1
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Sood A, Schuette G, Zhang B. Dynamical phase transition in models that couple chromatin folding with histone modifications. Phys Rev E 2024; 109:054411. [PMID: 38907407 DOI: 10.1103/physreve.109.054411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/25/2024] [Indexed: 06/24/2024]
Abstract
Genomic regions can acquire heritable epigenetic states through unique histone modifications, which lead to stable gene expression patterns without altering the underlying DNA sequence. However, the relationship between chromatin conformational dynamics and epigenetic stability is poorly understood. In this paper, we propose kinetic models to investigate the dynamic fluctuations of histone modifications and the spatial interactions between nucleosomes. Our model explicitly incorporates the influence of chemical modifications on the structural stability of chromatin and the contribution of chromatin contacts to the cooperative nature of chemical reactions. Through stochastic simulations and analytical theory, we have discovered distinct steady-state outcomes in different kinetic regimes, resembling a dynamical phase transition. Importantly, we have validated that the emergence of this transition, which occurs on biologically relevant timescales, is robust against variations in model design and parameters. Our findings suggest that the viscoelastic properties of chromatin and the timescale at which it transitions from a gel-like to a liquidlike state significantly impact dynamic processes that occur along the one-dimensional DNA sequence.
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2
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Gao GF, Li P, Leonard WJ. Co-localization of clusters of TCR-regulated genes with TAD rearrangements. BMC Genomics 2023; 24:650. [PMID: 37898735 PMCID: PMC10613383 DOI: 10.1186/s12864-023-09693-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/21/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Gene expression has long been known to be influenced by the relative proximity of DNA regulatory elements. Topologically associating domains (TADs) are self-interacting genomic regions involved in regulating gene expression by controlling the proximity of these elements. Prior studies of TADs and their biological roles have revealed correlations between TAD changes and cellular differentiation. Here, we used Hi-C and RNA-seq data to correlate TCR-induced changes in TAD structure and gene expression in human CD4+ T cells. RESULTS We developed a pipeline, Differentially Expressed Gene Enrichment Finder (DEGEF), that identifies regions of differentially expressed gene enrichment. Using DEGEF, we found that TCR-regulated genes cluster non-uniformly across the genome and that these clusters preferentially localized in regions of TAD rearrangement. Interestingly, clusters of upregulated genes preferentially formed new Hi-C contacts compared to downregulated clusters, suggesting that TCR-activated CD4+ T cells may regulate genes by changing stimulatory contacts rather than inhibitory contacts. CONCLUSIONS Our observations support a significant relationship between TAD rearrangements and changes in local gene expression. These findings indicate potentially important roles for TAD rearrangements in shaping their local regulatory environments and thus driving differential expression of nearby genes during CD4+ T cell activation. Moreover, they provide new insights into global mechanisms that regulate gene expression.
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Affiliation(s)
- Galen F Gao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA.
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3
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Orsi GA, Tortora MMC, Horard B, Baas D, Kleman JP, Bucevičius J, Lukinavičius G, Jost D, Loppin B. Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis. Nat Commun 2023; 14:4187. [PMID: 37443316 PMCID: PMC10345107 DOI: 10.1038/s41467-023-39908-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Spermiogenesis is a radical process of differentiation whereby sperm cells acquire a compact and specialized morphology to cope with the constraints of sexual reproduction while preserving their main cargo, an intact copy of the paternal genome. In animals, this often involves the replacement of most histones by sperm-specific nuclear basic proteins (SNBPs). Yet, how the SNBP-structured genome achieves compaction and accommodates shaping remain largely unknown. Here, we exploit confocal, electron and super-resolution microscopy, coupled with polymer modeling to identify the higher-order architecture of sperm chromatin in the needle-shaped nucleus of the emerging model cricket Gryllus bimaculatus. Accompanying spermatid differentiation, the SNBP-based genome is strikingly reorganized as ~25nm-thick fibers orderly coiled along the elongated nucleus axis. This chromatin spool is further found to achieve large-scale helical twisting in the final stages of spermiogenesis, favoring its ultracompaction. We reveal that these dramatic transitions may be recapitulated by a surprisingly simple biophysical principle based on a nucleated rigidification of chromatin linked to the histone-to-SNBP transition within a confined nuclear space. Our work highlights a unique, liquid crystal-like mode of higher-order genome organization in ultracompact cricket sperm, and establishes a multidisciplinary methodological framework to explore the diversity of non-canonical modes of DNA organization.
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Affiliation(s)
- Guillermo A Orsi
- Institute for Advanced Biosciences, University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, 38000, Grenoble, France.
| | - 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, Lyon, France
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Béatrice Horard
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Dominique Baas
- Laboratoire MeLiS, CNRS UMR 52684, Inserm U 1314, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Philippe Kleman
- Institut de Biologie Structurale, UMR5075, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jonas Bucevičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
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4
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Miné-Hattab J, Liu S, Taddei A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes (Basel) 2022; 13:1846. [PMID: 36292731 PMCID: PMC9602295 DOI: 10.3390/genes13101846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 07/26/2023] Open
Abstract
In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.
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Affiliation(s)
| | | | - Angela Taddei
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, CEDEX 05, 75248 Paris, France
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5
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Newar K, Abdulla AZ, Salari H, Fanchon E, Jost D. Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells. PLoS Comput Biol 2022; 18:e1010450. [PMID: 36054209 PMCID: PMC9477427 DOI: 10.1371/journal.pcbi.1010450] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 09/15/2022] [Accepted: 07/28/2022] [Indexed: 01/02/2023] Open
Abstract
The Polycomb system via the methylation of the lysine 27 of histone H3 (H3K27) plays central roles in the silencing of many lineage-specific genes during development. Recent experimental evidence suggested that the recruitment of histone modifying enzymes like the Polycomb repressive complex 2 (PRC2) at specific sites and their spreading capacities from these sites are key to the establishment and maintenance of a proper epigenomic landscape around Polycomb-target genes. Here, to test whether such mechanisms, as a minimal set of qualitative rules, are quantitatively compatible with data, we developed a mathematical model that can predict the locus-specific distributions of H3K27 modifications based on previous biochemical knowledge. Within the biological context of mouse embryonic stem cells, our model showed quantitative agreement with experimental profiles of H3K27 acetylation and methylation around Polycomb-target genes in wild-type and mutants. In particular, we demonstrated the key role of the reader-writer module of PRC2 and of the competition between the binding of activating and repressing enzymes in shaping the H3K27 landscape around transcriptional start sites. The predicted dynamics of establishment and maintenance of the repressive trimethylated H3K27 state suggest a slow accumulation, in perfect agreement with experiments. Our approach represents a first step towards a quantitative description of PcG regulation in various cellular contexts and provides a generic framework to better characterize epigenetic regulation in normal or disease situations.
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Affiliation(s)
- Kapil Newar
- Univ Grenoble Alpes, CNRS, TIMC laboratory, UMR 5525, Grenoble, France
| | - Amith Zafal Abdulla
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Hossein Salari
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Eric Fanchon
- Univ Grenoble Alpes, CNRS, TIMC laboratory, UMR 5525, Grenoble, France
| | - Daniel Jost
- Univ Grenoble Alpes, CNRS, TIMC laboratory, UMR 5525, Grenoble, France
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail:
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6
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Abstract
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription, RNA processing, DNA replication, and repair accumulate in self-organizing membraneless chromatin subcompartments. These structures contribute to efficiently conduct chromatin-mediated reactions and to establish specific cellular programs. However, the underlying mechanisms for their formation are only partly understood. Recent studies invoke liquid-liquid phase separation (LLPS) of proteins and RNAs in the establishment of chromatin activity patterns. At the same time, the folding of chromatin in the nucleus can drive genome partitioning into spatially distinct domains. Here, the interplay between chromatin organization, chromatin binding, and LLPS is discussed by comparing and contrasting three prototypical chromatin subcompartments: the nucleolus, clusters of active RNA polymerase II, and pericentric heterochromatin domains. It is discussed how the different ways of chromatin compartmentalization are linked to transcription regulation, the targeting of soluble factors to certain parts of the genome, and to disease-causing genetic aberrations.
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Affiliation(s)
- Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany
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7
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Laghmach R, Di Pierro M, Potoyan D. A Liquid State Perspective on Dynamics of Chromatin Compartments. Front Mol Biosci 2022; 8:781981. [PMID: 35096966 PMCID: PMC8793688 DOI: 10.3389/fmolb.2021.781981] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
The interior of the eukaryotic cell nucleus has a crowded and heterogeneous environment packed with chromatin polymers, regulatory proteins, and RNA molecules. Chromatin polymer, assisted by epigenetic modifications, protein and RNA binders, forms multi-scale compartments which help regulate genes in response to cellular signals. Furthermore, chromatin compartments are dynamic and tend to evolve in size and composition in ways that are not fully understood. The latest super-resolution imaging experiments have revealed a much more dynamic and stochastic nature of chromatin compartments than was appreciated before. An emerging mechanism explaining chromatin compartmentalization dynamics is the phase separation of protein and nucleic acids into membraneless liquid condensates. Consequently, concepts and ideas from soft matter and polymer systems have been rapidly entering the lexicon of cell biology. In this respect, the role of computational models is crucial for establishing a rigorous and quantitative foundation for the new concepts and disentangling the complex interplay of forces that contribute to the emergent patterns of chromatin dynamics and organization. Several multi-scale models have emerged to address various aspects of chromatin dynamics, ranging from equilibrium polymer simulations, hybrid non-equilibrium simulations coupling protein binding and chromatin folding, and mesoscopic field-theoretic models. Here, we review these emerging theoretical paradigms and computational models with a particular focus on chromatin’s phase separation and liquid-like properties as a basis for nuclear organization and dynamics.
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Affiliation(s)
- Rabia Laghmach
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, MA, United States
| | - Davit Potoyan
- Department of Chemistry, Iowa State University, Ames, IA, United States
- *Correspondence: Davit Potoyan,
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8
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Jost D. Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. Methods Mol Biol 2022; 2301:293-305. [PMID: 34415542 DOI: 10.1007/978-1-0716-1390-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mechanistic modeling in biology allows to investigate, based on first principles, if putative hypotheses are compatible with observations and to drive further experimental works. Along this line, polymer modeling has been instrumental in 3D genomics to better understand the impact of key mechanisms on the spatial genome organization. Here, I describe how polymer-based models can be practically used to study the role of epigenome in chromosome folding. I illustrate this methodology in the context of Drosophila epigenome folding.
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Affiliation(s)
- Daniel Jost
- University of Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.
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9
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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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10
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Using computational modelling to reveal mechanisms of epigenetic Polycomb control. Biochem Soc Trans 2021; 49:71-77. [PMID: 33616630 PMCID: PMC7925002 DOI: 10.1042/bst20190955] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
The Polycomb system is essential for stable gene silencing in many organisms. This regulation is achieved in part through addition of the histone modifications H3K27me2/me3 by Polycomb Repressive Complex 2 (PRC2). These modifications are believed to be the causative epigenetic memory elements of PRC2-mediated silencing. As these marks are stored locally in the chromatin, PRC2-based memory is a cis-acting system. A key feature of stable epigenetic memory in cis is PRC2-mediated, self-reinforcing feedback from K27-methylated histones onto nearby histones in a read-write paradigm. However, it was not clear under what conditions such feedback can lead to stable memory, able, for example, to survive the perturbation of histone dilution at DNA replication. In this context, computational modelling has allowed a rigorous exploration of possible underlying memory mechanisms and has also greatly accelerated our understanding of switching between active and silenced states. Specifically, modelling has predicted that switching and memory at Polycomb loci is digital, with a locus being either active or inactive, rather than possessing intermediate, smoothly varying levels of activation. Here, we review recent advances in models of Polycomb control, focusing on models of epigenetic switching through nucleation and spreading of H3K27me2/me3. We also examine models that incorporate transcriptional feedback antagonism and those including bivalent chromatin states. With more quantitative experimental data on histone modification kinetics, as well as single-cell resolution data on transcription and protein levels for PRC2 targets, we anticipate an expanded need for modelling to help dissect increasingly interconnected and complex memory mechanisms.
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11
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Chromatin as an active polymeric material. Emerg Top Life Sci 2020; 4:111-118. [PMID: 32830859 DOI: 10.1042/etls20200010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023]
Abstract
The patterns of the large-scale spatial organization of chromatin in interphase human somatic cells are not random. Such patterns include the radial separation of euchromatin and heterochromatin, the territorial organization of individual chromosomes, the non-random locations of chromosome territories and the differential positioning of the two X chromosomes in female cells. These features of large-scale nuclear architecture follow naturally from the hypothesis that ATP-consuming non-equilibrium processes associated with highly transcribed regions of chromosomes are a source of 'active' forces. These forces are in excess of those that arise from Brownian motion. Simulations of model chromosomes that incorporate such activity recapitulate these features. In addition, they reproduce many other aspects of the spatial organization of chromatin at large scales that are known from experiments. Our results, reviewed here, suggest that the distribution of transcriptional activity across chromosomes underlies many aspects of large-scale nuclear architecture that were hitherto believed to be unrelated.
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12
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Crippa M, Zhan Y, Tiana G. Effective model of loop extrusion predicts chromosomal domains. Phys Rev E 2020; 102:032414. [PMID: 33076010 DOI: 10.1103/physreve.102.032414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/03/2020] [Indexed: 11/07/2022]
Abstract
An active loop-extrusion mechanism is regarded as the main out-of-equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fiber by solving the kinetic equations associated with the motion of the extruder. By averaging out the position of the extruder along the chain, we build an effective equilibrium model capable of reproducing experimental contact maps based solely on the positions of extrusion-blocking proteins. We assessed the quality of the effective model using numerical simulations of chromosomal segments and comparing the results with explicit-extruder models and experimental data.
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Affiliation(s)
- Martina Crippa
- Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milano, Italy and Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Guido Tiana
- Department of Physics and Center for Complexity and Biosystems, Università degli Studi di Milano and INFN, via Celoria 16, 20133 Milano, Italy
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13
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Frank L, Rippe K. Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 2020; 432:4270-4286. [DOI: 10.1016/j.jmb.2020.04.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022]
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14
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Ghosh SK, Jost D. Genome organization via loop extrusion, insights from polymer physics models. Brief Funct Genomics 2020; 19:119-127. [PMID: 31711163 DOI: 10.1093/bfgp/elz023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/26/2019] [Accepted: 08/31/2019] [Indexed: 12/12/2022] Open
Abstract
Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.
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Affiliation(s)
- Surya K Ghosh
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India
| | - Daniel Jost
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.,Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, Inserm U1210, F-69007 Lyon, France
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15
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Erdel F, Rademacher A, Vlijm R, Tünnermann J, Frank L, Weinmann R, Schweigert E, Yserentant K, Hummert J, Bauer C, Schumacher S, Al Alwash A, Normand C, Herten DP, Engelhardt J, Rippe K. Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation. Mol Cell 2020; 78:236-249.e7. [PMID: 32101700 PMCID: PMC7163299 DOI: 10.1016/j.molcel.2020.02.005] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/20/2019] [Accepted: 02/04/2020] [Indexed: 12/14/2022]
Abstract
The formation of silenced and condensed heterochromatin foci involves enrichment of heterochromatin protein 1 (HP1). HP1 can bridge chromatin segments and form liquid droplets, but the biophysical principles underlying heterochromatin compartmentalization in the cell nucleus are elusive. Here, we assess mechanistically relevant features of pericentric heterochromatin compaction in mouse fibroblasts. We find that (1) HP1 has only a weak capacity to form liquid droplets in living cells; (2) the size, global accessibility, and compaction of heterochromatin foci are independent of HP1; (3) heterochromatin foci lack a separated liquid HP1 pool; and (4) heterochromatin compaction can toggle between two “digital” states depending on the presence of a strong transcriptional activator. These findings indicate that heterochromatin foci resemble collapsed polymer globules that are percolated with the same nucleoplasmic liquid as the surrounding euchromatin, which has implications for our understanding of chromatin compartmentalization and its functional consequences. HP1 has only a weak capacity to form droplets in living cells Size, accessibility, and compaction of heterochromatin foci are independent of HP1 Heterochromatin compaction is “digital” and can toggle between two distinct states Methodological framework to assess hallmarks of phase separation in living cells
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Affiliation(s)
- Fabian Erdel
- LBME, Centre de Biologie Intégrative (CBI), CNRS, UPS, Toulouse, France; Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
| | - Anne Rademacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Rifka Vlijm
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Jana Tünnermann
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Lukas Frank
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Robin Weinmann
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Elisabeth Schweigert
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Klaus Yserentant
- Department for Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Johan Hummert
- Department for Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Caroline Bauer
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Ahmad Al Alwash
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | | | - Dirk-Peter Herten
- Department for Physical Chemistry, Heidelberg University, Heidelberg, Germany; Institute of Cardiovascular Sciences, College of Medical and Dental Sciences and School of Chemistry, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, United Kingdom
| | - Johann Engelhardt
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
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16
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Agrawal A, Ganai N, Sengupta S, Menon GI. Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus. Biophys J 2019; 118:2229-2244. [PMID: 31818465 DOI: 10.1016/j.bpj.2019.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 10/25/2022] Open
Abstract
Model approaches to nuclear architecture have traditionally ignored the biophysical consequences of ATP-fueled active processes acting on chromatin. However, transcription-coupled activity is a source of stochastic forces that are substantially larger than the Brownian forces present at physiological temperatures. Here, we describe an approach to large-scale nuclear architecture in metazoans that incorporates cell-type-specific active processes. The model predicts the statistics of positional distributions, shapes, and overlaps of each chromosome. Simulations of the model reproduce common organizing principles underlying large-scale nuclear architecture across human cell nuclei in interphase. These include the differential positioning of euchromatin and heterochromatin, the territorial organization of chromosomes (including both gene-density-based and size-based chromosome radial positioning schemes), the nonrandom locations of chromosome territories, and the shape statistics of individual chromosomes. We propose that the biophysical consequences of the distribution of transcriptional activity across chromosomes should be central to any chromosome positioning code.
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Affiliation(s)
- Ankit Agrawal
- Computational Biology Group, The Institute of Mathematical Sciences, Taramani, Chennai, India; Homi Bhabha National Institute, Mumbai, India
| | - Nirmalendu Ganai
- Department of Physics, Nabadwip Vidyasagar College, Nabadwip, Nadia, India
| | - Surajit Sengupta
- TIFR Centre for Interdisciplinary Sciences, Serilingampally Mandal, Ranga Reddy District, Hyderabad, India
| | - Gautam I Menon
- Computational Biology Group, The Institute of Mathematical Sciences, Taramani, Chennai, India; Homi Bhabha National Institute, Mumbai, India; Department of Physics, Ashoka University, Rajiv Gandhi Education City, National Capital Region P.O.Rai, Sonepat, India.
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17
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Fiorillo L, Bianco S, Esposito A, Conte M, Sciarretta R, Musella F, Chiariello AM. A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luca Fiorillo
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Simona Bianco
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Andrea Esposito
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Mattia Conte
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Renato Sciarretta
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Francesco Musella
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
| | - Andrea M. Chiariello
- Dipartimento di Fisica Università di Napoli Federico II, and INFN Napoli Complesso Universitario di Monte Sant'Angelo Naples Italy
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18
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Merlotti A, Rosa A, Remondini D. Merging 1D and 3D genomic information: Challenges in modelling and validation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194415. [PMID: 31672524 DOI: 10.1016/j.bbagrm.2019.194415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/23/2022]
Abstract
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and structure of DNA and chromatin inside the nucleus of the cell. It is now clear that these mechanisms have a key role in important processes like gene regulation, yet the detailed ways they act simultaneously and, eventually, come to influence each other even across very different length-scales remain largely unexplored. In this paper, we recapitulate some of the main results concerning gene regulatory and physical mechanisms, in relation to the information encoded in the 1D sequence and the 3D folding structure of DNA. In particular, we stress how reciprocal crossfeeding between 1D and 3D models may provide original insight into how these complex processes work and influence each other. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Alessandra Merlotti
- Department of Physics and Astronomy (DIFA), University of Bologna, Viale Berti Pichat 6/2, Bologna 40127, Italy; INFN Sez., Bologna, Italy.
| | - Angelo Rosa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, (Italy).
| | - Daniel Remondini
- Department of Physics and Astronomy (DIFA), University of Bologna, Viale Berti Pichat 6/2, Bologna 40127, Italy; INFN Sez., Bologna, Italy.
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19
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Jost D, Vaillant C. Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance. Nucleic Acids Res 2019; 46:2252-2264. [PMID: 29365171 PMCID: PMC5861409 DOI: 10.1093/nar/gky009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/11/2018] [Indexed: 02/05/2023] Open
Abstract
Recent progresses of genome-wide chromatin conformation capture techniques have shown that the genome is segmented into hierarchically organized spatial compartments. However, whether this non-random 3D organization only reflects or indeed contributes—and how—to the regulation of genome function remain to be elucidated. The observation in many species that 3D domains correlate strongly with the 1D epigenomic information along the genome suggests a dynamic coupling between chromatin organization and epigenetic regulation. Here, we posit that chromosome folding may contribute to the maintenance of a robust epigenomic identity via the formation of spatial compartments like topologically-associating domains. Using a novel theoretical framework, the living chromatin model, we show that 3D compartmentalization leads to the spatial colocalization of epigenome regulators, thus increasing their local concentration and enhancing their ability to spread an epigenomic signal at long-range. Interestingly, we find that the presence of 1D insulator elements, like CTCF, may contribute greatly to the stable maintenance of adjacent antagonistic epigenomic domains. We discuss the generic implications of our findings in the light of various biological contexts from yeast to human. Our approach provides a modular framework to improve our understanding and to investigate in details the coupling between the structure and function of chromatin.
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Affiliation(s)
- Daniel Jost
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
- To whom correspondence should be addressed. Tel: +33 4 72 72 86 34; Fax: +33 4 72 72 89 50; . Correspondence may also be addressed to Daniel Jost. Tel: +33 4 56 52 00 69; Fax: +33 4 56 52 00 44;
| | - Cédric Vaillant
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, 69007 Lyon, France
- To whom correspondence should be addressed. Tel: +33 4 72 72 86 34; Fax: +33 4 72 72 89 50; . Correspondence may also be addressed to Daniel Jost. Tel: +33 4 56 52 00 69; Fax: +33 4 56 52 00 44;
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20
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Miné-Hattab J, Taddei A. Physical principles and functional consequences of nuclear compartmentalization in budding yeast. Curr Opin Cell Biol 2019; 58:105-113. [PMID: 30928833 DOI: 10.1016/j.ceb.2019.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/28/2019] [Accepted: 02/20/2019] [Indexed: 12/19/2022]
Abstract
One striking feature of eukaryotic nuclei is the existence of discrete regions, in which specific factors concentrate while others are excluded, thus forming microenvironments with different molecular compositions and biological functions. These domains are often referred to as subcompartments even though they are not membrane enclosed. Despite their functional importance the physical nature of these structures remains largely unknown. Here, we describe how the Saccharomyces cerevisiae nucleus is compartmentalized and discuss possible physical models underlying the formation and maintenance of chromatin associated subcompartments. Focusing on three particular examples, the nucleolus, silencing foci, and repair foci, we discuss the biological implications of these different models as well as possible approaches to challenge them in living cells.
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France
| | - Angela Taddei
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France.
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21
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Tan ZW, Guarnera E, Berezovsky IN. Exploring chromatin hierarchical organization via Markov State Modelling. PLoS Comput Biol 2018; 14:e1006686. [PMID: 30596637 PMCID: PMC6355033 DOI: 10.1371/journal.pcbi.1006686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/31/2019] [Accepted: 11/27/2018] [Indexed: 01/02/2023] Open
Abstract
We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling probe in the corresponding energy landscape, mimicking the motion of a biomolecule involved in chromatin function. By studying the metastability of the associated Markov State Model upon annealing, the hierarchical structure of individual chromosomes is observed, and corresponding set of structural partitions is identified at each level of hierarchy. Then, the notion of effective interaction between partitions is derived, delineating the overall topology and architecture of chromosomes. Mapping epigenetic data on the graphs of intra-chromosomal effective interactions helps in understanding how chromosome organization facilitates its function. A sketch of whole-genome interactions obtained from the analysis of 539 partitions from all 23 chromosomes, complemented by distributions of gene expression regulators and epigenetic factors, sheds light on the structure-function relationships in chromatin, delineating chromosomal territories, as well as structural partitions analogous to topologically associating domains and active / passive epigenomic compartments. In addition to the overall genome architecture shown by effective interactions, the affinity between partitions of different chromosomes was analyzed as an indicator of the degree of association between partitions in functionally relevant genomic interactions. The overall static picture of whole-genome interactions obtained with the method presented in this work provides a foundation for chromatin structural reconstruction, for the modelling of chromatin dynamics, and for exploring the regulation of genome function. The algorithms used in this study are implemented in a freely available Python package ChromaWalker (https://bitbucket.org/ZhenWahTan/chromawalker).
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore
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22
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He M, Li Y, Tang Q, Li D, Jin L, Tian S, Che T, He S, Deng L, Gao G, Gu Y, Jiang Z, Li X, Li M. Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis. Int J Biol Sci 2018; 14:1571-1585. [PMID: 30263009 PMCID: PMC6158721 DOI: 10.7150/ijbs.25328] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 07/29/2018] [Indexed: 12/14/2022] Open
Abstract
The recently developed high-throughput chromatin conformation capture (Hi-C) technology enables us to explore the spatial architecture of genomes, which is increasingly considered an important regulator of gene expression. To investigate the changes in three-dimensional (3D) chromatin structure and its mediated gene expression during adipogenesis and myogenesis, we comprehensively mapped 3D chromatin organization for four cell types (3T3-L1 pre-adipocytes, 3T3-L1-D adipocytes, C2C12 myoblasts, and C2C12-D myotubes). We demonstrate that the dynamic spatial genome architecture affected gene expression during cell differentiation. A considerable proportion (~22%) of the mouse genome underwent compartment A/B rearrangement during adipogenic and myogenic differentiation, and most (~80%) upregulated marker genes exhibited an active chromatin state with B to A switch or stable A compartment. More than half (65.4%-73.2%) of the topologically associating domains (TADs) are dynamic. The newly formed TAD and intensified local interactions in the Fabp gene cluster indicated more precise structural regulation of the expression of pro-differentiation genes during adipogenesis. About half (32.39%-59.04%) of the differential chromatin interactions (DCIs) during differentiation are promoter interactions, although these DCIs only account for a small proportion of genome-wide interactions (~9.67% in adipogenesis and ~4.24% in myogenesis). These differential promoter interactions were enriched with promoter-enhancer interactions (PEIs), which were mediated by typical adipogenic and myogenic transcription factors. Differential promoter interactions also included more differentially expressed genes than nonpromoter interactions. Our results provide a global view of dynamic chromatin interactions during adipogenesis and myogenesis and are a resource for studying long-range chromatin interactions mediating the expression of pro-differentiation genes.
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Affiliation(s)
- Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shen He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lamei Deng
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Guangliang Gao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.,Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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23
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Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA. Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci U S A 2018; 115:E6697-E6706. [PMID: 29967174 PMCID: PMC6055145 DOI: 10.1073/pnas.1717730115] [Citation(s) in RCA: 381] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mammalian chromatin is spatially organized at many scales showing two prominent features in interphase: (i) alternating regions (1-10 Mb) of active and inactive chromatin that spatially segregate into different compartments, and (ii) domains (<1 Mb), that is, regions that preferentially interact internally [topologically associating domains (TADs)] and are central to gene regulation. There is growing evidence that TADs are formed by active extrusion of chromatin loops by cohesin, whereas compartmentalization is established according to local chromatin states. Here, we use polymer simulations to examine how loop extrusion and compartmental segregation work collectively and potentially interfere in shaping global chromosome organization. A model with differential attraction between euchromatin and heterochromatin leads to phase separation and reproduces compartmentalization as observed in Hi-C. Loop extrusion, essential for TAD formation, in turn, interferes with compartmentalization. Our integrated model faithfully reproduces Hi-C data from puzzling experimental observations where altering loop extrusion also led to changes in compartmentalization. Specifically, depletion of chromatin-associated cohesin reduced TADs and revealed finer compartments, while increased processivity of cohesin strengthened large TADs and reduced compartmentalization; and depletion of the TAD boundary protein CTCF weakened TADs while leaving compartments unaffected. We reveal that these experimental perturbations are special cases of a general polymer phenomenon of active mixing by loop extrusion. Our results suggest that chromatin organization on the megabase scale emerges from competition of nonequilibrium active loop extrusion and epigenetically defined compartment structure.
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Affiliation(s)
- Johannes Nuebler
- Department of Physics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Geoffrey Fudenberg
- Gladstone Institutes of Data Science and Biotechnology, San Francisco, CA 94158
| | - Maxim Imakaev
- Department of Physics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Nezar Abdennur
- Department of Physics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Leonid A Mirny
- Department of Physics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139;
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24
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Ghosh SK, Jost D. How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes. PLoS Comput Biol 2018; 14:e1006159. [PMID: 29813054 PMCID: PMC6003694 DOI: 10.1371/journal.pcbi.1006159] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 06/15/2018] [Accepted: 04/28/2018] [Indexed: 11/19/2022] Open
Abstract
The 3D organization of chromosomes is crucial for regulating gene expression and cell function. Many experimental and polymer modeling efforts are dedicated to deciphering the mechanistic principles behind chromosome folding. Chromosomes are long and densely packed-topologically constrained-polymers. The main challenges are therefore to develop adequate models and simulation methods to investigate properly the multi spatio-temporal scales of such macromolecules. Here, we proposed a generic strategy to develop efficient coarse-grained models for self-avoiding polymers on a lattice. Accounting accurately for the polymer entanglement length and the volumic density, we show that our simulation scheme not only captures the steady-state structural and dynamical properties of the system but also tracks the same dynamics at different coarse-graining. This strategy allows a strong power-law gain in numerical efficiency and offers a systematic way to define reliable coarse-grained null models for chromosomes and to go beyond the current limitations by studying long chromosomes during an extended time period with good statistics. We use our formalism to investigate in details the time evolution of the 3D organization of chromosome 3R (20 Mbp) in drosophila during one cell cycle (20 hours). We show that a combination of our coarse-graining strategy with a one-parameter block copolymer model integrating epigenomic-driven interactions quantitatively reproduce experimental data at the chromosome-scale and predict that chromatin motion is very dynamic during the cell cycle.
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Affiliation(s)
- Surya K. Ghosh
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Daniel Jost
- Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
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25
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Abstract
Transcription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo. As large-scale ChIP-seq data sets have been collected for different TFs and histone modifications, their potential to predict gene expression can be used to test hypotheses about the mechanisms of gene regulation. In addition, complementary functional genomics assays provide a global view of chromatin accessibility and long-range cis-regulatory interactions that are being combined with TF binding and histone remodeling to study the regulation of gene expression. Thus, ChIP-seq analysis is now widely integrated with other functional genomics assays to better understand gene regulatory mechanisms. In this review, we discuss advances and challenges in integrating ChIP-seq data to identify context-specific chromatin states associated with gene activity. We describe the overall computational design of integrating ChIP-seq data with other functional genomics assays. We also discuss the challenges of extending these methods to low-input ChIP-seq assays and related single-cell assays.
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Affiliation(s)
| | - Ali Mortazavi
- Corresponding author: Ali Mortazavi, Department of Developmental and Cell Biology, 2300 Biological Sciences 3, University of California, Irvine, CA 92697, USA. Tel: (949)824-6762; E-mail:
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26
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Albritton SE, Ercan S. Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation. Trends Genet 2017; 34:41-53. [PMID: 29037439 DOI: 10.1016/j.tig.2017.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 01/05/2023]
Abstract
Recent work demonstrating the role of chromosome organization in transcriptional regulation has sparked substantial interest in the molecular mechanisms that control chromosome structure. Condensin, an evolutionarily conserved multisubunit protein complex, is essential for chromosome condensation during cell division and functions in regulating gene expression during interphase. In Caenorhabditis elegans, a specialized condensin forms the core of the dosage compensation complex (DCC), which specifically binds to and represses transcription from the hermaphrodite X chromosomes. DCC serves as a clear paradigm for addressing how condensins target large chromosomal domains and how they function to regulate chromosome structure and transcription. Here, we discuss recent research on C. elegans DCC in the context of canonical condensin mechanisms as have been studied in various organisms.
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Affiliation(s)
- Sarah Elizabeth Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA.
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27
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Haddad N, Vaillant C, Jost D. IC-Finder: inferring robustly the hierarchical organization of chromatin folding. Nucleic Acids Res 2017; 45:e81. [PMID: 28130423 PMCID: PMC5449546 DOI: 10.1093/nar/gkx036] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/13/2017] [Indexed: 11/22/2022] Open
Abstract
The spatial organization of the genome plays a crucial role in the regulation of gene expression. Recent experimental techniques like Hi-C have emphasized the segmentation of genomes into interaction compartments that constitute conserved functional domains participating in the maintenance of a proper cell identity. Here, we propose a novel method, IC-Finder, to identify interaction compartments (IC) from experimental Hi-C maps. IC-Finder is based on a hierarchical clustering approach that we adapted to account for the polymeric nature of chromatin. Based on a benchmark of realistic in silico Hi-C maps, we show that IC-Finder is one of the best methods in terms of reliability and is the most efficient numerically. IC-Finder proposes two original options: a probabilistic description of the inferred compartments and the possibility to explore the various hierarchies of chromatin organization. Applying the method to experimental data in fly and human, we show how the predicted segmentation may depend on the normalization scheme and how 3D compartmentalization is tightly associated with epigenomic information. IC-Finder provides a robust and generic ‘all-in-one’ tool to uncover the general principles of 3D chromatin folding and their influence on gene regulation. The software is available at http://membres-timc.imag.fr/Daniel.Jost/DJ-TIMC/Software.html.
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Affiliation(s)
- Noelle Haddad
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69007 Lyon, France
| | - Cédric Vaillant
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69007 Lyon, France
| | - Daniel Jost
- Univ. Grenoble Alpes, CNRS, TIMC-IMAG, F-38000 Grenoble, France
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28
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Fudenberg G, Imakaev M. FISH-ing for captured contacts: towards reconciling FISH and 3C. Nat Methods 2017; 14:673-678. [PMID: 28604723 PMCID: PMC5517086 DOI: 10.1038/nmeth.4329] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/03/2017] [Indexed: 11/20/2022]
Abstract
Chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) are two widely used technologies that provide distinct readouts of 3D chromosome organization. While both technologies can assay locus-specific organization, how to integrate views from 3C, or genome-wide Hi-C, and FISH is far from solved. Contact frequency, measured by Hi-C, and spatial distance, measured by FISH, are often assumed to quantify the same phenomena and used interchangeably. Here, however, we demonstrate that contact frequency is distinct from average spatial distance, both in polymer simulations and in experimental data. Performing a systematic analysis of the technologies, we show that this distinction can create a seemingly paradoxical relationship between 3C and FISH, both in minimal polymer models with dynamic looping interactions and in loop-extrusion simulations. Together, our results indicate that cross-validation of Hi-C and FISH should be carefully designed, and that jointly considering contact frequency and spatial distance is crucial for fully understanding chromosome organization.
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Affiliation(s)
- Geoffrey Fudenberg
- Center for the 3D Structure and Physics of the Genome, and Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Maxim Imakaev
- Center for the 3D Structure and Physics of the Genome, and Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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29
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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] [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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