1
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Attar AG, Paturej J, Banigan EJ, Erbaş A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. Nucleus 2024; 15:2351957. [PMID: 38753956 DOI: 10.1080/19491034.2024.2351957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a "wetting"-like interaction. In contrast, fluctuations are insensitive to heterochromatin's internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.
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Affiliation(s)
- Ali Goktug Attar
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
| | | | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey
- Institute of Physics, University of Silesia, Chorzów, Poland
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2
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He X, Dias Lopes C, Pereyra-Bistrain LI, Huang Y, An J, Chaouche RB, Zalzalé H, Wang Q, Ma X, Antunez-Sanchez J, Bergounioux C, Piquerez S, Fragkostefanakis S, Zhang Y, Zheng S, Crespi M, Mahfouz MM, Mathieu O, Ariel F, Gutierrez-Marcos J, Li X, Bouché N, Raynaud C, Latrasse D, Benhamed M. Genetic-epigenetic interplay in the determination of plant 3D genome organization. Nucleic Acids Res 2024:gkae690. [PMID: 39149894 DOI: 10.1093/nar/gkae690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/25/2024] [Accepted: 08/07/2024] [Indexed: 08/17/2024] Open
Abstract
The 3D chromatin organization plays a major role in the control of gene expression. However, our comprehension of the governing principles behind nuclear organization remains incomplete. Particularly, the spatial segregation of loci with similar repressive transcriptional states in plants poses a significant yet poorly understood puzzle. In this study, employing a combination of genetics and advanced 3D genomics approaches, we demonstrated that a redistribution of facultative heterochromatin marks in regions usually occupied by constitutive heterochromatin marks disrupts the 3D genome compartmentalisation. This disturbance, in turn, triggers novel chromatin interactions between genic and transposable element (TE) regions. Interestingly, our results imply that epigenetic features, constrained by genetic factors, intricately mold the landscape of 3D genome organisation. This study sheds light on the profound genetic-epigenetic interplay that underlies the regulation of gene expression within the intricate framework of the 3D genome. Our findings highlight the complexity of the relationships between genetic determinants and epigenetic features in shaping the dynamic configuration of the 3D genome.
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Affiliation(s)
- Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Chloé Dias Lopes
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Leonardo I Pereyra-Bistrain
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Jing An
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Rim Brik Chaouche
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Hugo Zalzalé
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Qingyi Wang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Xing Ma
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | | | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Sophie Piquerez
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zheijang University, Hangzhou 310058, China
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, Clermont-Ferrand, F-63000, France
| | - Federico Ariel
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | | | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvment, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070 Hubei, China
| | - Nicolas Bouché
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000 Versailles, France
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay 91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
- Institut Universitaire de France (IUF), Orsay, France
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3
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An J, Brik Chaouche R, Pereyra-Bistraín LI, Zalzalé H, Wang Q, Huang Y, He X, Dias Lopes C, Antunez-Sanchez J, Bergounioux C, Boulogne C, Dupas C, Gillet C, Pérez-Pérez JM, Mathieu O, Bouché N, Fragkostefanakis S, Zhang Y, Zheng S, Crespi M, Mahfouz MM, Ariel F, Gutierrez-Marcos J, Raynaud C, Latrasse D, Benhamed M. An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution. Proc Natl Acad Sci U S A 2024; 121:e2400737121. [PMID: 38968127 PMCID: PMC11252963 DOI: 10.1073/pnas.2400737121] [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: 01/12/2024] [Accepted: 05/21/2024] [Indexed: 07/07/2024] Open
Abstract
In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.
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Affiliation(s)
- Jing An
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Rim Brik Chaouche
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Leonardo I. Pereyra-Bistraín
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
| | - Hugo Zalzalé
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
| | - Qingyi Wang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Chloé Dias Lopes
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | | | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Claire Boulogne
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | - Cynthia Dupas
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | - Cynthia Gillet
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | | | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, Clermont-FerrandF-63000, France
| | - Nicolas Bouché
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles78000, France
| | | | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal23955-6900, Saudi Arabia
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, SantaFe 3000, Argentina
| | | | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
- Institut Universitaire de France, Orsay, Gif-sur-Yvette91190, France
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4
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Girard M, de la Cruz MO, Marko JF, Erbaş A. Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus. Phys Rev E 2024; 110:014403. [PMID: 39160964 PMCID: PMC11371272 DOI: 10.1103/physreve.110.014403] [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: 10/18/2023] [Accepted: 05/29/2024] [Indexed: 08/21/2024]
Abstract
The highly and slightly condensed forms of chromatin, heterochromatin and euchromatin, respectively, segregate in the cell nucleus. Heterochromatin is more abundant in the nucleus periphery. Here we study the mechanism of heterochromatin segregation by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell using molecular dynamics simulations. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses only, while an interaction potential between the spherical shell and chromatin is used to model lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, most heterochromatin segregates towards the nuclear interior due to the depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution,which is opposite to the conventional case with heterochromatin dominating at the periphery, is in accord with experimental observations in rod cells. This "inversion" is also found to be independent of the heterochromatin concentration and chromosome number. The chromatin distribution at the periphery found in vivo can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Our results indicate that the bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP1α-driven phase segregation and of loop extruders and interactions with the nuclear envelope and topological constraints.
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Affiliation(s)
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Department of Chemistry, Department of Chemical and Biological Engineering, and Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
| | | | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey
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5
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Simon L, Probst AV. Maintenance and dynamic reprogramming of chromatin organization during development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:657-670. [PMID: 36700345 DOI: 10.1111/tpj.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Abstract
Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.
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Affiliation(s)
- Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
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6
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Attar AG, Paturej J, Banigan EJ, Erbas A. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.16.571697. [PMID: 38168411 PMCID: PMC10760070 DOI: 10.1101/2023.12.16.571697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Abnormalities in the shapes of mammalian cell nuclei are hallmarks of a variety of diseases, including progeria, muscular dystrophy, and various cancers. Experiments have shown that there is a causal relationship between chromatin organization and nuclear morphology. Decreases in heterochromatin levels, perturbations to heterochromatin organization, and increases in euchromatin levels all lead to misshapen nuclei, which exhibit deformations, such as nuclear blebs and nuclear ruptures. However, the polymer physical mechanisms of how chromatin governs nuclear shape and integrity are poorly understood. To investigate how heterochromatin and euchromatin, which are thought to microphase separate in vivo , govern nuclear morphology, we implemented a composite coarse-grained polymer and elastic shell model. By varying chromatin volume fraction (density), heterochromatin levels and structure, and heterochromatin-lamina interactions, we show how the spatial organization of chromatin polymer phases within the nucleus could perturb nuclear shape in some scenarios. Increasing the volume fraction of chromatin in the cell nucleus stabilizes the nuclear lamina against large fluctuations. However, surprisingly, we find that increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations in our simulations by a "wetting"-like interaction. In contrast, shape fluctuations are largely insensitive to the internal structure of the heterochromatin, such as the presence or absence of chromatin-chromatin crosslinks. Therefore, our simulations suggest that heterochromatin accumulation at the nuclear periphery could perturb nuclear morphology in a nucleus or nuclear region that is sufficiently soft, while stabilization of the nucleus via heterochromatin likely occurs through mechanisms other than chromatin microphase organization.
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7
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Tourdot E, Grob S. Three-dimensional chromatin architecture in plants - General features and novelties. Eur J Cell Biol 2023; 102:151344. [PMID: 37562220 DOI: 10.1016/j.ejcb.2023.151344] [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: 02/23/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.
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Affiliation(s)
- Edouard Tourdot
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
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8
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [PMID: 37974978 PMCID: PMC10643749 DOI: 10.1007/s12551-023-01136-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 11/19/2023] Open
Abstract
Nuclear cytoplasmic transport is mediated by many receptors that recognize specific nuclear localization signals on proteins and RNA and transport these substrates through nuclear pore complexes. Facilitated diffusion through nuclear pore complexes requires the attachment of transport receptors. Despite the relatively large tunnel diameter, some even small proteins (less than 20-30 kDa), such as histones, pass through the nuclear pore complex only with transport receptors. Over several decades, considerable material has been accumulated on the structure, architecture, and amino acid composition of the proteins included in this complex and the sequence of many receptors. We consider the data available in the literature on the structure of the nuclear pore complex and possible mechanisms of nuclear-cytoplasmic transport, applying the theory of electrostatic interactions in the context of our data on changes in the electrokinetic potential of nuclei and our previously proposed physical model of the mechanism of facilitated diffusion through the nuclear pore complex (NPC). According to our data, the main contribution to the charge of the nuclear membrane is made by anionic phospholipids, which are part of both the nuclear membrane and the nuclear matrix, which creates a potential difference between them. The nuclear membrane is a four-layer phospholipid dielectric, so the potential vector can only pass through the NPC, creating an electrostatic funnel that "pulls in" the positively charged load-NLS-NTR trigger complexes. Considering the newly obtained data, an improved model of the previously proposed physical model of the mechanism of nuclear-cytoplasmic transport is proposed. This model considers the contribution of electrostatic fields to the transportation speed when changing the membrane's thickness in the NPC basket at a higher load.
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Affiliation(s)
- Liya A. Minasbekyan
- Scientific Research Institute of Biology, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
| | - Hamlet G. Badalyan
- Chair of General Physics, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
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9
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [DOI: https:/doi.org/10.1007/s12551-023-01136-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 02/27/2024] Open
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10
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Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV, Schrumpfová PP, Fajkus J, Amiard S, Grob S, Bourbousse C, Barneche F. Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis. Cell Rep 2023; 42:112894. [PMID: 37515769 DOI: 10.1016/j.celrep.2023.112894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 12/02/2022] [Accepted: 07/13/2023] [Indexed: 07/31/2023] Open
Abstract
While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.
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Affiliation(s)
- Gianluca Teano
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Lorenzo Concia
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léopold Carron
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Ivona Biocanin
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Amira Kramdi
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vincent Colot
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Chris Bowler
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Aline V Probst
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Simon Amiard
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Stefan Grob
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.
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11
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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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12
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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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13
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Huang YF, Liu L, Wang F, Yuan XW, Chen HC, Liu ZF. High-Resolution 3D Genome Map of Brucella Chromosomes in Exponential and Stationary Phases. Microbiol Spectr 2023; 11:e0429022. [PMID: 36847551 PMCID: PMC10100373 DOI: 10.1128/spectrum.04290-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
The three-dimensional (3D) genome structure of an organism or cell is highly relevant to its biological activities, but the availability of 3D genome information for bacteria, especially intracellular pathogens, is still limited. Here, we used Hi-C (high-throughput chromosome conformation capture) technology to determine the 3D chromosome structures of exponential- and stationary-phase Brucella melitensis at a 1-kb resolution. We observed that the contact heat maps of the two B. melitensis chromosomes contain a prominent diagonal and a secondary diagonal. Then, 79 chromatin interaction domains (CIDs) were detected at an optical density at 600 nm (OD600) of 0.4 (exponential phase), with the longest CID being 106 kb and the shortest being 12 kb. Moreover, we obtained 49,363 significant cis-interaction loci and 59,953 significant trans-interaction loci. Meanwhile, 82 CIDs of B. melitensis at an OD600 of 1.5 (stationary phase) were detected, with the longest CID being 94 kb and the shortest being 16 kb. In addition, 25,965 significant cis-interaction loci and 35,938 significant trans-interaction loci were obtained in this phase. Furthermore, we found that as the B. melitensis cells grew from the logarithmic to the plateau phase, the frequency of short-range interactions increased, while that of long-range interactions decreased. Finally, combined analysis of 3D genome and whole-genome transcriptome (RNA-seq) data revealed that the strength of short-range interactions in Chr1 is specifically and strongly correlated with gene expression. Overall, our study provides a global view of the chromatin interactions in the B. melitensis chromosomes, which will serve as a resource for further study of the spatial regulation of gene expression in Brucella. IMPORTANCE The spatial structure of chromatin plays important roles in normal cell functions and in the regulation of gene expression. Three-dimensional genome sequencing has been performed in many mammals and plants, but the availability of such data for bacteria, especially intracellular pathogens, is still limited. Approximately 10% of sequenced bacterial genomes contain more than one replicon. However, how multiple replicons are organized within bacterial cells, how they interact, and whether these interactions help to maintain or segregate these multipartite genomes are unresolved issues. Brucella is a Gram-negative, facultative intracellular, and zoonotic bacterium. Except for Brucella suis biovar 3, Brucella species have two chromosomes. Here, we applied Hi-C technology to determine the 3D genome structures of exponential- and stationary-phase Brucella melitensis chromosomes at a 1-kb resolution. Combined analysis of the 3D genome and RNA-seq data indicated that the strength of short-range interactions in B. melitensis Chr1 is specifically and strongly correlated with gene expression. Our study provides a resource to achieve a deeper understanding of the spatial regulation of gene expression in Brucella.
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Affiliation(s)
- Yong-Fang Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lin Liu
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, Hubei, China
| | - Fei Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xin-Wei Yuan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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14
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Consistencies and contradictions in different polymer models of chromatin architecture. Comput Struct Biotechnol J 2023; 21:1084-1091. [PMID: 36789261 PMCID: PMC9900451 DOI: 10.1016/j.csbj.2023.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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15
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Kariti H, Feld T, Kaplan N. Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments. Nucleic Acids Res 2023; 51:1103-1119. [PMID: 36629266 PMCID: PMC9943678 DOI: 10.1093/nar/gkac1258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/30/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
The Hi-C method has revolutionized the study of genome organization, yet interpretation of Hi-C interaction frequency maps remains a major challenge. Genomic compartments are a checkered Hi-C interaction pattern suggested to represent the partitioning of the genome into two self-interacting states associated with active and inactive chromatin. Based on a few elementary mechanistic assumptions, we derive a generative probabilistic model of genomic compartments, called deGeco. Testing our model, we find it can explain observed Hi-C interaction maps in a highly robust manner, allowing accurate inference of interaction probability maps from extremely sparse data without any training of parameters. Taking advantage of the interpretability of the model parameters, we then test hypotheses regarding the nature of genomic compartments. We find clear evidence of multiple states, and that these states self-interact with different affinities. We also find that the interaction rules of chromatin states differ considerably within and between chromosomes. Inspecting the molecular underpinnings of a four-state model, we show that a simple classifier can use histone marks to predict the underlying states with 87% accuracy. Finally, we observe instances of mixed-state loci and analyze these loci in single-cell Hi-C maps, finding that mixing of states occurs mainly at the cell level.
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Affiliation(s)
- Hagai Kariti
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
| | - Tal Feld
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel,Viterbi Faculty of Electrical & Computer Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Noam Kaplan
- To whom correspondence should be addressed. Tel: +972 4 8295293;
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16
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Di Stefano M, Cavalli G. Integrative studies of 3D genome organization and chromatin structure. Curr Opin Struct Biol 2022; 77:102493. [PMID: 36335845 DOI: 10.1016/j.sbi.2022.102493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The structural organization of the genome is emerging as a crucial regulator of the cell state, affecting gene transcription, DNA replication, and repair. Over the last twenty years, increasing evidence prompted the development of new experimental techniques to study genome structure. In parallel with the complexity of the novel techniques, computational approaches have become an essential tool in any structural genomics laboratory to analyze and model the data. For biologists to be able to apply the most appropriate modeling approach, it is fundamental to understand the conceptual bases of distinct methods and the insights they can provide. Here, we will discuss recent advances that were possible thanks to 3D genome modeling, discuss their limitations and highlight future perspectives.
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Affiliation(s)
- Marco Di Stefano
- Institute of Human Genetics, CNRS and University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090, Montpellier, France. https://twitter.com/@MarcDiEsse
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090, Montpellier, France.
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17
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Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Nat Methods 2022; 19:938-949. [PMID: 35817938 PMCID: PMC9349046 DOI: 10.1038/s41592-022-01527-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 05/18/2022] [Indexed: 02/07/2023]
Abstract
A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin. We demonstrate that multimodal data integration can compensate for systematic errors in some of the data and can greatly increase accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency (‘rare’) interchromosomal contacts to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multimodal data integration for genome structure analysis, available through the Integrative Genome Modeling software package. The Integrative Genome Modeling platform is a tool for population-based three-dimensional genome structure modeling and analysis by integrating various experimental data sources.
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18
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Generation of dynamic three-dimensional genome structure through phase separation of chromatin. Proc Natl Acad Sci U S A 2022; 119:e2109838119. [PMID: 35617433 PMCID: PMC9295772 DOI: 10.1073/pnas.2109838119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Significance DNA functions in living cells are crucially affected by the three-dimensional genome structure and dynamics. We analyze the whole genome of human cells by developing a polymer model of interphase nuclei. The model reveals the essential importance of the unfolding process of chromosomes from the condensed mitotic state for describing the interphase nuclei; through the unfolding process, heterogeneous repulsive interactions among chromatin chains induce phase separation of chromatin, which quantitatively explains the experimentally observed various genomic data. We can use this model structure as a platform to analyze the relationship among genome structure, dynamics, and functions.
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19
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Brahmachari S, Contessoto V, Di Pierro M, Onuchic J. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. Nucleic Acids Res 2022; 50:4258-4271. [PMID: 35420130 PMCID: PMC9071446 DOI: 10.1093/nar/gkac231] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/02/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023] Open
Abstract
The link between genomic structure and biological function is yet to be consolidated, it is, however, clear that physical manipulation of the genome, driven by the activity of a variety of proteins, is a crucial step. To understand the consequences of the physical forces underlying genome organization, we build a coarse-grained polymer model of the genome, featuring three fundamentally distinct classes of interactions: lengthwise compaction, i.e., compaction of chromosomes along its contour, self-adhesion among epigenetically similar genomic segments, and adhesion of chromosome segments to the nuclear envelope or lamina. We postulate that these three types of interactions sufficiently represent the concerted action of the different proteins organizing the genome architecture and show that an interplay among these interactions can recapitulate the architectural variants observed across the tree of life. The model elucidates how an interplay of forces arising from the three classes of genomic interactions can drive drastic, yet predictable, changes in the global genome architecture, and makes testable predictions. We posit that precise control over these interactions in vivo is key to the regulation of genome architecture.
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Affiliation(s)
| | | | - Michele Di Pierro
- Department of Physics, and Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics and Astronomy, Department of Chemistry, Department of BioSciences, Rice University, Houston TX 77005, USA
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20
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Dergilev AI, Orlova NG, Dobrovolskaya OB, Orlov YL. Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data. J Integr Bioinform 2021; 19:jib-2020-0036. [PMID: 34953471 PMCID: PMC9069649 DOI: 10.1515/jib-2020-0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/25/2021] [Indexed: 12/03/2022] Open
Abstract
The development of high-throughput genomic sequencing coupled with chromatin immunoprecipitation technologies allows studying the binding sites of the protein transcription factors (TF) in the genome scale. The growth of data volume on the experimentally determined binding sites raises qualitatively new problems for the analysis of gene expression regulation, prediction of transcription factors target genes, and regulatory gene networks reconstruction. Genome regulation remains an insufficiently studied though plants have complex molecular regulatory mechanisms of gene expression and response to environmental stresses. It is important to develop new software tools for the analysis of the TF binding sites location and their clustering in the plant genomes, visualization, and the following statistical estimates. This study presents application of the analysis of multiple TF binding profiles in three evolutionarily distant model plant organisms. The construction and analysis of non-random ChIP-seq binding clusters of the different TFs in mammalian embryonic stem cells were discussed earlier using similar bioinformatics approaches. Such clusters of TF binding sites may indicate the gene regulatory regions, enhancers and gene transcription regulatory hubs. It can be used for analysis of the gene promoters as well as a background for transcription networks reconstruction. We discuss the statistical estimates of the TF binding sites clusters in the model plant genomes. The distributions of the number of different TFs per binding cluster follow same power law distribution for all the genomes studied. The binding clusters in Arabidopsis thaliana genome were discussed here in detail.
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Affiliation(s)
- Arthur I. Dergilev
- Novosibirsk State University, 630090Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090Novosibirsk, Russia
| | - Nina G. Orlova
- Financial University under the Government of the Russian Federation, 125993Moscow, Russia
- Moscow State Technical University of Civil Aviation, 125993Moscow, Russia
| | - Oxana B. Dobrovolskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia,117198Moscow, Russia
| | - Yuriy L. Orlov
- Novosibirsk State University, 630090Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090Novosibirsk, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia,117198Moscow, Russia
- The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991Moscow, Russia
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21
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Liu L, Zhang B, Hyeon C. Extracting multi-way chromatin contacts from Hi-C data. PLoS Comput Biol 2021; 17:e1009669. [PMID: 34871311 PMCID: PMC8675768 DOI: 10.1371/journal.pcbi.1009669] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/16/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
There is a growing realization that multi-way chromatin contacts formed in chromosome structures are fundamental units of gene regulation. However, due to the paucity and complexity of such contacts, it is challenging to detect and identify them using experiments. Based on an assumption that chromosome structures can be mapped onto a network of Gaussian polymer, here we derive analytic expressions for n-body contact probabilities (n > 2) among chromatin loci based on pairwise genomic contact frequencies available in Hi-C, and show that multi-way contact probability maps can in principle be extracted from Hi-C. The three-body (triplet) contact probabilities, calculated from our theory, are in good correlation with those from measurements including Tri-C, MC-4C and SPRITE. Maps of multi-way chromatin contacts calculated from our analytic expressions can not only complement experimental measurements, but also can offer better understanding of the related issues, such as cell-line dependent assemblies of multiple genes and enhancers to chromatin hubs, competition between long-range and short-range multi-way contacts, and condensates of multiple CTCF anchors.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Optical Field Manipulation of Zhejiang Province, Department of Physics, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bokai Zhang
- Key Laboratory of Optical Field Manipulation of Zhejiang Province, Department of Physics, Zhejiang Sci-Tech University, Hangzhou, China
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
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22
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Di Stefano M, Nützmann HW. Modeling the 3D genome of plants. Nucleus 2021; 12:65-81. [PMID: 34057011 PMCID: PMC8168717 DOI: 10.1080/19491034.2021.1927503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022] Open
Abstract
Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the transcription machinery, histone modifications, and their three-dimensional folding. The synergistic application of experimental approaches and computer simulations has helped to unveil how these organizational layers of the genome interplay in various organisms. However, such multidisciplinary approaches are still rarely explored in the plant kingdom. Here, we provide an overview of our current knowledge on plant 3D genome organization and review recent efforts to integrate cutting-edge experiments from microscopy and next-generation sequencing approaches with theoretical models. Building on these recent approaches, we propose possible avenues to extend the application of theoretical modeling in the characterization of the 3D genome organization in plants.
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Affiliation(s)
- Marco Di Stefano
- Institute of Human Genetics, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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23
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Three-dimensional genome organization via triplex-forming RNAs. Nat Struct Mol Biol 2021; 28:945-954. [PMID: 34759378 DOI: 10.1038/s41594-021-00678-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 09/30/2021] [Indexed: 11/08/2022]
Abstract
An increasing number of long noncoding RNAs (lncRNAs) have been proposed to act as nuclear organization factors during interphase. Direct RNA-DNA interactions can be achieved by the formation of triplex helix structures where a single-stranded RNA molecule hybridizes by complementarity into the major groove of double-stranded DNA. However, whether and how these direct RNA-DNA associations influence genome structure in interphase chromosomes remain poorly understood. Here we theorize that RNA organizes the genome in space via a triplex-forming mechanism. To test this theory, we apply a computational modeling approach of chromosomes that combines restraint-based modeling with polymer physics. Our models suggest that colocalization of triplex hotspots targeted by lncRNAs could contribute to large-scale chromosome compartmentalization cooperating, rather than competing, with architectural transcription factors such as CTCF.
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Câmara AS, Schubert V, Mascher M, Houben A. A simple model explains the cell cycle-dependent assembly of centromeric nucleosomes in holocentric species. Nucleic Acids Res 2021; 49:9053-9065. [PMID: 34352103 PMCID: PMC8450114 DOI: 10.1093/nar/gkab648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Centromeres are essential for chromosome movement. In independent taxa, species with holocentric chromosomes exist. In contrast to monocentric species, where no obvious dispersion of centromeres occurs during interphase, the organization of holocentromeres differs between condensed and decondensed chromosomes. During interphase, centromeres are dispersed into a large number of CENH3-positive nucleosome clusters in a number of holocentric species. With the onset of chromosome condensation, the centromeric nucleosomes join and form line-like holocentromeres. Using polymer simulations, we propose a mechanism relying on the interaction between centromeric nucleosomes and structural maintenance of chromosomes (SMC) proteins. Different sets of molecular dynamic simulations were evaluated by testing four parameters: (i) the concentration of Loop Extruders (LEs) corresponding to SMCs, (ii) the distribution and number of centromeric nucleosomes, (iii) the effect of centromeric nucleosomes on interacting LEs and (iv) the assembly of kinetochores bound to centromeric nucleosomes. We observed the formation of a line-like holocentromere, due to the aggregation of the centromeric nucleosomes when the chromosome was compacted into loops. A groove-like holocentromere structure formed after a kinetochore complex was simulated along the centromeric line. Similar mechanisms may also organize a monocentric chromosome constriction, and its regulation may cause different centromere types during evolution.
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Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
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Brandão HB, Ren Z, Karaboja X, Mirny LA, Wang X. DNA-loop-extruding SMC complexes can traverse one another in vivo. Nat Struct Mol Biol 2021; 28:642-651. [PMID: 34312537 DOI: 10.1038/s41594-021-00626-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
Chromosome organization mediated by structural maintenance of chromosomes (SMC) complexes is vital in many organisms. SMC complexes act as motors that extrude DNA loops, but it remains unclear what happens when multiple complexes encounter one another on the same DNA in living cells and how these interactions may help to organize an active genome. We therefore created a crash-course track system to study SMC complex encounters in vivo by engineering defined SMC loading sites in the Bacillus subtilis chromosome. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of chromosome folding patterns. Through three-dimensional polymer simulations and theory, we determine that these patterns require SMC complexes to bypass each other in vivo, as recently seen in an in vitro study. We posit that the bypassing activity enables SMC complexes to avoid traffic jams while spatially organizing the genome.
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Affiliation(s)
- Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Xheni Karaboja
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Leonid A Mirny
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA. .,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN, USA.
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Bishop J, Swan H, Valente F, Nützmann HW. The Plant Nuclear Envelope and Its Role in Gene Transcription. FRONTIERS IN PLANT SCIENCE 2021; 12:674209. [PMID: 33995467 PMCID: PMC8119737 DOI: 10.3389/fpls.2021.674209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/25/2021] [Indexed: 05/12/2023]
Abstract
Chromosomes are dynamic entities in the eukaryotic nucleus. During cell development and in response to biotic and abiotic change, individual sections as well as entire chromosomes re-organise and reposition within the nuclear space. A focal point for these processes is the nuclear envelope (NE) providing both barrier and anchor for chromosomal movement. In plants, positioning of chromosome regions and individual genes at the nuclear envelope has been shown to be associated with distinct transcriptional patterns. Here, we will review recent findings on the interplay between transcriptional activity and gene positioning at the nuclear periphery (NP). We will discuss potential mechanisms of transcriptional regulation at the nuclear envelope and outline future perspectives in this research area.
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