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Câmara AS, Mascher M. Consistencies and contradictions in different polymer models of chromatin architecture. Comput Struct Biotechnol J 2023; 21:1084-91. [PMID: 36789261 DOI: 10.1016/j.csbj.2023.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Genetic information is stored in very long DNA molecules, which are folded to form chromatin, a similarly long polymer fibre that is ultimately organised into chromosomes. The organisation of chromatin is fundamental to many cellular functions, from the expression of the genetic information to cell division. As a long polymer, chromatin is very flexible and may adopt a myriad of shapes. Globally, the polymer physics governing chromatin dynamics is very well understood. But chromatin is not uniform and regions of it, with chemical modifications and bound effectors, form domains and compartments through mechanisms not yet clear. Polymer models have been successfully used to investigate these mechanisms to explain cytological observations and build hypothesis for experimental validation. Many different approaches to conceptualise chromatin in polymer models can be envisioned and each reflects different aspects. Here, we compare recent approaches that aim at reproducing prominent features of interphase chromatin organisation: the compartmentalisation into eu- and heterochromatin compartments, the formation of a nucleolus, chromatin loops and the rosette and Rabl conformations of interphase chromosomes. We highlight commonalities and contradictions that point to a modulation of the mechanisms involved to fine degree. Consolidating models will require the inclusion of yet hidden or neglected parameters.
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2
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Komoto T, Fujii M, Awazu A. Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells. Biophys Physicobiol 2022; 19:1-14. [PMID: 35797402 PMCID: PMC9174021 DOI: 10.2142/biophysico.bppb-v19.0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
X chromosome inactivation center (Xic) pairing occurs during the differentiation of embryonic stem (ES) cells from female mouse embryos, and is related to X chromosome inactivation, the circadian clock, intra-nucleus architecture, and metabolism. However, the mechanisms underlying the identification and approach of X chromosome pairs in the crowded nucleus are unclear. To elucidate the driving force of Xic pairing, we developed a coarse-grained molecular dynamics model of intranuclear chromosomes in ES cells and in cells 2 days after the onset of differentiation (2-day cells) by considering intrachromosomal epigenetic-structural feature-dependent mechanics. The analysis of the experimental data showed that X-chromosomes exhibit the rearrangement of their distributions of open/closed chromatin regions on their surfaces during cell differentiation. By simulating models where the excluded volume effects of closed chromatin regions are stronger than those of open chromatin regions, such rearrangement of open/closed chromatin regions on X-chromosome surfaces promoted the mutual approach of the Xic pair. These findings suggested that local intrachromosomal epigenetic features may contribute to the regulation of cell species-dependent differences in intranuclear architecture.
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Affiliation(s)
- Tetsushi Komoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masashi Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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3
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Seirin-Lee S, Yamamoto K, Kimura A. The extra-embryonic space and the local contour are crucial geometric constraints regulating cell arrangement. Development 2022; 149:275369. [PMID: 35552395 PMCID: PMC9148568 DOI: 10.1242/dev.200401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
In multicellular systems, cells communicate with adjacent cells to determine their positions and fates, an arrangement important for cellular development. Orientation of cell division, cell-cell interactions (i.e. attraction and repulsion) and geometric constraints are three major factors that define cell arrangement. In particular, geometric constraints are difficult to reveal in experiments, and the contribution of the local contour of the boundary has remained elusive. In this study, we developed a multicellular morphology model based on the phase-field method so that precise geometric constraints can be incorporated. Our application of the model to nematode embryos predicted that the amount of extra-embryonic space, the empty space within the eggshell that is not occupied by embryonic cells, affects cell arrangement in a manner dependent on the local contour and other factors. The prediction was validated experimentally by increasing the extra-embryonic space in the Caenorhabditis elegans embryo. Overall, our analyses characterized the roles of geometrical contributors, specifically the amount of extra-embryonic space and the local contour, on cell arrangements. These factors should be considered for multicellular systems. Summary: The local contour and the extra-embryonic space, the empty space within the eggshell not occupied by embryonic cells, are important geometric constraints in cell arrangement of nematode embryos.
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Affiliation(s)
- Sungrim Seirin-Lee
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study, Kyoto University, Kyoto 606-8315, Japan.,JST CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazunori Yamamoto
- Department of Applied Bioscience, Faculty of Applied Bioscience, Kanagawa Institute of Technology, Atsugi 243-0292, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, Sokendai, Mishima 411-8540, Japan
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4
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Cheng Q, Delafrouz P, Liang J, Liu C, Shen J. Modeling and simulation of cell nuclear architecture reorganization process. J Comput Phys 2022; 449:110808. [PMID: 36185393 PMCID: PMC9524197 DOI: 10.1016/j.jcp.2021.110808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We develop a special phase field/diffusive interface method to model the nuclear architecture reorganization process. In particular, we use a Lagrange multiplier approach in the phase field model to preserve the specific physical and geometrical constraints for the biological events. We develop several efficient and robust linear and weakly nonlinear schemes for this new model. To validate the model and numerical methods, we present ample numerical simulations which in particular reproduce several processes of nuclear architecture reorganization from the experiment literature.
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Affiliation(s)
- Qing Cheng
- Department of Mathematics,Purdue University, West Lafayette, IN 47907, USA
| | - Pourya Delafrouz
- Department of Bioengineering, University of Illinois at Chicago, SEO, MC-063, Chicago, IL, 60607-7052, USA
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, SEO, MC-063, Chicago, IL, 60607-7052, USA
| | - Chun Liu
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jie Shen
- Department of Mathematics,Purdue University, West Lafayette, IN 47907, USA
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5
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Abstract
In the process of asymmetric cell division, the mother cell induces polarity in both the membrane and the cytosol by distributing substrates and components asymmetrically. Such polarity formation results from the harmonization of the upstream and downstream polarities between the cell membrane and the cytosol. MEX-5/6 is a well-investigated downstream cytoplasmic protein, which is deeply involved in the membrane polarity of the upstream transmembrane protein PAR in the Caenorhabditis elegans embryo. In contrast to the extensive exploration of membrane PAR polarity, cytoplasmic polarity is poorly understood, and the precise contribution of cytoplasmic polarity to the membrane PAR polarity remains largely unknown. In this study, we explored the interplay between the cytoplasmic MEX-5/6 polarity and the membrane PAR polarity by developing a mathematical model that integrates the dynamics of PAR and MEX-5/6 and reflects the cell geometry. Our investigations show that the downstream cytoplasmic protein MEX-5/6 plays an indispensable role in causing a robust upstream PAR polarity, and the integrated understanding of their interplay, including the effect of the cell geometry, is essential for the study of polarity formation in asymmetric cell division.
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Affiliation(s)
- Sungrim Seirin-Lee
- Department of Mathematics, Department of Mathematical and Life Sciences, Graduate School of Integrated Science for Life, Hiroshima University, Kagamiyama 1-3-1, Hiroshima, 700-0046, Japan.
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6
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Cheng RR, Contessoto VG, Lieberman Aiden E, Wolynes PG, Di Pierro M, Onuchic JN. Exploring chromosomal structural heterogeneity across multiple cell lines. eLife 2020; 9:60312. [PMID: 33047670 PMCID: PMC7593087 DOI: 10.7554/elife.60312] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscopy. We demonstrate using machine learning and polymer physics simulations that epigenetic information can be used to predict the structural ensembles of multiple human cell lines. Theory predicts that chromosome structures are fluid and can only be described by an ensemble, which is consistent with the observation that chromosomes exhibit no unique fold. Nevertheless, our analysis of both structures from simulation and microscopy reveals that short segments of chromatin make two-state transitions between closed conformations and open dumbbell conformations. Finally, we study the conformational changes associated with the switching of genomic compartments observed in human cell lines. The formation of genomic compartments resembles hydrophobic collapse in protein folding, with the aggregation of denser and predominantly inactive chromatin driving the positioning of active chromatin toward the surface of individual chromosomal territories.
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Affiliation(s)
- Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Vinicius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Brazilian Biorenewables National Laboratory - LNBR, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, Brazil
| | - Erez Lieberman Aiden
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Center for Genome Architecture, Baylor College of Medicine, Houston, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Chemistry, Rice University, Houston, United States.,Department of Physics & Astronomy, Rice University, Houston, United States.,Department of Biosciences, Rice University, Houston, United States
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Physics, Northeastern University, Boston, United States
| | - Jose N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Chemistry, Rice University, Houston, United States.,Department of Physics & Astronomy, Rice University, Houston, United States.,Department of Biosciences, Rice University, Houston, United States
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7
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Myers CG, Olins DE, Olins AL, Schlick T. Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes. Biophys J 2020; 118:2066-2076. [PMID: 31668748 PMCID: PMC7202932 DOI: 10.1016/j.bpj.2019.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/25/2019] [Accepted: 08/15/2019] [Indexed: 12/28/2022] Open
Abstract
Interactions of chromatin with bivalent immunoglobin nucleosome-binding antibodies and their monovalent (papain-derived) antigen-binding fragment analogs are useful probes for examining chromatin conformational states. To help interpret antibody-chromatin interactions and explore how antibodies might compete for interactions with chromatin components, we incorporate coarse-grained PL2-6 antibody modeling into our mesoscale chromatin model. We analyze interactions and fiber structures for the antibody-chromatin complexes in open and condensed chromatin, with and without H1 linker histone (LH). Despite minimal and transient interactions at physiological salt, we capture significant differences in antibody-chromatin complex configurations in open fibers, with more intense interactions between the bivalent antibody and chromatin compared to monovalent antigen-binding fragments. For these open chromatin fiber morphologies, antibody binding to histone tails is increased and compaction is greater for bivalent compared to monovalent and antibody-free systems. Differences between monovalent and bivalent binding result from antibody competition with internal chromatin fiber components (nucleosome core and linker DNA) for histone tail (H3, H4, H2A, H2B) interactions. This antibody competition for tail contacts reduces tail-core and tail-linker interactions and increases tail-antibody interactions. Such internal structural changes in open fibers resemble mechanisms of LH condensation, driven by charge screening and entropy changes. For condensed fibers at physiological salt, the three systems are much more similar overall, but some subtle tail interaction differences can be noted. Adding LH results in less-dramatic changes for all systems, except that the bivalent complex at physiological salt shows cooperative effects between LH and the antibodies in condensing chromatin fibers. Such dynamic interactions that depend on the internal structure and complex-stabilizing interactions within the chromatin fiber have implications for gene regulation and other chromatin complexes such as with LH, remodeling proteins, and small molecular chaperones that bind and modulate chromatin structure.
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Affiliation(s)
| | - Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, Maine
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, Maine
| | - 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 at New York University Shanghai, Shanghai, China.
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8
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Laghmach R, Di Pierro M, Potoyan DA. Mesoscale Liquid Model of Chromatin Recapitulates Nuclear Order of Eukaryotes. Biophys J 2019; 118:2130-2140. [PMID: 31623887 DOI: 10.1016/j.bpj.2019.09.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 02/01/2023] Open
Abstract
The nuclear envelope segregates the genome of Eukaryota from the cytoplasm. Within the nucleus, chromatin is further compartmentalized into architectures that change throughout the lifetime of the cell. Epigenetic patterns along the chromatin polymer strongly correlate with chromatin compartmentalization and, accordingly, also change during the cell life cycle and at differentiation. Recently, it has been suggested that subnuclear chromatin compartmentalization might result from a process of liquid-liquid phase separation orchestrated by the epigenetic marking and operated by proteins that bind to chromatin. Here, we translate these observations into a diffuse interface model of chromatin, which we named the mesoscale liquid model of nucleus. Using this streamlined continuum model of the genome, we study the large-scale rearrangements of chromatin that happen at different stages of the growth and senescence of the cell and during nuclear inversion events. In particular, we investigate the role of droplet diffusion, fluctuations, and heterochromatin-lamina interactions during nuclear remodeling. Our results indicate that the physical process of liquid-liquid phase separation, together with surface effects, is sufficient to recapitulate much of the large-scale morphology and dynamics of chromatin along the life cycle of cells.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, Iowa
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, Iowa; Department of Biochemistry and Molecular Biology, Iowa State University, Ames, Iowa; Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa.
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9
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Seirin-Lee S, Osakada F, Takeda J, Tashiro S, Kobayashi R, Yamamoto T, Ochiai H. Role of dynamic nuclear deformation on genomic architecture reorganization. PLoS Comput Biol 2019; 15:e1007289. [PMID: 31509522 PMCID: PMC6738595 DOI: 10.1371/journal.pcbi.1007289] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/28/2019] [Indexed: 11/18/2022] Open
Abstract
Higher-order genomic architecture varies according to cell type and changes dramatically during differentiation. One of the remarkable examples of spatial genomic reorganization is the rod photoreceptor cell differentiation in nocturnal mammals. The inverted nuclear architecture found in adult mouse rod cells is formed through the reorganization of the conventional architecture during terminal differentiation. However, the mechanisms underlying these changes remain largely unknown. Here, we found that the dynamic deformation of nuclei via actomyosin-mediated contractility contributes to chromocenter clustering and promotes genomic architecture reorganization during differentiation by conducting an in cellulo experiment coupled with phase-field modeling. Similar patterns of dynamic deformation of the nucleus and a concomitant migration of the nuclear content were also observed in rod cells derived from the developing mouse retina. These results indicate that the common phenomenon of dynamic nuclear deformation, which accompanies dynamic cell behavior, can be a universal mechanism for spatiotemporal genomic reorganization. The motion and spatial reorganization of sub-nuclear domains have been extensively studied using microscopy, but the underlying mechanisms that promote the reorganization are still poorly understood. We found that dynamic nuclear deformation provides a driving force for long-range migration and aggressive clustering of chromocenters, which ultimately induces nuclear architecture reorganization. This study significantly contributes to an improved understanding of the role of nuclear deformation and reorganization of nuclear architecture that seems complex but is based on simple physical properties of the cell.
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Affiliation(s)
- Sungrim Seirin-Lee
- Department of Mathematics, School of Science, Hiroshima University, Higashi-Hiroshima, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
- * E-mail: (SSL); (HO)
| | - Fumitaka Osakada
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
- Laboratory of Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Junichi Takeda
- Laboratory of Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Ryo Kobayashi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroshi Ochiai
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
- * E-mail: (SSL); (HO)
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10
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Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature 2019; 570:395-9. [PMID: 31168090 DOI: 10.1038/s41586-019-1275-3] [Citation(s) in RCA: 326] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/26/2019] [Indexed: 01/18/2023]
Abstract
The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic and inactive heterochromatic regions of the genome1,2. In conventional nuclei, microscopy shows that euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery1,2. Genome-wide chromosome conformation capture (Hi-C) analyses show this segregation as a plaid pattern of contact enrichment within euchromatin and heterochromatin compartments3, and depletion between them. Many mechanisms for the formation of compartments have been proposed, such as attraction of heterochromatin to the nuclear lamina2,4, preferential attraction of similar chromatin to each other1,4-12, higher levels of chromatin mobility in active chromatin13-15 and transcription-related clustering of euchromatin16,17. However, these hypotheses have remained inconclusive, owing to the difficulty of disentangling intra-chromatin and chromatin-lamina interactions in conventional nuclei18. The marked reorganization of interphase chromosomes in the inverted nuclei of rods in nocturnal mammals19,20 provides an opportunity to elucidate the mechanisms that underlie spatial compartmentalization. Here we combine Hi-C analysis of inverted rod nuclei with microscopy and polymer simulations. We find that attractions between heterochromatic regions are crucial for establishing both compartmentalization and the concentric shells of pericentromeric heterochromatin, facultative heterochromatin and euchromatin in the inverted nucleus. When interactions between heterochromatin and the lamina are added, the same model recreates the conventional nuclear organization. In addition, our models allow us to rule out mechanisms of compartmentalization that involve strong euchromatin interactions. Together, our experiments and modelling suggest that attractions between heterochromatic regions are essential for the phase separation of the active and inactive genome in inverted and conventional nuclei, whereas interactions of the chromatin with the lamina are necessary to build the conventional architecture from these segregated phases.
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Sugawara T, Kimura A. Physical properties of the chromosomes and implications for development. Dev Growth Differ 2017; 59:405-414. [PMID: 28573677 DOI: 10.1111/dgd.12363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/13/2017] [Accepted: 04/13/2017] [Indexed: 01/15/2023]
Abstract
Remarkable progress has been made in understanding chromosome structures inside the cell nucleus. Recent advances in Hi-C technologies enable the detection of genome-wide chromatin interactions, providing insight into three-dimensional (3D) genome organization. Advancements in the spatial and temporal resolutions of imaging as well as in molecular biological techniques allow the tracking of specific chromosomal loci, improving our understanding of chromosome movements. From these data, we are beginning to understand how the intra-nuclear locations of chromatin loci and the 3D genome structure change during development and differentiation. This emerging field of genome structure and dynamics research requires an interdisciplinary approach including efficient collaborations between experimental biologists and physicists, informaticians, or engineers. Quantitative and mathematical analyses based on polymer physics are becoming increasingly important for processing and interpreting experimental data on 3D chromosome structures and dynamics. In this review, we aim to provide an overview of recent research on the physical aspects of chromosome structure and dynamics oriented for biologists. These studies have mainly focused on chromosomes at the cellular level, using unicellular organisms and cultured cells. However, physical parameters that change during development, such as nuclear size, may impact genome structure and dynamics. Here, we discuss how chromatin dynamics and genome structures in early embryos change during development, which we expect will be a hot topic in the field of chromatin dynamics in the near future. We hope this review helps developmental biologists to quantitatively investigate the physical natures of chromosomes in developmental biology research.
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Affiliation(s)
- Takeshi Sugawara
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, 739-8530, Japan.,Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, 411-8540, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (Sokendai), Mishima, 411-8540, Japan
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