1
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Iso N, Norizoe Y, Sakaue T. Phase separation in soft repulsive polymer mixtures: foundation and implication for chromatin organization. SOFT MATTER 2024; 20:6848-6856. [PMID: 39157948 DOI: 10.1039/d4sm00309h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Given the wide range of length scales, the analysis of polymer systems often requires coarse-graining, for which various levels of description may be possible depending on the phenomenon under consideration. Here, we provide a super-coarse grained description, where polymers are represented as a succession of mesosopic soft beads which are allowed to overlap with others. We then investigate the phase separation behaviors in a mixture of such homopolymers based on mean-field theory, and discuss universal aspects of the miscibility phase diagram in comparison with the numerical simulation. We also discuss an extension of our analysis to mixtures involving random copolymers, which might be interesting in the context of chromatin organization in a cell nucleus.
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Affiliation(s)
- Naoki Iso
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Japan.
| | - Yuki Norizoe
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Japan.
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Japan.
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2
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Lao Z, Kamat KD, Jiang Z, Zhang B. OpenNucleome for high-resolution nuclear structural and dynamical modeling. eLife 2024; 13:RP93223. [PMID: 39146200 PMCID: PMC11326778 DOI: 10.7554/elife.93223] [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] [Indexed: 08/17/2024] Open
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of 'fixed points' within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Kartik D Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
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3
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Liu S, Athreya A, Lao Z, Zhang B. From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization. Annu Rev Biophys 2024; 53:221-245. [PMID: 38346246 PMCID: PMC11369498 DOI: 10.1146/annurev-biophys-030822-032650] [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] [Indexed: 07/18/2024]
Abstract
Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due to its complex, multiscale nature. Significant progress has been made in studying in vitro systems, uncovering the structure of individual nucleosomes and their arrays, and elucidating the role of physicochemical forces in stabilizing these structures. Additionally, remarkable advancements have been achieved in characterizing chromatin organization in vivo, particularly at the whole-chromosome level, revealing important features such as chromatin loops, topologically associating domains, and nuclear compartments. However, bridging the gap between in vitro and in vivo studies remains challenging. The resemblance between in vitro and in vivo chromatin conformations and the relevance of internucleosomal interactions for chromatin folding in vivo are subjects of debate. This article reviews experimental and computational studies conducted at various length scales, highlighting the significance of intrinsic interactions between nucleosomes and their roles in chromatin folding in vivo.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Advait Athreya
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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4
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Bonato A, Chiang M, Corbett D, Kitaev S, Marenduzzo D, Morozov A, Orlandini E. Topological Spectra and Entropy of Chromatin Loop Networks. PHYSICAL REVIEW LETTERS 2024; 132:248403. [PMID: 38949344 DOI: 10.1103/physrevlett.132.248403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/19/2024] [Indexed: 07/02/2024]
Abstract
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here, we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin. Unlike polymer networks previously studied, our chromatin networks have finite average distances between successive binding sites, and this leads to giant differences between the weights of topologies with the same number of edges and nodes but different wiring. These weights strongly favor rosettelike structures with a local cloud of loops with respect to more complicated nonlocal topologies. Our results suggest that genes should overwhelmingly fold into a small fraction of all possible 3D topologies, which can be robustly characterized by the framework we propose here.
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Affiliation(s)
- Andrea Bonato
- Department of Physics, University of Strathclyde, Glasgow G4 0NG, Scotland, United Kingdom
| | - Michael Chiang
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Dom Corbett
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Sergey Kitaev
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow G1 1XH, United Kingdom
| | - Davide Marenduzzo
- Department of Physics, University of Strathclyde, Glasgow G4 0NG, Scotland, United Kingdom
| | - Alexander Morozov
- Department of Physics, University of Strathclyde, Glasgow G4 0NG, Scotland, United Kingdom
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova and INFN, Sezione Padova, Via Marzolo 8, I-35131 Padova, Italy
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5
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Chaboche Q, Campos-Villalobos G, Giunta G, Dijkstra M, Cosentino Lagomarsino M, Scolari VF. A mean-field theory for predicting single polymer collapse induced by neutral crowders. SOFT MATTER 2024; 20:3271-3282. [PMID: 38456237 DOI: 10.1039/d3sm01522j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Macromolecular crowding can induce the collapse of a single long polymer into a globular form due to depletion forces of entropic nature. This phenomenon has been shown to play a significant role in compacting the genome within the bacterium Escherichia coli into a well-defined region of the cell known as the nucleoid. Motivated by the biological significance of this process, numerous theoretical and computational studies have searched for the primary determinants of the behavior of polymer-crowder phases. However, our understanding of this process remains incomplete and there is debate on a quantitatively unified description. In particular, different simulation studies with explicit crowders have proposed different order parameters as potential predictors for the collapse transition. In this work, we present a comprehensive analysis of published simulation data obtained from different sources. Based on the common behavior we find in this data, we develop a unified phenomenological model that we show to be predictive. Finally, to further validate the accuracy of the model, we conduct new simulations on polymers of various sizes, and investigate the role of jamming of the crowders.
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Affiliation(s)
- Quentin Chaboche
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, 75005 Paris, France
- IFOM ETS, The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
| | - Gerardo Campos-Villalobos
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Giuliana Giunta
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Marco Cosentino Lagomarsino
- IFOM ETS, The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
- Physics Department, University of Milan, and INFN, Milan, Italy
| | - Vittore F Scolari
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, 75005 Paris, France
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.
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6
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Lao Z, Kamat K, Jiang Z, Zhang B. OpenNucleome for high resolution nuclear structural and dynamical modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562451. [PMID: 37905090 PMCID: PMC10614770 DOI: 10.1101/2023.10.16.562451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The intricate structural organization of the human nucleus is fundamental to cellular function and gene regulation. Recent advancements in experimental techniques, including high-throughput sequencing and microscopy, have provided valuable insights into nuclear organization. Computational modeling has played significant roles in interpreting experimental observations by reconstructing high-resolution structural ensembles and uncovering organization principles. However, the absence of standardized modeling tools poses challenges for furthering nuclear investigations. We present OpenNucleome-an open-source software designed for conducting GPU-accelerated molecular dynamics simulations of the human nucleus. OpenNucleome offers particle-based representations of chromosomes at a resolution of 100 KB, encompassing nuclear lamina, nucleoli, and speckles. This software furnishes highly accurate structural models of nuclear architecture, affording the means for dynamic simulations of condensate formation, fusion, and exploration of non-equilibrium effects. We applied OpenNucleome to uncover the mechanisms driving the emergence of "fixed points" within the nucleus-signifying genomic loci robustly anchored in proximity to specific nuclear bodies for functional purposes. This anchoring remains resilient even amidst significant fluctuations in chromosome radial positions and nuclear shapes within individual cells. Our findings lend support to a nuclear zoning model that elucidates genome functionality. We anticipate OpenNucleome to serve as a valuable tool for nuclear investigations, streamlining mechanistic explorations and enhancing the interpretation of experimental observations.
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Affiliation(s)
- Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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7
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Portillo-Ledesma S, Chung S, Hoffman J, Schlick T. Regulation of chromatin architecture by transcription factor binding. eLife 2024; 12:RP91320. [PMID: 38241351 PMCID: PMC10945602 DOI: 10.7554/elife.91320] [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] [Indexed: 01/21/2024] Open
Abstract
Transcription factors (TF) bind to chromatin and regulate the expression of genes. The pair Myc:Max binds to E-box regulatory DNA elements throughout the genome to control the transcription of a large group of specific genes. We introduce an implicit modeling protocol for Myc:Max binding to mesoscale chromatin fibers at nucleosome resolution to determine TF effect on chromatin architecture and shed light into its mechanism of gene regulation. We first bind Myc:Max to different chromatin locations and show how it can direct fiber folding and formation of microdomains, and how this depends on the linker DNA length. Second, by simulating increasing concentrations of Myc:Max binding to fibers that differ in the DNA linker length, linker histone density, and acetylation levels, we assess the interplay between Myc:Max and other chromatin internal parameters. Third, we study the mechanism of gene silencing by Myc:Max binding to the Eed gene loci. Overall, our results show how chromatin architecture can be regulated by TF binding. The position of TF binding dictates the formation of microdomains that appear visible only at the ensemble level. At the same time, the level of linker histone and tail acetylation, or different linker DNA lengths, regulates the concentration-dependent effect of TF binding. Furthermore, we show how TF binding can repress gene expression by increasing fiber folding motifs that help compact and occlude the promoter region. Importantly, this effect can be reversed by increasing linker histone density. Overall, these results shed light on the epigenetic control of the genome dictated by TF binding.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York UniversityNew YorkUnited States
| | - Suckwoo Chung
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
| | - Jill Hoffman
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
- New York University-East China Normal University Center for Computational Chemistry, New York University ShanghaiShanghaiChina
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