1
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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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2
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Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M. Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603769. [PMID: 39071404 PMCID: PMC11275793 DOI: 10.1101/2024.07.16.603769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in-silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in-situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.
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Affiliation(s)
- Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Johan H. Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Krishna M. Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655
| | - Francesca Vercellone
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Fontana
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Florinda Di Pierno
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
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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 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] [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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Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Cell type- and transcription-independent spatial proximity between enhancers and promoters. Mol Biol Cell 2024; 35:ar96. [PMID: 38717453 PMCID: PMC11244156 DOI: 10.1091/mbc.e24-02-0082] [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] [Indexed: 06/07/2024] Open
Abstract
Cell type-specific enhancers are critically important for lineage specification. The mechanisms that determine cell-type specificity of enhancer activity, however, are not fully understood. Most current models for how enhancers function invoke physical proximity between enhancer elements and their target genes. Here, we use an imaging-based approach to examine the spatial relationship of cell type-specific enhancers and their target genes with single-cell resolution. Using high-throughput microscopy, we measure the spatial distance from target promoters to their cell type-specific active and inactive enhancers in individual pancreatic cells derived from distinct lineages. We find increased proximity of all promoter-enhancer pairs relative to non-enhancer pairs separated by similar genomic distances. Strikingly, spatial proximity between enhancers and target genes was unrelated to tissue-specific enhancer activity. Furthermore, promoter-enhancer proximity did not correlate with the expression status of target genes. Our results suggest that promoter-enhancer pairs exist in a distinctive chromatin environment but that genome folding is not a universal driver of cell-type specificity in enhancer function.
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Affiliation(s)
- Yasmine Mian
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Li Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Adib Keikhosravi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Konnie Guo
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - H Efsun Arda
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth H Finn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104
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5
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Sahoo S, Kadam S, Padinhateeri R, Kumar PBS. Nonequilibrium switching of segmental states can influence compaction of chromatin. SOFT MATTER 2024; 20:4621-4632. [PMID: 38819321 DOI: 10.1039/d4sm00274a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Knowledge about the dynamic nature of chromatin organization is essential to understand the regulation of processes like DNA transcription and repair. The existing models of chromatin assume that protein organization and chemical states along chromatin are static and the 3D organization is purely a result of protein-mediated intra-chromatin interactions. Here we present a new hypothesis that certain nonequilibrium processes, such as switching of chemical and physical states due to nucleosome assembly/disassembly or gene repression/activation, can also simultaneously influence chromatin configurations. To understand the implications of this inherent nonequilibrium switching, we present a block copolymer model of chromatin, with switching of its segmental states between two states, mimicking active/repressed or protein unbound/bound states. We show that competition between switching timescale Tt, polymer relaxation timescale τp, and segmental relaxation timescale τs can lead to non-trivial changes in chromatin organization, leading to changes in local compaction and contact probabilities. As a function of the switching timescale, the radius of gyration of chromatin shows a non-monotonic behavior with a prominent minimum when Tt ≈ τp and a maximum when Tt ≈ τs. We find that polymers with a small segment length exhibit a more compact structure than those with larger segment lengths. We also find that the switching can lead to higher contact probability and better mixing of far-away segments. Our study also shows that the nature of the distribution of chromatin clusters varies widely as we change the switching rate.
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Affiliation(s)
- Soudamini Sahoo
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad, 678623, India
- Department of Physics and Astronomy, National Institute of Technology Rourkela, Rourkela, 769008, India
| | - Sangram Kadam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad, 678623, India
- Department of Physics, Indian Institute of Technology Madras, Chennai, 600036, India
- Center for Soft and Biological Matter, Indian Institute of Technology Madras, Chennai, 600036, India
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6
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Korabel N, Warmenhoven JW, Henthorn NT, Ingram S, Fedotov S, Heaven CJ, Kirkby KJ, Taylor MJ, Merchant MJ. Modelling Heterogeneous Anomalous Dynamics of Radiation-Induced Double-Strand Breaks in DNA during Non-Homologous End-Joining Pathway. ENTROPY (BASEL, SWITZERLAND) 2024; 26:502. [PMID: 38920510 PMCID: PMC11202905 DOI: 10.3390/e26060502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024]
Abstract
The process of end-joining during nonhomologous repair of DNA double-strand breaks (DSBs) after radiation damage is considered. Experimental evidence has revealed that the dynamics of DSB ends exhibit subdiffusive motion rather than simple diffusion with rare directional movement. Traditional models often overlook the rare long-range directed motion. To address this limitation, we present a heterogeneous anomalous diffusion model consisting of subdiffusive fractional Brownian motion interchanged with short periods of long-range movement. Our model sheds light on the underlying mechanisms of heterogeneous diffusion in DSB repair and could be used to quantify the DSB dynamics on a time scale inaccessible to single particle tracking analysis. The model predicts that the long-range movement of DSB ends is responsible for the misrepair of DSBs in the form of dicentric chromosome lesions.
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Affiliation(s)
- Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, UK;
| | - John W. Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Nicholas T. Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Samuel Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Sergei Fedotov
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, UK;
| | - Charlotte J. Heaven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Karen J. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Michael J. Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Michael J. Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
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7
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Kant A, Guo Z, Vinayak V, Neguembor MV, Li WS, Agrawal V, Pujadas E, Almassalha L, Backman V, Lakadamyali M, Cosma MP, Shenoy VB. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nat Commun 2024; 15:4338. [PMID: 38773126 PMCID: PMC11109243 DOI: 10.1038/s41467-024-48698-z] [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: 04/24/2023] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, histone modifications, and chromatin extrusion. We predict that the size of heterochromatic domains is governed by a balance among the diffusive flux of methylated histones sustaining them and the acetylation reactions in the domains and the process of loop extrusion via supercoiling by RNAPII at their periphery, which contributes to size reduction. Super-resolution and nano-imaging of five distinct cell lines confirm the predictions indicating that the absence of transcription leads to larger heterochromatin domains. Furthermore, the model accurately reproduces the findings regarding how transcription-mediated supercoiling loss can mitigate the impacts of excessive cohesin loading. Our findings shed light on the role of transcription in genome organization, offering insights into chromatin dynamics and potential therapeutic targets.
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Affiliation(s)
- Aayush Kant
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zixian Guo
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vinayak Vinayak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Wing Shun Li
- Department of Applied Physics, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Vasundhara Agrawal
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Emily Pujadas
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Luay Almassalha
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA
| | - Vadim Backman
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- ICREA, Barcelona, 08010, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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8
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Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nat Commun 2024; 15:4178. [PMID: 38755200 PMCID: PMC11099156 DOI: 10.1038/s41467-024-48562-0] [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: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.
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Affiliation(s)
- Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yu Shi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA
| | - Katie L Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Hosein Rostamian
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Joseph Rodriguez
- National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA.
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9
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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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10
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Jeong D, Shi G, Li X, Thirumalai D. Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion. eLife 2024; 12:RP88564. [PMID: 38502563 PMCID: PMC10950330 DOI: 10.7554/elife.88564] [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: 03/21/2024] Open
Abstract
Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer-promoter/promoter-promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.
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Affiliation(s)
- Davin Jeong
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Guang Shi
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Xin Li
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - D Thirumalai
- Department of Chemistry, University of Texas at AustinAustinUnited States
- Department of Physics, University of Texas at AustinAustinUnited States
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11
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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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12
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Wei J, Xue Y, Liu Y, Tian H, Shao Y, Gao YQ. Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins. J Chem Phys 2024; 160:054904. [PMID: 38341710 DOI: 10.1063/5.0189692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024] Open
Abstract
Within the confines of a densely populated cell nucleus, chromatin undergoes intricate folding, forming loops, domains, and compartments under the governance of topological constraints and phase separation. This coordinated process inevitably introduces interference between different folding strategies. In this study, we model interphase chromatins as block copolymers with hetero-hierarchical loops within a confined system. Employing dissipative particle dynamics simulations and scaling analysis, we aim to explain how the structure and distribution of loop domains modulate the microphase separation of chromatins. Our results highlight the correlation between the microphase separation of the copolymer and the length, heterogeneity, and hierarchically nested levels of the loop domains. This correlation arises from steric repulsion intrinsic to loop domains. The steric repulsion induces variations in chain stiffness (including local orientation correlations and the persistence length), thereby influencing the degree of phase separation. Through simulations of block copolymers with distinct groups of hetero-hierarchical loop anchors, we successfully reproduce changes in phase separation across diverse cell lines, under fixed interaction parameters. These findings, in qualitative alignment with Hi-C data, suggest that the variations of loop constraints alone possess the capacity to regulate higher-order structures and the gene expressions of interphase chromatins.
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Affiliation(s)
| | - Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Yawei Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Hao Tian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Yingfeng Shao
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Qin Gao
- Changping Laboratory, Beijing 102206, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- Shenzhen Bay Laboratory, 5F, No. 9 Duxue Rd., Nanshan District, Shenzhen 518055, Guangdong, China
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13
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Das R, Sakaue T, Shivashankar GV, Prost J, Hiraiwa T. Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics. PHYSICAL REVIEW LETTERS 2024; 132:058401. [PMID: 38364140 DOI: 10.1103/physrevlett.132.058401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus-some of those transiently link and pass two chromatin segments. Here, we study how such an active perturbation affects fluctuating dynamics of an inclusion in the chromatic medium. Using numerical simulations and a versatile effective model, we categorize inclusion dynamics into three distinct modes. The transient-link-and-pass activity speeds up inclusion dynamics by affecting a slow mode related to chromatin remodeling, viz., size and shape of the chromatin meshes.
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Affiliation(s)
- Rakesh Das
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, Kanagawa 252-5258, Japan
| | - G V Shivashankar
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Villigen 8092, Switzerland
- Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Jacques Prost
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Laboratoire Physico Chimie Curie, Institut Curie, Paris Science et Lettres Research University, 75005 Paris, France
| | - Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
- Institute of Physics, Academia Sinica, Taipei City 115201, Taiwan
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14
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Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet 2024; 25:123-141. [PMID: 37673975 PMCID: PMC11127719 DOI: 10.1038/s41576-023-00638-1] [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] [Accepted: 07/12/2023] [Indexed: 09/08/2023]
Abstract
Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease.
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Affiliation(s)
- Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Lorenzo Boninsegna
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Muyu Yang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tom Misteli
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Frank Alber
- Department of Microbiology, Immunology and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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15
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Jung Y, Sadeghi A, Ha BY. Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS. Sci Rep 2024; 14:139. [PMID: 38167921 PMCID: PMC10762067 DOI: 10.1038/s41598-023-50355-2] [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: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Cells orchestrate the action of various molecules toward organizing their chromosomes. Using a coarse-grained computational model, we study the compaction of bacterial chromosomes by the cross-linking protein H-NS and cellular crowders. In this work, H-NS, modeled as a mobile "binder," can bind to a chromosome-like polymer with a characteristic binding energy. The simulation results reported here clarify the relative role of biomolecular crowding and H-NS in condensing a bacterial chromosome in a quantitative manner. In particular, they shed light on the nature and degree of crowder and H-NS synergetics: while the presence of crowders enhances H-NS binding to a chromosome-like polymer, the presence of H-NS makes crowding effects more efficient, suggesting two-way synergetics in chain compaction. Also, the results show how crowding effects promote clustering of bound H-NS. For a sufficiently large concentration of H-NS, the cluster size increases with the volume fraction of crowders.
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Affiliation(s)
- Youngkyun Jung
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon, 34141, South Korea.
| | - Amir Sadeghi
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Bae-Yeun Ha
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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16
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Singh A, Chakrabarti S. Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture. PLoS Comput Biol 2023; 19:e1011725. [PMID: 38109423 PMCID: PMC10760866 DOI: 10.1371/journal.pcbi.1011725] [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: 07/24/2023] [Revised: 01/02/2024] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
The dynamics of inheritance of histones and their associated modifications across cell divisions can have major consequences on maintenance of the cellular epigenomic state. Recent experiments contradict the long-held notion that histone inheritance during replication is always local, suggesting that active and repressed regions of the genome exhibit fundamentally different histone dynamics independent of transcription-coupled turnover. Here we develop a stochastic model of histone dynamics at the replication fork and demonstrate that differential diffusivity of histones in active versus repressed chromatin is sufficient to quantitatively explain these recent experiments. Further, we use the model to predict patterns in histone mark similarity between pairs of genomic loci that should be developed as a result of diffusion, but cannot originate from either PRC2 mediated mark spreading or transcriptional processes. Interestingly, using a combination of CHIP-seq, replication timing and Hi-C datasets we demonstrate that all the computationally predicted patterns are consistently observed for both active and repressive histone marks in two different cell lines. While direct evidence for histone diffusion remains controversial, our results suggest that dislodged histones in euchromatin and facultative heterochromatin may exhibit some level of diffusion within "Diffusion-Accessible-Domains" (DADs), leading to redistribution of epigenetic marks within and across chromosomes. Preservation of the epigenomic state across cell divisions therefore might be achieved not by passing on strict positional information of histone marks, but by maintaining the marks in somewhat larger DADs of the genome.
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Affiliation(s)
- Archit Singh
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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17
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Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566470. [PMID: 38014222 PMCID: PMC10680651 DOI: 10.1101/2023.11.09.566470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we developed an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrated that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacted nucleosome diffusive properties in a manner that was dependent on local chromatin density and supportive of a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Our results reveal that nuclear heterogeneity arises from both active and passive process and highlights the need to account for different organizational principals when modeling different chromatin environments.
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18
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Abstract
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
- Department of Physics, University of Maryland, College Park, Maryland, USA;
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, Maryland, USA;
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
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19
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Dutta S, Ghosh A, Boettiger AN, Spakowitz AJ. Leveraging polymer modeling to reconstruct chromatin connectivity from live images. Biophys J 2023; 122:3532-3540. [PMID: 37542372 PMCID: PMC10502477 DOI: 10.1016/j.bpj.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/19/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023] Open
Abstract
Chromosomal dynamics plays a central role in a number of critical biological processes, such as transcriptional regulation, genetic recombination, and DNA replication. However, visualization of chromatin is generally limited to live imaging of a few fluorescently labeled chromosomal loci or high-resolution reconstruction of multiple loci from a single time frame. To aid in mapping the underlying chromosomal structure based on parsimonious experimental measurements, we present an exact analytical expression for the evolution of the polymer configuration based on a flexible-polymer model, and we propose an algorithm that tracks the polymer configuration from live images of chromatin marked with several fluorescent marks. Our theory identifies the resolution of microscopy needed to achieve high-accuracy tracking for a given spacing of markers, establishing the statistical confidence in the assignment of genome identity to the visualized marks. We then leverage experimental data of locus-tracking measurements to demonstrate the validity of our modeling approach and to establish a basis for the design of experiments with a desired resolution. Altogether, this work provides a computational approach founded on polymer physics that vastly improves the interpretation of in vivo measurements of biopolymer dynamics.
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Affiliation(s)
- Sayantan Dutta
- Department of Chemical Engineering, Stanford University, Stanford, California
| | - Ashesh Ghosh
- Department of Chemical Engineering, Stanford University, Stanford, California
| | | | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California.
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20
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Liu S, Wang C, Latham AP, Ding X, Zhang B. OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates. PLoS Comput Biol 2023; 19:e1011442. [PMID: 37695778 PMCID: PMC10513381 DOI: 10.1371/journal.pcbi.1011442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/21/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023] Open
Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performance on a single GPU that rivals the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that OpenABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Cong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew P. Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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21
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Eshghi I, Zidovska A, Grosberg AY. Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:69. [PMID: 37540478 DOI: 10.1140/epje/s10189-023-00327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of motors having polar symmetry, both in the linear response regime as well as in the long-term, fully nonlinear regime of the flows. The introduction of a boundary induces a particular geometry in the flows of chromatin, which we describe using vector spherical harmonics, a tool which greatly simplifies both our analytical and numerical approaches. We find that the long-term behavior of this model in confinement is dominated by steady, transverse flows of chromatin which circulate around the spherical domain. These circulating flows are found to be robust to perturbations, and their characteristic size is set by the size of the domain. This gives us further insight into active chromatin dynamics in the cell nucleus, and provides a foundation for development of further, more complex models of active chromatin dynamics.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA.
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22
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Chiariello AM, Abraham A, Bianco S, Esposito A, Vercellone F, Conte M, Fontana A, Nicodemi M. Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550709. [PMID: 37546924 PMCID: PMC10402158 DOI: 10.1101/2023.07.27.550709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
SARS-CoV-2 is able to re-structure chromatin organization and alters the epigenomic landscape of the host genome, though the mechanisms that produce such changes are still poorly understood. Here, we investigate with polymer physics chromatin re-organization of the host genome, in space and time upon SARS-CoV-2 viral infection. We show that re-structuring of A/B compartments is well explained by a re-modulation of intra-compartment homotypic affinities, which leads to the weakening of A-A interactions and enhances A-B mixing. At TAD level, re-arrangements are physically described by a general reduction of the loop extrusion activity coupled with an alteration of chromatin phase-separation properties, resulting in more intermingling between different TADs and spread in space of TADs themselves. In addition, the architecture of loci relevant to the antiviral interferon (IFN) response, such as DDX58 or IFIT, results more variable within the 3D single-molecule population of the infected model, suggesting that viral infection leads to a loss of chromatin structural specificity. Analysis of time trajectories of pairwise gene-enhancer and higher-order contacts reveals that such variability derives from a more fluctuating dynamics in infected case, suggesting that SARS-CoV-2 alters gene regulation by impacting the stability of the contact network in time. Overall, our study provides the first polymer-physics based 4D reconstruction of SARS-CoV-2 infected genome with mechanistic insights on the consequent gene mis-regulation.
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Affiliation(s)
- Andrea M. Chiariello
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Simona Bianco
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Francesca Vercellone
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Mattia Conte
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Andrea Fontana
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
- Berlin Institute for Medical Systems Biology at the Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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23
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Eshghi I, Zidovska A, Grosberg AY. Activity-Driven Phase Transition Causes Coherent Flows of Chromatin. PHYSICAL REVIEW LETTERS 2023; 131:048401. [PMID: 37566839 DOI: 10.1103/physrevlett.131.048401] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 08/13/2023]
Abstract
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular motors tethered to chromatin. Cooperation occurs if each motor acts simultaneously on the polymer and the surrounding solvent, exerting on them equal and opposite forces. This drives the flow of solvent past the polymer, which in turn affects the orientation of nearby motors and, if the drive is strong enough, an active polar ("ferromagnetic") phase of motors can spontaneously form. Depending on boundary conditions, either transverse flows or sustained longitudinal oscillations and waves are possible. Predicted length scales are consistent with experiments. We now have in hand a coarse-grained description of chromatin dynamics which reproduces the directed coherent flows of chromatin seen in experiments. This field-theoretic description can be analytically coupled to other features of the nuclear environment such as fluctuating or porous boundaries, local heterogeneities in the distribution of chromatin or its activity, leading to insights on the effects of activity on the cell nucleus and its contents.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, New York 10003, USA
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24
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Li Z, Portillo-Ledesma S, Schlick T. Brownian dynamics simulations of mesoscale chromatin fibers. Biophys J 2023; 122:2884-2897. [PMID: 36116007 PMCID: PMC10397810 DOI: 10.1016/j.bpj.2022.09.013] [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: 05/31/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The relationship between chromatin architecture and function defines a central problem in biology and medicine. Many computational chromatin models with atomic, coarse-grained, mesoscale, and polymer resolution have been used to shed light onto the mechanisms that dictate genome folding and regulation of gene expression. The associated simulation techniques range from Monte Carlo to molecular, Brownian, and Langevin dynamics. Here, we present an efficient Compute Unified Device Architecture (CUDA) implementation of Brownian dynamics (BD) to simulate chromatin fibers at the nucleosome resolution with our chromatin mesoscale model. With the CUDA implementation for computer architectures with graphic processing units (GPUs), we significantly accelerate compute-intensive hydrodynamic tensor calculations in the BD simulations by massive parallelization, boosting the performance a hundred-fold compared with central processing unit calculations. We validate our BD simulation approach by reproducing experimental trends on fiber diffusion and structure as a function of salt, linker histone binding, and histone-tail composition, as well as Monte Carlo equilibrium sampling results. Our approach proves to be physically accurate with performance that makes feasible the study of chromatin fibers in the range of kb or hundreds of nucleosomes (small gene). Such simulations are essential to advance the study of biological processes such as gene regulation and aberrant genome-structure related diseases.
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Affiliation(s)
- Zilong Li
- Department of Chemistry, New York University, New York, New York
| | | | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York; Courant Institute of Mathematical Sciences, New York University, New York, New York; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, China; Simons Center for Computational Physical Chemistry, New York University, New York, New York.
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25
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Kadam S, Kumari K, Manivannan V, Dutta S, Mitra MK, Padinhateeri R. Predicting scale-dependent chromatin polymer properties from systematic coarse-graining. Nat Commun 2023; 14:4108. [PMID: 37433821 PMCID: PMC10336007 DOI: 10.1038/s41467-023-39907-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
Simulating chromatin is crucial for predicting genome organization and dynamics. Although coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
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Affiliation(s)
- Sangram Kadam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Kiran Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Vinoth Manivannan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Shuvadip Dutta
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Mithun K Mitra
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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26
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Tolokh IS, Kinney NA, Sharakhov IV, Onufriev AV. Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin. Epigenetics Chromatin 2023; 16:21. [PMID: 37254161 PMCID: PMC10228000 DOI: 10.1186/s13072-023-00492-9] [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: 01/19/2023] [Accepted: 05/04/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics; however, relevant genome-wide experiments that may provide statistically significant conclusions remain difficult. RESULTS We have developed a coarse-grained dynamical model of D. melanogaster nuclei at TAD resolution that explicitly accounts for four distinct epigenetic classes of TADs and LAD-NE interactions. The model is parameterized to reproduce the experimental Hi-C map of the wild type (WT) nuclei; it describes time evolution of the chromatin over the G1 phase of the interphase. The simulations include an ensemble of nuclei, corresponding to the experimentally observed set of several possible mutual arrangements of chromosomal arms. The model is validated against multiple structural features of chromatin from several different experiments not used in model development. Predicted positioning of all LADs at the NE is highly dynamic-the same LAD can attach, detach and move far away from the NE multiple times during interphase. The probabilities of LADs to be in contact with the NE vary by an order of magnitude, despite all having the same affinity to the NE in the model. These probabilities are mostly determined by a highly variable local linear density of LADs along the genome, which also has the same strong effect on the predicted positioning of individual TADs -- higher probability of a TAD to be near NE is largely determined by a higher linear density of LADs surrounding this TAD. The distribution of LADs along the chromosome chains plays a notable role in maintaining a non-random average global structure of chromatin. Relatively high affinity of LADs to the NE in the WT nuclei substantially reduces sensitivity of the global radial chromatin distribution to variations in the strength of TAD-TAD interactions compared to the lamin depleted nuclei, where a small (0.5 kT) increase of cross-type TAD-TAD interactions doubles the chromatin density in the central nucleus region. CONCLUSIONS A dynamical model of the entire fruit fly genome makes multiple genome-wide predictions of biological interest. The distribution of LADs along the chromatin chains affects their probabilities to be in contact with the NE and radial positioning of highly mobile TADs, playing a notable role in creating a non-random average global structure of the chromatin. We conjecture that an important role of attractive LAD-NE interactions is to stabilize global chromatin structure against inevitable cell-to-cell variations in TAD-TAD interactions.
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Affiliation(s)
- Igor S. Tolokh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
| | - Nicholas Allen Kinney
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Entomology, Virginia Tech, Blacksburg, VA 24061 USA
- Edward Via College of Osteopathic Medicine, 2265 Kraft Drive, Blacksburg, VA 24060 USA
| | | | - Alexey V. Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
- Department of Physics, Virginia Tech, Blacksburg, VA 24061 USA
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061 USA
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27
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Amin A, Kadam S, Mieczkowski J, Ahmed I, Bhat YA, Shah F, Tolstorukov MY, Kingston RE, Padinhateeri R, Wani AH. Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility. Life Sci Alliance 2023; 6:e202201768. [PMID: 36849253 PMCID: PMC9973501 DOI: 10.26508/lsa.202201768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Abstract
Chromatin attains its three-dimensional (3D) conformation by establishing contacts between different noncontiguous regions. Sterile Alpha Motif (SAM)-mediated polymerization of the polyhomeotic (PH) protein regulates subnuclear clustering of Polycomb Repressive Complex 1 (PRC1) and chromatin topology. The mutations that perturb the ability of the PH to polymerize, disrupt long-range chromatin contacts, alter Hox gene expression, and lead to developmental defects. To understand the underlying mechanism, we combined the experiments and theory to investigate the effect of this SAM domain mutation on nucleosome occupancy and accessibility on a genome wide scale. Our data show that disruption of PH polymerization because of SAM domain mutation decreases nucleosome occupancy and alters accessibility. Polymer simulations investigating the interplay between distant chromatin contacts and nucleosome occupancy, both of which are regulated by PH polymerization, suggest that nucleosome density increases when contacts between different regions of chromatin are established. Taken together, it appears that SAM domain-mediated PH polymerization biomechanically regulates the organization of chromatin at multiple scales from nucleosomes to chromosomes and we suggest that higher order organization can have a top-down causation effect on nucleosome occupancy.
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Affiliation(s)
- Adfar Amin
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Sangram Kadam
- Department of Biosciences and Bioengineering, IIT, Bombay, India
| | - Jakub Mieczkowski
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Ikhlak Ahmed
- CIRI, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Younus A Bhat
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Fouziya Shah
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | | | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Ajazul H Wani
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
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28
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Dey A, Shi G, Takaki R, Thirumalai D. Structural changes in chromosomes driven by multiple condensin motors during mitosis. Cell Rep 2023; 42:112348. [PMID: 37027299 DOI: 10.1016/j.celrep.2023.112348] [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: 06/29/2022] [Revised: 11/10/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
We create a computational framework that utilizes loop extrusion (LE) by multiple condensin I/II motors to predict changes in chromosome organization during mitosis. The theory accurately reproduces the experimental contact probability profiles for the mitotic chromosomes in HeLa and DT40 cells. The LE rate is smaller at the start of mitosis and increases as the cells approach metaphase. Condensin II-mediated mean loop size is about six times larger than loops because of condensin I. The loops, which overlap each other, are stapled to a central dynamically changing helical scaffold formed by the motors during the LE process. A polymer physics-based data-driven method that uses the Hi-C contact map as the only input shows that the helix is characterized as random helix perversions (RHPs) in which the handedness changes randomly along the scaffold. The theoretical predictions, which are testable using imaging experiments, do not contain any parameters.
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Affiliation(s)
- Atreya Dey
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Guang Shi
- Department of Materials Science, University of Illinois, Urbana, IL 61801, USA
| | - Ryota Takaki
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str.38, 01187 Dresden, Saxony, Germany
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA; Department of Physics, The University of Texas at Austin, Austin, TX 78712, USA.
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29
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Liu S, Wang C, Latham A, Ding X, Zhang B. OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537533. [PMID: 37131742 PMCID: PMC10153273 DOI: 10.1101/2023.04.19.537533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performances on a single GPU that rival the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that Open-ABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates. Open-ABC is available at https://github.com/ZhangGroup-MITChemistry/OpenABC.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cong Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xinqiang Ding
- 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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30
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Erdel F. Phase transitions in heterochromatin organization. Curr Opin Struct Biol 2023; 80:102597. [PMID: 37087823 DOI: 10.1016/j.sbi.2023.102597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Heterochromatin formation has been proposed to involve phase transitions on the level of the three-dimensional folding of heterochromatin regions and the liquid-liquid demixing of heterochromatin proteins. Here, I outline the hallmarks of such transitions and the current challenges to detect them in living cells. I further discuss the abundance and properties of prominent heterochromatin proteins and relate them to their potential role in driving phase transitions. Recent data from mouse fibroblasts indicate that pericentric heterochromatin is organized via a reordering transition on the level of heterochromatin regions that does not necessarily involve liquid-liquid demixing of heterochromatin proteins. Evaluating key hallmarks of the different candidate phase transition mechanisms across cell types and species will be needed to complete the current picture.
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Affiliation(s)
- Fabian Erdel
- MCD, Center for Integrative Biology (CBI), CNRS, UPS, Toulouse, France.
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31
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Kamat K, Lao Z, Qi Y, Wang Y, Ma J, Zhang B. Compartmentalization with nuclear landmarks yields random, yet precise, genome organization. Biophys J 2023; 122:1376-1389. [PMID: 36871158 PMCID: PMC10111368 DOI: 10.1016/j.bpj.2023.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The 3D organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made in deciphering the folding mechanisms of individual chromosomes, the principles of the dynamic large-scale spatial arrangement of all chromosomes inside the nucleus are poorly understood. We use polymer simulations to model the diploid human genome compartmentalization relative to nuclear bodies such as nuclear lamina, nucleoli, and speckles. We show that a self-organization process based on a cophase separation between chromosomes and nuclear bodies can capture various features of genome organization, including the formation of chromosome territories, phase separation of A/B compartments, and the liquid property of nuclear bodies. The simulated 3D structures quantitatively reproduce both sequencing-based genomic mapping and imaging assays that probe chromatin interaction with nuclear bodies. Importantly, our model captures the heterogeneous distribution of chromosome positioning across cells while simultaneously producing well-defined distances between active chromatin and nuclear speckles. Such heterogeneity and preciseness of genome organization can coexist due to the nonspecificity of phase separation and the slow chromosome dynamics. Together, our work reveals that the cophase separation provides a robust mechanism for us to produce functionally important 3D contacts without requiring thermodynamic equilibration that can be difficult to achieve.
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Affiliation(s)
- Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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32
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Abdulla AZ, Salari H, Tortora MMC, Vaillant C, Jost D. 4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling. Curr Opin Genet Dev 2023; 79:102033. [PMID: 36893485 DOI: 10.1016/j.gde.2023.102033] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023]
Abstract
Recent experimental observations suggest a strong coupling between the 3D nuclear chromosome organization and epigenomics. However, the mechanistic and functional bases of such interplay remain elusive. In this review, we describe how biophysical modeling has been instrumental in characterizing how genome folding may impact the formation of epigenomic domains and, conversely, how epigenomic marks may affect chromosome conformation. Finally, we discuss how this mutual feedback loop between chromatin organization and epigenome regulation, via the formation of physicochemical nanoreactors, may represent a key functional role of 3D compartmentalization in the assembly and maintenance of stable - but yet plastic - epigenomic landscapes.
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Affiliation(s)
- Amith Z Abdulla
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France; École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France. https://twitter.com/@AmithZafal
| | - Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France; École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France. https://twitter.com/@hosseinsalari65
| | - Maxime M C Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France
| | - Cédric Vaillant
- École Normale Supérieure de Lyon, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France.
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, 46 Allée d'Italie, 69007 Lyon, France.
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33
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Shi G, Thirumalai D. A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants. Nat Commun 2023; 14:1150. [PMID: 36854665 PMCID: PMC9974990 DOI: 10.1038/s41467-023-36412-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023] Open
Abstract
The principles that govern the organization of genomes, which are needed for an understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three-dimensional (3D) structures are known. Recently, single-cell imaging techniques have been developed to determine the 3D coordinates of genomic loci in vivo. Here, we introduce a computational method (Distance Matrix to Ensemble of Structures, DIMES), based on the maximum entropy principle, with experimental pairwise distances between loci as constraints, to generate a unique ensemble of 3D chromatin structures. Using the ensemble of structures, we quantitatively account for the distribution of pairwise distances, three-body co-localization, and higher-order interactions. The DIMES method can be applied to both small and chromosome-scale imaging data to quantify the extent of heterogeneity and fluctuations in the shapes across various length scales. We develop a perturbation method in conjunction with DIMES to predict the changes in 3D structures from structural variations. Our method also reveals quantitative differences between the 3D structures inferred from Hi-C and those measured in imaging experiments. Finally, the physical interpretation of the parameters extracted from DIMES provides insights into the origin of phase separation between euchromatin and heterochromatin domains.
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Affiliation(s)
- Guang Shi
- Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712, USA. .,Department of Materials Science, University of Illinois, Urbana, Illinois, 61801, USA.
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712, USA. .,Department of Physics, University of Texas at Austin, Austin, Texas, 78712, USA.
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34
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Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling. Int J Mol Sci 2023; 24:ijms24043660. [PMID: 36835064 PMCID: PMC9967178 DOI: 10.3390/ijms24043660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Understanding the mechanisms underlying the complex 3D architecture of mammalian genomes poses, at a more fundamental level, the problem of how two or multiple genomic sites can establish physical contacts in the nucleus of the cells. Beyond stochastic and fleeting encounters related to the polymeric nature of chromatin, experiments have revealed specific, privileged patterns of interactions that suggest the existence of basic organizing principles of folding. In this review, we focus on two major and recently proposed physical processes of chromatin organization: loop-extrusion and polymer phase-separation, both supported by increasing experimental evidence. We discuss their implementation into polymer physics models, which we test against available single-cell super-resolution imaging data, showing that both mechanisms can cooperate to shape chromatin structure at the single-molecule level. Next, by exploiting the comprehension of the underlying molecular mechanisms, we illustrate how such polymer models can be used as powerful tools to make predictions in silico that can complement experiments in understanding genome folding. To this aim, we focus on recent key applications, such as the prediction of chromatin structure rearrangements upon disease-associated mutations and the identification of the putative chromatin organizing factors that orchestrate the specificity of DNA regulatory contacts genome-wide.
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35
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Contessoto VG, Dudchenko O, Aiden EL, Wolynes PG, Onuchic JN, Di Pierro M. Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nat Commun 2023; 14:326. [PMID: 36658127 PMCID: PMC9852290 DOI: 10.1038/s41467-023-35909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
We use data-driven physical simulations to study the three-dimensional architecture of the Aedes aegypti genome. Hi-C maps exhibit both a broad diagonal and compartmentalization with telomeres and centromeres clustering together. Physical modeling reveals that these observations correspond to an ensemble of 3D chromosomal structures that are folded over and partially condensed. Clustering of the centromeres and telomeres near the nuclear lamina appears to be a necessary condition for the formation of the observed structures. Further analysis of the mechanical properties of the genome reveals that the chromosomes of Aedes aegypti, by virtue of their atypical structural organization, are highly sensitive to the deformation of the nuclei. This last finding provides a possible physical mechanism linking mechanical cues to gene regulation.
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Affiliation(s)
- Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Instituto de Biociências, Letras e Ciências Exatas, UNESP - Univ. Estadual Paulista, Departamento de Física, São José do Rio Preto, SP, Brazil.
| | - Olga Dudchenko
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erez Lieberman Aiden
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Physics & Astronomy, Rice University, Houston, TX, USA.,Department of Chemistry, Rice University, Houston, TX, USA.,Department of Biosciences, Rice University, Houston, TX, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Physics & Astronomy, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Biosciences, Rice University, Houston, TX, USA.
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA, USA. .,Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA.
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36
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Abstract
In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.
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37
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Finn EH, Misteli T. Nuclear position modulates long-range chromatin interactions. PLoS Genet 2022; 18:e1010451. [PMID: 36206323 PMCID: PMC9581366 DOI: 10.1371/journal.pgen.1010451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/19/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022] Open
Abstract
The human genome is non-randomly organized within the cell nucleus. Spatial mapping of genome folding by biochemical methods and imaging has revealed extensive variation in locus interaction frequencies between cells in a population and between homologs within an individual cell. Commonly used mapping approaches typically examine either the relative position of genomic sites to each other or the position of individual loci relative to nuclear landmarks. Whether the frequency of specific chromatin-chromatin interactions is affected by where in the nuclear space a locus is located is unknown. Here, we have simultaneously mapped at the single cell level the interaction frequencies and radial position of more than a hundred locus pairs using high-throughput imaging to ask whether the location within the nucleus affects interaction frequency. We find strong enrichment of many interactions at specific radial positions. Position-dependency of interactions was cell-type specific, correlated with local chromatin type, and cell-type-specific enriched associations were marked by increased variability, sometimes without a significant decrease in mean spatial distance. These observations demonstrate that the folding of the chromatin fiber, which brings genomically distant loci into proximity, and the position of that chromatin fiber relative to nuclear landmarks, are closely linked.
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Affiliation(s)
- Elizabeth H. Finn
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail: (EHF); (TM)
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (EHF); (TM)
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38
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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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39
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Locatelli M, Lawrimore J, Lin H, Sanaullah S, Seitz C, Segall D, Kefer P, Salvador Moreno N, Lietz B, Anderson R, Holmes J, Yuan C, Holzwarth G, Bloom KS, Liu J, Bonin K, Vidi PA. DNA damage reduces heterogeneity and coherence of chromatin motions. Proc Natl Acad Sci U S A 2022; 119:e2205166119. [PMID: 35858349 PMCID: PMC9304018 DOI: 10.1073/pnas.2205166119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 01/14/2023] Open
Abstract
Chromatin motions depend on and may regulate genome functions, in particular the DNA damage response. In yeast, DNA double-strand breaks (DSBs) globally increase chromatin diffusion, whereas in higher eukaryotes the impact of DSBs on chromatin dynamics is more nuanced. We mapped the motions of chromatin microdomains in mammalian cells using diffractive optics and photoactivatable chromatin probes and found a high level of spatial heterogeneity. DNA damage reduces heterogeneity and imposes spatially defined shifts in motions: Distal to DNA breaks, chromatin motions are globally reduced, whereas chromatin retains higher mobility at break sites. These effects are driven by context-dependent changes in chromatin compaction. Photoactivated lattices of chromatin microdomains are ideal to quantify microscale coupling of chromatin motion. We measured correlation distances up to 2 µm in the cell nucleus, spanning chromosome territories, and speculate that this correlation distance between chromatin microdomains corresponds to the physical separation of A and B compartments identified in chromosome conformation capture experiments. After DNA damage, chromatin motions become less correlated, a phenomenon driven by phase separation at DSBs. Our data indicate tight spatial control of chromatin motions after genomic insults, which may facilitate repair at the break sites and prevent deleterious contacts of DSBs, thereby reducing the risk of genomic rearrangements.
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Affiliation(s)
- Maëlle Locatelli
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Hua Lin
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Sarvath Sanaullah
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Clayton Seitz
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Dave Segall
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Paul Kefer
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Naike Salvador Moreno
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Benton Lietz
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Rebecca Anderson
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Julia Holmes
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907
| | - George Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jing Liu
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
- Laboratoire InGenO, Institut de Cancérologie de l’Ouest, 49055 Angers, France
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40
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Kumari K, Ravi Prakash J, Padinhateeri R. Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains. Biophys J 2022; 121:2794-2812. [PMID: 35672951 PMCID: PMC9382282 DOI: 10.1016/j.bpj.2022.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
Abstract
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene regulation and DNA replication occur in the context of these domains, it is important to understand their organization, fluctuation, and dynamics. To simulate chromatin domains, one requires knowledge of interaction strengths among chromatin segments. Here, we derive interaction-strength parameters from experimentally known contact maps and use them to predict chromatin organization and dynamics. Taking two domains on the human chromosome as examples, we investigate its three-dimensional organization, size/shape fluctuations, and dynamics of different segments within a domain, accounting for hydrodynamic effects. Considering different cell types, we quantify changes in interaction strengths and chromatin shape fluctuations in different epigenetic states. Perturbing the interaction strengths systematically, we further investigate how epigenetic-like changes can alter the spatio-temporal nature of the domains. Our results show that heterogeneous weak interactions are crucial in determining the organization of the domains. Computing effective stiffness and relaxation times, we investigate how perturbations in interactions affect the solid- and liquid-like nature of chromatin domains. Quantifying dynamics of chromatin segments within a domain, we show how the competition between polymer entropy and interaction energy influence the timescales of loop formation and maintenance of stable loops.
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Affiliation(s)
- Kiran Kumari
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai, Maharashtra, 400076, India; Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India; Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia.
| | - J Ravi Prakash
- Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia.
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India.
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41
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Williams MR, Xiaokang Y, Hathaway NA, Kireev D. A simulation model of heterochromatin formation at submolecular detail. iScience 2022; 25:104590. [PMID: 35800764 PMCID: PMC9254115 DOI: 10.1016/j.isci.2022.104590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/16/2021] [Accepted: 06/08/2022] [Indexed: 11/15/2022] Open
Abstract
Heterochromatin is a physical state of the chromatin fiber that maintains gene repression during cell development. Although evidence exists on molecular mechanisms involved in heterochromatin formation, a detailed structural mechanism of heterochromatin formation needs a better understanding. We made use of a simple Monte Carlo simulation model with explicit representation of key molecular events to observe molecular self-organization leading to heterochromatin formation. Our simulations provide a structural interpretation of several important traits of the heterochromatinization process. In particular, this study provides a depiction of how small amounts of HP1 are able to induce a highly condensed chromatin state through HP1 dimerization and bridging of sequence-remote nucleosomes. It also elucidates structural roots of a yet poorly understood phenomenon of a nondeterministic nature of heterochromatin formation and subsequent gene repression. Experimental chromatin in vivo assay provides an unbiased estimate of time scale of repressive response to a heterochromatin-triggering event.
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Affiliation(s)
- Michael R. Williams
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
| | - Yan Xiaokang
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
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42
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Conte M, Irani E, Chiariello AM, Abraham A, Bianco S, Esposito A, Nicodemi M. Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding. Nat Commun 2022; 13:4070. [PMID: 35831310 PMCID: PMC9279381 DOI: 10.1038/s41467-022-31856-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
Loop-extrusion and phase-separation have been proposed as mechanisms that shape chromosome spatial organization. It is unclear, however, how they perform relative to each other in explaining chromatin architecture data and whether they compete or co-exist at the single-molecule level. Here, we compare models of polymer physics based on loop-extrusion and phase-separation, as well as models where both mechanisms act simultaneously in a single molecule, against multiplexed FISH data available in human loci in IMR90 and HCT116 cells. We find that the different models recapitulate bulk Hi-C and average multiplexed microscopy data. Single-molecule chromatin conformations are also well captured, especially by phase-separation based models that better reflect the experimentally reported segregation in globules of the considered genomic loci and their cell-to-cell structural variability. Such a variability is consistent with two main concurrent causes: single-cell epigenetic heterogeneity and an intrinsic thermodynamic conformational degeneracy of folding. Overall, the model combining loop-extrusion and polymer phase-separation provides a very good description of the data, particularly higher-order contacts, showing that the two mechanisms can co-exist in shaping chromatin architecture in single cells.
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Affiliation(s)
- Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Ehsan Irani
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre (MDC) for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health (BIH), MDC-Berlin, Berlin, Germany
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Simona Bianco
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre (MDC) for Molecular Medicine, Berlin, Germany
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126, Naples, Italy.
- Berlin Institute for Medical Systems Biology, Max-Delbrück Centre (MDC) for Molecular Medicine, Berlin, Germany.
- Berlin Institute of Health (BIH), MDC-Berlin, Berlin, Germany.
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43
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Contessoto VG, Cheng RR, Onuchic JN. Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling. Curr Opin Struct Biol 2022; 75:102418. [PMID: 35839701 DOI: 10.1016/j.sbi.2022.102418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/04/2022] [Accepted: 06/03/2022] [Indexed: 11/03/2022]
Abstract
In recent years, much effort has been devoted to understanding the three-dimensional (3D) organization of the genome and how genomic structure mediates nuclear function. The development of experimental techniques that combine DNA proximity ligation with high-throughput sequencing, such as Hi-C, have substantially improved our knowledge about chromatin organization. Numerous experimental advancements, not only utilizing DNA proximity ligation but also high-resolution genome imaging (DNA tracing), have required theoretical modeling to determine the structural ensembles consistent with such data. These 3D polymer models of the genome provide an understanding of the physical mechanisms governing genome architecture. Here, we present an overview of the recent advances in modeling the ensemble of 3D chromosomal structures by employing the maximum entropy approach combined with polymer physics. Particularly, we discuss the minimal chromatin model (MiChroM) along with the "maximum entropy genomic annotations from biomarkers associated with structural ensembles" (MEGABASE) model, which have been remarkably successful in the accurate modeling of chromosomes consistent with both Hi-C and DNA-tracing data.
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Affiliation(s)
- Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. https://twitter.com/Vini_Contessoto
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. https://twitter.com/ryanrcheng
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Department of Physics and Astronomy, Rice University, Houston, TX, USA; Department of Chemistry, Rice University, Houston, TX, USA; Department of Biosciences, Rice University, Houston, TX, USA.
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44
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Katava M, Shi G, Thirumalai D. Chromatin dynamics controls epigenetic domain formation. Biophys J 2022; 121:2895-2905. [PMID: 35799447 PMCID: PMC9388564 DOI: 10.1016/j.bpj.2022.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/17/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022] Open
Abstract
In multicellular organisms, nucleosomes carry epigenetic information that defines distinct patterns of gene expression, which are inherited over multiple generations. The enhanced capacity for information storage arises by nucleosome modifications, which are triggered by enzymes. Modified nucleosomes can transfer the mark to others that are in proximity by a positive-feedback (modification begets modification) mechanism. We created a generic polymer model, referred to as 3DSpreader, in which each bead, representing a nucleosome, stochastically switches between unmodified (U) and modified (M) states depending on the states of the neighbors. Modification begins at a specific nucleation site (NS) that is permanently in the M state, and could spread to other loci that is dictated by chromatin dynamics. Transfer of marks among the non-nucleation loci occurs stochastically as chromatin evolves in time. If the spreading rate is slower than the chromatin relaxation rate, which is biologically pertinent, then finite-sized domains form, driven by contacts between nucleosomes through a three-dimensional looping mechanism. Surprisingly, simulations based on the 3DSpreader model result in finite bounded domains that arise without the need for any boundary elements. Maintenance of spatially and temporally stable domains requires the presence of the NS, whose removal eliminates finite-sized modified domains. The theoretical predictions are in excellent agreement with experimental data for H3K9me3 spreading in mouse embryonic stem cells.
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Affiliation(s)
- Marina Katava
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, Paris, France
| | - Guang Shi
- Department of Chemistry, The University of Texas, Austin, Texas
| | - D Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas.
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45
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Yildirim A, Boninsegna L, Zhan Y, Alber F. Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. Cold Spring Harb Perspect Biol 2022; 14:a039693. [PMID: 34400556 PMCID: PMC9248826 DOI: 10.1101/cshperspect.a039693] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still accessible for vital cellular processes, has grown dramatically over recent years with advances in microscopy and genomics technologies. Computational methods have played a pivotal role in the structural interpretation of experimental data, which helped unravel some organizational principles of genome folding. Here, we give an overview of current computational efforts in mechanistic and data-driven 3D chromatin structure modeling. We discuss strengths and limitations of different methods and evaluate the added value and benefits of computational approaches to infer the 3D structural and dynamic properties of the genome and its underlying mechanisms at different scales and resolution, ranging from the dynamic formation of chromatin loops and topological associated domains to nuclear compartmentalization of chromatin and nuclear bodies.
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Affiliation(s)
- Asli Yildirim
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Lorenzo Boninsegna
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Yuxiang Zhan
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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46
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Michieletto D, Fosado YAG, Melas E, Baiesi M, Tubiana L, Orlandini E. Dynamic and facilitated binding of topoisomerase accelerates topological relaxation. Nucleic Acids Res 2022; 50:4659-4668. [PMID: 35474478 PMCID: PMC9071436 DOI: 10.1093/nar/gkac260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expected of proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc. Intriguingly, this in turn implies that the timescale of topological relaxation is virtually independent of the substrate length. We then discover that considering binding biases due to facilitated diffusion on looped substrates steers the sampling of the topological space closer to the boundaries between different topoisomers yielding an optimally fast topological relaxation. We discuss our findings in the context of topological simplification in vitro and in vivo.
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Affiliation(s)
| | | | - Elias Melas
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy,INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Luca Tubiana
- Physics Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy,Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy,INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
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47
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Paul S, Majumder S, Das SK, Janke W. Effects of alignment activity on the collapse kinetics of a flexible polymer. SOFT MATTER 2022; 18:1978-1990. [PMID: 35023525 DOI: 10.1039/d1sm01055g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an alignment rule adapted from the Vicsek model. Following quenching from the high-temperature coil phase to a low-temperature state point, we study the coarsening kinetics via molecular dynamics (MD) simulations using the Langevin thermostat. For the passive polymer case the low-temperature equilibrium state is a compact globule. The results from our MD simulations reveal that though the globular state is also the typical final state in the active case, the nonequilibrium pathways to arrive at such a state differ from the picture for the passive case due to the alignment interaction among the beads. We notice that deviations from the intermediate "pearl-necklace"-like arrangement, which is observed in the passive case, and the formation of more elongated dumbbell-like structures increase with increasing activity. Furthermore, it appears that while a small active force on the beads certainly makes the coarsening process much faster, there exists a nonmonotonic dependence of the collapse time on the strength of active interaction. We quantify these observations by comparing the scaling laws for the collapse time and growth of pearls with the passive case.
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Affiliation(s)
- Subhajit Paul
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Suman Majumder
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Subir K Das
- Theoretical Sciences Unit and School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore-560064, India.
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
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48
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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] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Indexed: 11/30/2022]
Abstract
We study active topological glass under spherical confinement, allowing us to exceed the chain lengths simulated previously and determine the critical exponents of the arrested conformations. We find a previously unresolved "tank-treading" dynamic mode of active segments along the ring contour. This mode can enhance active-passive phase separation in the state of active topological glass when both diffusional and conformational relaxation of the rings are significantly suppressed. Within the observational time, we see no systematic trends in the positioning of the separated active domains within the confining sphere. The arrested state exhibits coherent stochastic rotations. We discuss possible connections of the conformational and dynamic features of the system to chromosomes enclosed in the nucleus of a living cell.
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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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49
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Laghmach R, Di Pierro M, Potoyan D. A Liquid State Perspective on Dynamics of Chromatin Compartments. Front Mol Biosci 2022; 8:781981. [PMID: 35096966 PMCID: PMC8793688 DOI: 10.3389/fmolb.2021.781981] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
The interior of the eukaryotic cell nucleus has a crowded and heterogeneous environment packed with chromatin polymers, regulatory proteins, and RNA molecules. Chromatin polymer, assisted by epigenetic modifications, protein and RNA binders, forms multi-scale compartments which help regulate genes in response to cellular signals. Furthermore, chromatin compartments are dynamic and tend to evolve in size and composition in ways that are not fully understood. The latest super-resolution imaging experiments have revealed a much more dynamic and stochastic nature of chromatin compartments than was appreciated before. An emerging mechanism explaining chromatin compartmentalization dynamics is the phase separation of protein and nucleic acids into membraneless liquid condensates. Consequently, concepts and ideas from soft matter and polymer systems have been rapidly entering the lexicon of cell biology. In this respect, the role of computational models is crucial for establishing a rigorous and quantitative foundation for the new concepts and disentangling the complex interplay of forces that contribute to the emergent patterns of chromatin dynamics and organization. Several multi-scale models have emerged to address various aspects of chromatin dynamics, ranging from equilibrium polymer simulations, hybrid non-equilibrium simulations coupling protein binding and chromatin folding, and mesoscopic field-theoretic models. Here, we review these emerging theoretical paradigms and computational models with a particular focus on chromatin’s phase separation and liquid-like properties as a basis for nuclear organization and dynamics.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA, United States
| | - Davit Potoyan
- Department of Chemistry, Iowa State University, Ames, IA, United States
- *Correspondence: Davit Potoyan,
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50
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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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