavity. Macromolecules 2022; 55:956-964. [PMID: 35153336 PMCID: PMC8830202 DOI: 10.1021/acs.macromol.1c02471] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Iurii Chubak
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, Sorbonne Université CNRS, F-75005 Paris, France
| | | | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christos N. Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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15
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Mahajan A, Saintillan D. Self-induced hydrodynamic coil-stretch transition of active polymers. Phys Rev E 2022; 105:014608. [PMID: 35193223 DOI: 10.1103/physreve.105.014608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
We analyze the conformational dynamics and statistical properties of an active polymer model. The polymer is described as a freely jointed bead-rod chain subject to stochastic active force dipoles that act on the suspending solvent where they drive long-ranged fluid flows. Using Langevin simulations of isolated chains in unconfined domains, we show how the coupling of active flows with polymer conformations leads to emergent dynamics. Systems with contractile dipoles behave similarly to passive Brownian chains with enhanced fluctuations due to dipolar flows. In systems with extensile dipoles, however, our simulations uncover an active coil-stretch transition whereby the polymer spontaneously unfolds and stretches out in its own self-induced hydrodynamic flow, and we characterize this transition in terms of a dimensionless activity parameter comparing active dipolar forces to thermal fluctuations. We discuss our findings in the context of the classic coil-stretch transition of passive polymers in extensional flows and complement our simulations with a simple kinetic model for an active trimer.
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Affiliation(s)
- Achal Mahajan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - David Saintillan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California 92093, USA
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16
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Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin. Genome Res 2021; 32:28-43. [PMID: 34963660 PMCID: PMC8744683 DOI: 10.1101/gr.275827.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022]
Abstract
Chromosome organization and dynamics are involved in regulating many fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical heterogeneities may emerge from the same structural mechanisms. We found that the formation of topologically associating domains (TADs) is a key driver of chromatin motion heterogeneity. In particular, we showed that the local degree of compaction of the TAD regulates the transition from a weakly compact, fluid state of chromatin to a more compact, gel state exhibiting anomalous diffusion and coherent motion. Our work provides a comprehensive study of chromosome dynamics and a unified view of chromatin motion enabling interpretation of the wide variety of dynamical behaviors observed experimentally across different biological conditions, suggesting that the "liquid" or "solid" state of chromatin are in fact two sides of the same coin.
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17
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Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, Scalzo D, Telling A, Groudine M, Brangwynne CP, Marko JF, Stephens AD. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. eLife 2021; 10:e63972. [PMID: 34106828 PMCID: PMC8233041 DOI: 10.7554/elife.63972] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1α (CBX5) is unknown. We used a novel HP1α auxin-inducible degron human cell line to rapidly degrade HP1α. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1α is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1αI165E indicate that chromatin crosslinking via HP1α dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1α similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1α is therefore a critical chromatin-crosslinking protein that provides mechanical strength to chromosomes and the nucleus throughout the cell cycle and supports cellular functions.
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Affiliation(s)
- Amy R Strom
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Ronald J Biggs
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Katherine Chiu
- Biology Department, University of Massachusetts AmherstAmherstUnited States
| | - Cameron Herman
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Jimena Collado
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | | | - Leah J Tait
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - David Scalzo
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Agnes Telling
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Mark Groudine
- The Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Clifford P Brangwynne
- Howard Hughes Medical Institute, Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Andrew D Stephens
- Biology Department, University of Massachusetts AmherstAmherstUnited States
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