1
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Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Di Pierno F, Dekker J, Nicodemi M. Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations. Int J Mol Sci 2024; 25:10215. [PMID: 39337699 PMCID: PMC11432541 DOI: 10.3390/ijms251810215] [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: 07/14/2024] [Revised: 09/17/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024] Open
Abstract
Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2 Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.
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Affiliation(s)
- Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Alex Abraham
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Liyan Yang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Johan H. Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Krishna M. Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Francesca Vercellone
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, Italy
- INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Fontana
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Florinda Di Pierno
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, Italy
- INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
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2
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Chaboche Q, Campos-Villalobos G, Giunta G, Dijkstra M, Cosentino Lagomarsino M, Scolari VF. A mean-field theory for predicting single polymer collapse induced by neutral crowders. SOFT MATTER 2024; 20:3271-3282. [PMID: 38456237 DOI: 10.1039/d3sm01522j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Macromolecular crowding can induce the collapse of a single long polymer into a globular form due to depletion forces of entropic nature. This phenomenon has been shown to play a significant role in compacting the genome within the bacterium Escherichia coli into a well-defined region of the cell known as the nucleoid. Motivated by the biological significance of this process, numerous theoretical and computational studies have searched for the primary determinants of the behavior of polymer-crowder phases. However, our understanding of this process remains incomplete and there is debate on a quantitatively unified description. In particular, different simulation studies with explicit crowders have proposed different order parameters as potential predictors for the collapse transition. In this work, we present a comprehensive analysis of published simulation data obtained from different sources. Based on the common behavior we find in this data, we develop a unified phenomenological model that we show to be predictive. Finally, to further validate the accuracy of the model, we conduct new simulations on polymers of various sizes, and investigate the role of jamming of the crowders.
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Affiliation(s)
- Quentin Chaboche
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, 75005 Paris, France
- IFOM ETS, The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
| | - Gerardo Campos-Villalobos
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Giuliana Giunta
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen am Rhein, Germany
| | - Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Marco Cosentino Lagomarsino
- IFOM ETS, The AIRC Institute of Molecular Oncology, 20139, Milan, Italy.
- Physics Department, University of Milan, and INFN, Milan, Italy
| | - Vittore F Scolari
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, 75005 Paris, France
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.
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3
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Remini L, Segers M, Palmeri J, Walter JC, Parmeggiani A, Carlon E. Chromatin structure from high resolution microscopy: Scaling laws and microphase separation. Phys Rev E 2024; 109:024408. [PMID: 38491617 DOI: 10.1103/physreve.109.024408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/11/2024] [Indexed: 03/18/2024]
Abstract
Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50 nm) of the three-dimensional physical location of multiple (up to ∼10^{2}) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr21 obtained from multiplexed fluorescence in situ hybridization (FISH) methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags with the aim being to unravel the chromatin conformational arrangements. We show that for any specific genomic site, there are (at least) two different conformational arrangements of chromatin, implying coexisting distinct topologies which we refer to as phase α and phase β. These two phases show different scaling behaviors: the former is consistent with a crumpled globule, while the latter indicates a confined, but more extended conformation, such as a looped domain. The identification of these distinct phases sheds light on the coexistence of multiple chromatin topologies and provides insights into the effects of cellular context and/or treatments on chromatin structure.
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Affiliation(s)
- Loucif Remini
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Midas Segers
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS UMR5221, Montpellier, France
| | - Enrico Carlon
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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4
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Jung Y, Sadeghi A, Ha BY. Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS. Sci Rep 2024; 14:139. [PMID: 38167921 PMCID: PMC10762067 DOI: 10.1038/s41598-023-50355-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Cells orchestrate the action of various molecules toward organizing their chromosomes. Using a coarse-grained computational model, we study the compaction of bacterial chromosomes by the cross-linking protein H-NS and cellular crowders. In this work, H-NS, modeled as a mobile "binder," can bind to a chromosome-like polymer with a characteristic binding energy. The simulation results reported here clarify the relative role of biomolecular crowding and H-NS in condensing a bacterial chromosome in a quantitative manner. In particular, they shed light on the nature and degree of crowder and H-NS synergetics: while the presence of crowders enhances H-NS binding to a chromosome-like polymer, the presence of H-NS makes crowding effects more efficient, suggesting two-way synergetics in chain compaction. Also, the results show how crowding effects promote clustering of bound H-NS. For a sufficiently large concentration of H-NS, the cluster size increases with the volume fraction of crowders.
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Affiliation(s)
- Youngkyun Jung
- Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon, 34141, South Korea.
| | - Amir Sadeghi
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Bae-Yeun Ha
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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5
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Mitra D, Pande S, Chatterji A. Polymer architecture orchestrates the segregation and spatial organization of replicating E. coli chromosomes in slow growth. SOFT MATTER 2022; 18:5615-5631. [PMID: 35861071 DOI: 10.1039/d2sm00734g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The mechanism of chromosome segregation and organization in the bacterial cell cycle of E. coli is one of the least understood aspects in its life cycle. The E. coli chromosome is often modelled as a bead spring ring polymer. We introduce cross-links in the DNA-ring polymer, resulting in the formation of loops within each replicating bacterial chromosome. We use simulations to show that the chosen polymer-topology ensures its self-organization along the cell long-axis, such that various chromosomal loci get spatially localized as seen in vivo. The localization of loci arises due to entropic repulsion between polymer loops within each daughter DNA confined in a cylinder. The cellular addresses of the loci in our model are in fair agreement with those seen in experiments as given in J. A. Cass et al., Biophys. J., 2016, 110, 2597-2609. We also show that the adoption of such modified polymer architectures by the daughter DNAs leads to an enhanced propensity of their spatial segregation. Secondly, we match other experimentally reported results, including observation of the cohesion time and the ter-transition. Additionally, the contact map generated from our simulations reproduces the macro-domain like organization as seen in the experimentally obtained Hi-C map. Lastly, we have also proposed a plausible reconciliation of the 'Train Track' and the 'Replication Factory' models which provide conflicting descriptions of the spatial organization of the replication forks. Thus, we reconcile observations from complementary experimental techniques probing bacterial chromosome organization.
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6
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Cristofalo M, Marrano CA, Salerno D, Corti R, Cassina V, Mammola A, Gherardi M, Sclavi B, Cosentino Lagomarsino M, Mantegazza F. Cooperative effects on the compaction of DNA fragments by the nucleoid protein H-NS and the crowding agent PEG probed by Magnetic Tweezers. Biochim Biophys Acta Gen Subj 2020; 1864:129725. [PMID: 32891648 DOI: 10.1016/j.bbagen.2020.129725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 08/30/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND DNA bridging promoted by the H-NS protein, combined with the compaction induced by cellular crowding, plays a major role in the structuring of the E. coli genome. However, only few studies consider the effects of the physical interplay of these two factors in a controlled environment. METHODS We apply a single molecule technique (Magnetic Tweezers) to study the nanomechanics of compaction and folding kinetics of a 6 kb DNA fragment, induced by H-NS bridging and/or PEG crowding. RESULTS In the presence of H-NS alone, the DNA shows a step-wise collapse driven by the formation of multiple bridges, and little variations in the H-NS concentration-dependent unfolding force. Conversely, the DNA collapse force observed with PEG was highly dependent on the volume fraction of the crowding agent. The two limit cases were interpreted considering the models of loop formation in a pulled chain and pulling of an equilibrium globule respectively. CONCLUSIONS We observed an evident cooperative effect between H-NS activity and the depletion of forces induced by PEG. GENERAL SIGNIFICANCE Our data suggest a double role for H-NS in enhancing compaction while forming specific loops, which could be crucial in vivo for defining specific mesoscale domains in chromosomal regions in response to environmental changes.
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Affiliation(s)
- M Cristofalo
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - C A Marrano
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - D Salerno
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - R Corti
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - V Cassina
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy
| | - A Mammola
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - M Gherardi
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - B Sclavi
- Université Pierre et Marie Curie, Institut de Biologie Paris Seine, 7-9 Quai Saint Bernard, 75005 Paris, France
| | - M Cosentino Lagomarsino
- Università degli Studi di Milano, Via Celoria 16, 20133 Milano (MI), Italy; IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano (MI), Italy; I.N.F.N. Sezione di Milano, Via Celoria 16, 20133 Milano (MI), Italy
| | - F Mantegazza
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, via Raoul Follereau 3, 20854, Vedano al Lambro (MB), Italy.
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7
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Michieletto D, Colì D, Marenduzzo D, Orlandini E. Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus. PHYSICAL REVIEW LETTERS 2019; 123:228101. [PMID: 31868408 DOI: 10.1103/physrevlett.123.228101] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Understanding the spatial organization of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical-or epigenetic-marks that are deposited along the genome are thought to play an important, yet poorly understood, role in determining genome organization and cell identity. The physical principles underlying the interplay between epigenetic dynamics and genome folding remain elusive. Here we propose and study a theory that assumes a coupling between epigenetic mark and genome densities, and which can be applied at the scale of the whole nucleus. We show that equilibrium models are not compatible with experiments and a qualitative agreement is recovered by accounting for nonequilibrium processes that can stabilize microphase separated epigenomic domains. We finally discuss the potential biophysical origin of these terms.
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Affiliation(s)
- Davide Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
- Centre for Mathematical Biology, and Department of Mathematical Sciences, University of Bath, North Rd, Bath BA2 7AY, United Kingdom
| | - Davide Colì
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
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8
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Yamamoto T, Schiessel H. Dilution of contact frequency between superenhancers by loop extrusion at interfaces. SOFT MATTER 2019; 15:7635-7643. [PMID: 31482924 DOI: 10.1039/c9sm01454c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The loop extrusion theory predicts that cohesin acts as a molecular motor that extrudes chromatin fibers to produce loops. Hi-C experiments have detected relatively high contact frequencies between superenhancers. These probably result from the fact that superenhancers are localized at condensates of transcriptional activators and coactivators. The contact frequency between superenhancers is enhanced by auxin treatment that removes cohesin from chromatin. Motivated by these experimental results, we here treat chromatin at the surface of a condensate as a loop extruding polymer brush. Our theory predicts that the lateral pressure generated by the brush decreases with decreasing the loading rate of cohesin. This is because loop extrusion actively transfers chain segments at the vicinity of the interface. Our theory thus predicts that the increase of contact frequency by auxin treatment results from the fact that suppressing the loop extrusion process induces the dissolution of molecular components to the nucleoplasm, decreasing the average distance between superenhancers.
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Affiliation(s)
- Tetsuya Yamamoto
- Department of Materials Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan. and PRESTO, Japan Science and Technology Agency (JST) - 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Helmut Schiessel
- Instituut-Lorentz for Theoretical Physics, Leiden University - Niels Bohrweg 2, Leiden, 2333 CA, The Netherlands
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9
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Santra A, Kumari K, Padinhateeri R, Dünweg B, Prakash JR. Universality of the collapse transition of sticky polymers. SOFT MATTER 2019; 15:7876-7887. [PMID: 31531489 DOI: 10.1039/c9sm01361j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The universality of the swelling of the radius of gyration of a homopolymer relative to its value in the θ state, independent of polymer-solvent chemistry, in the crossover regime between θ and athermal solvent conditions, is well known. Here we study, by Brownian dynamics, a polymer model where a subset of monomers is labelled as "stickers". The mutual interaction of the stickers is more attractive than those of the other ("backbone") monomers, and has an additional important characteristic of "functionality" φ, i.e., the maximum number of stickers that can locally bind to a given sticker. A saturated bond formed in this manner remains bound until it breaks due to thermal fluctuations, a requirement which can be viewed as an additional Boolean degree of freedom that describes the bonding. This, in turn, makes the question of the order of the collapse transition a non-trivial one. Nevertheless, for the parameters that we have studied (in particular, φ = 1), we find a standard second-order θ collapse, using a renormalised solvent quality parameter that takes into account the increased average attraction due to the presence of stickers. We examine the swelling of the radius of gyration of such a sticky polymer relative to its value in the altered θ state, using a novel potential to model the various excluded volume interactions that occur between the monomers on the chain. We find that the swelling of such sticky polymers is identical to the universal swelling of homopolymers in the thermal crossover regime. Additionally, for our model, the Kuhn segment length under θ conditions is found to be the same for chains with and without stickers.
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Affiliation(s)
- Aritra Santra
- Department of Chemical Engineering, Monash University, Melbourne, VIC 3800, Australia.
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10
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Kumar A, Chaudhuri D. Cross-linker mediated compaction and local morphologies in a model chromosome. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:354001. [PMID: 31112939 DOI: 10.1088/1361-648x/ab2350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The binders cluster together via the polymer mediated attraction, in turn, folding the polymer. Using molecular dynamics simulations, and a mean field description, we explicitly demonstrate the continuous nature of the folding transition, characterized by unimodal distributions of the polymer size across the transition. At the transition point the chromatin size and cross-linker clusters display large fluctuations, and a maximum in their negative cross-correlation, apart from a critical slowing down. Along the transition, we distinguish the local chain morphologies in terms of topological loops, inter-loop gaps, and zippering. The topologies are dominated by simply connected loops at the criticality, and by zippering in the folded phase.
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Affiliation(s)
- Amit Kumar
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India. Homi Bhaba National Institute, Anushaktigar, Mumbai 400094, India
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11
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Liu S, Zhang L, Quan H, Tian H, Meng L, Yang L, Feng H, Gao YQ. From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective. Nucleic Acids Res 2019; 46:9367-9383. [PMID: 30053116 PMCID: PMC6182157 DOI: 10.1093/nar/gky633] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/12/2018] [Indexed: 11/28/2022] Open
Abstract
The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism, especially the sequence dependence for the formation of varied chromatin structures in different cells remains to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI (CpG island) forest and prairie genomic domains based on CGI densities of a species, dividing the genome into two sequentially, epigenetically, and transcriptionally distinct regions. These two megabase-sized domains also spatially segregate to different extents in different cell types. Forests and prairies show enhanced segregation from each other in development, differentiation, and senescence, meanwhile the multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, helping to define cell identity. We propose that the phase separation of the 1D mosaic sequence in space serves as a potential driving force, and together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types. The mosaicity in genome of different species in terms of forests and prairies could relate to observations in their biological processes like development and aging. In this way, we provide a bottoms-up theory to explain the chromatin structural and epigenetic changes in different processes.
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Affiliation(s)
- Sirui Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ling Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hao Tian
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luming Meng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Huajie Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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12
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Ross BC, Costello JC. Improved inference of chromosome conformation from images of labeled loci. F1000Res 2019; 7. [PMID: 31363407 PMCID: PMC6644830 DOI: 10.12688/f1000research.16252.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/26/2019] [Indexed: 11/29/2022] Open
Abstract
We previously published a method that infers chromosome conformation from images of fluorescently-tagged genomic loci, for the case when there are many loci labeled with each distinguishable color. Here we build on our previous work and improve the reconstruction algorithm to address previous limitations. We show that these improvements 1) increase the reconstruction accuracy and 2) allow the method to be used on large-scale problems involving several hundred labeled loci. Simulations indicate that full-chromosome reconstructions at 1/2 Mb resolution are possible using existing labeling and imaging technologies. The updated reconstruction code and the script files used for this paper are available at:
https://github.com/heltilda/align3d.
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Affiliation(s)
- Brian C Ross
- Computational Bioscience Program, Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - James C Costello
- Computational Bioscience Program, Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, CO, 80045, USA
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13
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Joyeux M. A segregative phase separation scenario of the formation of the bacterial nucleoid. SOFT MATTER 2018; 14:7368-7381. [PMID: 30204212 DOI: 10.1039/c8sm01205a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a volume about a thousand times larger outside the cell. Here, by performing numerical simulations using coarse-grained models, we elaborate on the conjecture that the formation of the nucleoid may result from a segregative phase separation mechanism driven by the demixing of the DNA coil and non-binding globular macromolecules present in the cytoplasm, presumably functional ribosomes. Simulations performed with crowders having a spherical, dumbbell or octahedral geometry highlight the sensitive dependence of the level of DNA compaction on the dissymmetry of DNA/DNA, DNA/crowder, and crowder/crowder repulsive interactions, thereby supporting the segregative phase separation scenario. Simulations also consistently predict a much stronger DNA compaction close to the jamming threshold. Moreover, simulations performed with crowders of different sizes suggest that the final density distribution of each species results from the competition between thermodynamic forces and steric hindrance, so that bigger crowders are expelled selectively from the nucleoid only at moderate total crowder concentrations. This work leads to several predictions, which may eventually be tested experimentally.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
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14
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Scolari VF, Mercy G, Koszul R, Lesne A, Mozziconacci J. Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer. PHYSICAL REVIEW LETTERS 2018; 121:057801. [PMID: 30118310 DOI: 10.1103/physrevlett.121.057801] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/11/2018] [Indexed: 06/08/2023]
Abstract
We investigate the kinetics of a polymer collapse due to the formation of irreversible cross-links between its monomers. Using the contact probability P(s) as a scale-dependent order parameter depending on the chemical distance s, our simulations show the emergence of a cooperative pearling instability. Namely, the polymer undergoes a sharp conformational transition to a set of absorbing states characterized by a length scale ξ corresponding to the mean pearl size. This length and the transition time depend on the polymer equilibrium dynamics and the cross-linking rate. We confirm experimentally this transition using a DNA conformation capture experiment in yeast.
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Affiliation(s)
- Vittore F Scolari
- Spatial Regulation of Genomes, Genomes and Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Guillaume Mercy
- Spatial Regulation of Genomes, Genomes and Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Romain Koszul
- Spatial Regulation of Genomes, Genomes and Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Annick Lesne
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, Montpellier, France
- University of Montpellier, Montpellier, France
| | - Julien Mozziconacci
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
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15
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Negri M, Gherardi M, Tiana G, Cosentino Lagomarsino M. Spontaneous domain formation in disordered copolymers as a mechanism for chromosome structuring. SOFT MATTER 2018; 14:6128-6136. [PMID: 29998272 DOI: 10.1039/c8sm00468d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Motivated by the problem of domain formation in chromosomes, we studied a co-polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus introducing some quenched disorder in the system. Previous work has shown that in the case of regularly-spaced interacting monomers this chain can fold into structures characterized by multiple distinct domains of consecutive segments. In each domain, attractive interactions are balanced by the entropy cost of forming loops. We show by advanced replica-exchange simulations that adding disorder in the position of the interacting monomers further stabilizes these domains. The model suggests that the partitioning of the chain into well-defined domains of consecutive monomers is a spontaneous property of heteropolymers. In the case of chromosomes, evolution could have acted on the spacing of interacting monomers to modulate in a simple way the underlying domains for functional reasons.
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Affiliation(s)
- Matteo Negri
- Department of Physics, Universitá degli Studi di Milano, via Celoria 16, 20133 Milano, Italy.
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16
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Pereira MCF, Brackley CA, Lintuvuori JS, Marenduzzo D, Orlandini E. Entropic elasticity and dynamics of the bacterial chromosome: A simulation study. J Chem Phys 2018; 147:044908. [PMID: 28764377 DOI: 10.1063/1.4995992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a "piston"-a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein sizes and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the "piston": while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they "pop-off" one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.
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Affiliation(s)
- M C F Pereira
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J S Lintuvuori
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Universite Paris-Saclay, 91405 Orsay Cedex, France
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - E Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova, 35131 PD, Italy
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17
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Hacker WC, Li S, Elcock AH. Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome. Nucleic Acids Res 2017. [PMID: 28645155 PMCID: PMC5570083 DOI: 10.1093/nar/gkx541] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of ‘fractal globules,’ and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome.
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Affiliation(s)
- William C Hacker
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Shuxiang Li
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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18
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Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains. Biophys J 2017; 112:1085-1093. [PMID: 28355537 DOI: 10.1016/j.bpj.2017.01.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/20/2016] [Accepted: 01/06/2017] [Indexed: 12/18/2022] Open
Abstract
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear bodies exchange rapidly with the soluble pool while the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins able to switch between an "on" (binding) and an "off" (nonbinding) state. This system provides a model for any DNA-binding protein that can be posttranslationally modified to change its affinity for DNA (e.g., through phosphorylation). Protein switching is a nonequilibrium process, and it leads to the formation of clusters of self-limiting size, where individual proteins in a cluster exchange with the soluble pool with kinetics similar to those seen in photobleaching experiments. This behavior contrasts sharply with that exhibited by nonswitching proteins, which are permanently in the on-state; when these bind to DNA nonspecifically, they form clusters that grow indefinitely in size. To explain these findings, we propose a mean-field theory from which we obtain a scaling relation between the typical cluster size and the protein switching rate. Protein switching also reshapes intrachromatin contacts to give networks resembling those seen in topologically associating domains, as switching markedly favors local (short-range) contacts over distant ones. Our results point to posttranslational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, nonequilibrium, protein clusters with the properties of nuclear bodies.
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Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of Chromosomal Domains by Loop Extrusion. Cell Rep 2016; 15:2038-49. [PMID: 27210764 PMCID: PMC4889513 DOI: 10.1016/j.celrep.2016.04.085] [Citation(s) in RCA: 1204] [Impact Index Per Article: 150.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/01/2015] [Accepted: 04/20/2016] [Indexed: 12/31/2022] Open
Abstract
Topologically associating domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain unclear. Here, we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. Using polymer simulations, we show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops. Loop extrusion both explains diverse experimental observations-including the preferential orientation of CTCF motifs, enrichments of architectural proteins at TAD boundaries, and boundary deletion experiments-and makes specific predictions for the depletion of CTCF versus cohesin. Finally, loop extrusion has potentially far-ranging consequences for processes such as enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes.
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Affiliation(s)
- Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 01238, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Maxim Imakaev
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Carolyn Lu
- Program for Research in Mathematics, Engineering and Science for High School Students (PRIMES) and Undergraduate Research Opportunities Program (UROP), MIT, Cambridge, MA 02139, USA
| | - Anton Goloborodko
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Nezar Abdennur
- PhD Program in Computational and Systems Biology, MIT, Cambridge, MA 02139, USA
| | - Leonid A Mirny
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 01238, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
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20
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Vandebroek H, Vanderzande C. Dynamics of a polymer in an active and viscoelastic bath. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:060601. [PMID: 26764617 DOI: 10.1103/physreve.92.060601] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Indexed: 06/05/2023]
Abstract
We study the dynamics of an ideal polymer chain in a viscoelastic medium and in the presence of active forces. The motion of the center of mass and of individual monomers is calculated. On time scales that are comparable to the persistence time of the active forces, monomers can move superdiffusively, while on larger time scales subdiffusive behavior occurs. The difference between this subdiffusion and that in the absence of active forces is quantified. We show that the polymer swells in response to active processes and determine how this swelling depends on the viscoelastic properties of the environment. Our results are compared to recent experiments on the motion of chromosomal loci in bacteria.
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Affiliation(s)
- Hans Vandebroek
- Faculty of Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Carlo Vanderzande
- Faculty of Sciences, Hasselt University, 3590 Diepenbeek, Belgium
- Instituut Theoretische Fysica, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
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21
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Imakaev MV, Fudenberg G, Mirny LA. Modeling chromosomes: Beyond pretty pictures. FEBS Lett 2015; 589:3031-6. [PMID: 26364723 DOI: 10.1016/j.febslet.2015.09.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/03/2015] [Indexed: 10/23/2022]
Abstract
Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data-driven ensembles, and two classes of de novo models: structural ensembles and mechanistic ensembles. Finally, we highlight specific questions mechanistic ensembles can address.
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Affiliation(s)
- Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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22
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Abstract
In rapidly growing populations of bacterial cells, including those of the model organism Escherichia coli, genes essential for growth--such as those involved in protein synthesis--are expressed at high levels; this is in contrast to many horizontally-acquired genes, which are maintained at low transcriptional levels. (1) This balance in gene expression states between 2 distinct classes of genes is established by a galaxy of transcriptional regulators, including the so-called nucleoid associated proteins (NAP) that contribute to shaping the chromosome. (2) Besides these active players in gene regulation, it is not too far-fetched to anticipate that genome organization in terms of how genes are arranged on the chromosome, (3) which is the result of long-drawn transactions among genome rearrangement processes and selection, and the manner in which it is structured inside the cell, plays a role in establishing this balance. A recent study from our group has contributed to the literature investigating the interplay between global transcriptional regulators and genome organization in establishing gene expression homeostasis. (4) In particular, we address a triangle of functional interactions among genome organization, gene expression homeostasis and horizontal gene transfer.
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23
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Scolari VF, Sclavi B, Cosentino Lagomarsino M. The nucleoid as a smart polymer. Front Microbiol 2015; 6:424. [PMID: 26005440 PMCID: PMC4424877 DOI: 10.3389/fmicb.2015.00424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/21/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
- Vittore F Scolari
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France
| | - Bianca Sclavi
- Centre National de la Recherche Scientifique, LBPA, UMR 8113, ENS Cachan Cachan, France
| | - Marco Cosentino Lagomarsino
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France ; Centre National de la Recherche Scientifique, UMR 7238 Paris, France
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24
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Hofmann A, Heermann DW. The role of loops on the order of eukaryotes and prokaryotes. FEBS Lett 2015; 589:2958-65. [PMID: 25912650 DOI: 10.1016/j.febslet.2015.04.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/14/2015] [Accepted: 04/14/2015] [Indexed: 11/29/2022]
Abstract
The study of the three-dimensional organization of chromatin has recently gained much focus in the context of novel techniques for detecting genome-wide contacts using next-generation sequencing. These chromosome conformation capture-based methods give a deep topological insight into the architecture of the genome inside the nucleus. Several recent studies observe a compartmentalization of chromatin interactions into spatially confined domains. This structural feature of interphase chromosomes is not only supported by conventional studies assessing the interaction data of millions of cells, but also by analysis on the level of a single cell. We first present and examine the different models that have been proposed to elucidate these topological domains in eukaryotes. Then we show that a model which relies on the dynamic formation of loops within domains can account for the experimentally observed contact maps. Interestingly, the topological domain structure is not only found in mammalian genomes, but also in bacterial chromosomes.
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Affiliation(s)
- Andreas Hofmann
- Institute for Theoretical Physics, University of Heidelberg, Philosophenweg 19, 69120 Heidelberg, Germany.
| | - Dieter W Heermann
- Institute for Theoretical Physics, University of Heidelberg, Philosophenweg 19, 69120 Heidelberg, Germany; Institute for Molecular Biophysics, The Jackson Laboratory, Bar Harbor, ME, USA; Shanghai Institute of Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, PR China; Shanghai Center for Bioinformation Technology (SCBIT), Shanghai, PR China
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