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Fouziya S, Krietenstein N, Mir US, Mieczkowski J, Khan MA, Baba A, Dar MA, Altaf M, Wani AH. Genome wide nucleosome landscape shapes 3D chromatin organization. SCIENCE ADVANCES 2024; 10:eadn2955. [PMID: 38848364 PMCID: PMC11160460 DOI: 10.1126/sciadv.adn2955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
The hierarchical chromatin organization begins with formation of nucleosomes, which fold into chromatin domains punctuated by boundaries and ultimately chromosomes. In a hierarchal organization, lower levels shape higher levels. However, the dependence of higher-order 3D chromatin organization on the nucleosome-level organization has not been studied in cells. We investigated the relationship between nucleosome-level organization and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation SWItch (ISWI) and Chromodomain Helicase DNA-binding (CHD1) chromatin remodeling factors in budding yeast. We find that changes in nucleosome-level properties are accompanied by changes in 3D chromatin organization. Short-range chromatin contacts up to a few kilo-base pairs decrease, chromatin domains weaken, and boundary strength decreases. Boundary strength scales with accessibility and moderately with width of nucleosome-depleted region. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical "bottom-up" mechanism by which nucleosome distribution across genome shapes 3D chromatin organization.
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Affiliation(s)
- Shah Fouziya
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Nils Krietenstein
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Ulfat Syed Mir
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Jakub Mieczkowski
- International Research Agenda 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Masood A. Khan
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Aemon Baba
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohmmad Abaas Dar
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohammad Altaf
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Ajazul H. Wani
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
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Jain N, Thakur S. Structure and dynamics of chemically active ring polymers: swelling to collapse. SOFT MATTER 2023; 19:7358-7369. [PMID: 37740385 DOI: 10.1039/d3sm00839h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
The ring structures are common in many synthetic or natural systems and experience both local and long-range forces by chemical sensing. This work is an effort to investigate the structural and dynamical properties of a chemically active ring in an explicit solvent bath utilizing hybrid molecular dynamics (MD) and multiparticle collision dynamics (MPCD) simulation techniques. We show that by tuning the chemical properties of the ring, it can be converted from a chemo-attractant to a chemo-repellent, thereby changing the steady state to be either collapsed or swelled as compared to its passive limit. We quantify these observations by comparing the scaling laws, local structures and the dynamics of active and passive rings. Furthermore, we show the impact of varying numbers of active sites by calculating the contact probability of the collapse state that highlights diverse structures. We also analyze the dynamics of the ring by finding the relaxation time and the mean square displacement of the centre of mass. A faster relaxation with enhanced diffusion is observed for the active rings.
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Affiliation(s)
- Namita Jain
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India.
| | - Snigdha Thakur
- Department of Physics, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India.
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3
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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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Nakahata S, Komoto T, Fujii M, Awazu A. Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast. Biophys Physicobiol 2022; 19:1-12. [PMID: 35749629 PMCID: PMC9160732 DOI: 10.2142/biophysico.bppb-v19.0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
During the repair of double-strand breaks (DSBs) in DNA, active mobilizations for conformational changes in chromosomes have been widely observed in eukaryotes, from yeast to animal and plant cells. DSB-damaged loci in the yeast genome showed increased mobility and relocation to the nuclear periphery. However, the driving forces behind DSB-induced chromatin dynamics remain unclear. In this study, mathematical models of normal and DSB-damaged yeast chromosomes were developed to simulate their structural dynamics. The effects of histone degradation in the whole nucleus and the change in the physical properties of damaged loci due to the binding of SUMOylated repair proteins were considered in the model of DSB-induced chromosomes based on recent experimental results. The simulation results reproduced DSB-induced changes to structural and dynamical features by which the combination of whole nuclear histone degradation and the rigid structure formation of repair protein accumulations on damaged loci were suggested to be primary contributors to the process by which damaged loci are relocated to the nuclear periphery.
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Affiliation(s)
- Shinjiro Nakahata
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Tetsushi Komoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masashi Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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5
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Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions. Nat Commun 2021; 12:2883. [PMID: 34001913 PMCID: PMC8129070 DOI: 10.1038/s41467-021-23090-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) is an important mechanism that helps explain the membraneless compartmentalization of the nucleus. Because chromatin compaction and LLPS are collective phenomena, linking their modulation to the physicochemical features of nucleosomes is challenging. Here, we develop an advanced multiscale chromatin model-integrating atomistic representations, a chemically-specific coarse-grained model, and a minimal model-to resolve individual nucleosomes within sub-Mb chromatin domains and phase-separated systems. To overcome the difficulty of sampling chromatin at high resolution, we devise a transferable enhanced-sampling Debye-length replica-exchange molecular dynamics approach. We find that nucleosome thermal fluctuations become significant at physiological salt concentrations and destabilize the 30-nm fiber. Our simulations show that nucleosome breathing favors stochastic folding of chromatin and promotes LLPS by simultaneously boosting the transient nature and heterogeneity of nucleosome-nucleosome contacts, and the effective nucleosome valency. Our work puts forward the intrinsic plasticity of nucleosomes as a key element in the liquid-like behavior of nucleosomes within chromatin, and the regulation of chromatin LLPS.
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Affiliation(s)
- Stephen E Farr
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
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6
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Tortora MMC, Salari H, Jost D. Chromosome dynamics during interphase: a biophysical perspective. Curr Opin Genet Dev 2020; 61:37-43. [DOI: 10.1016/j.gde.2020.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/24/2020] [Accepted: 03/02/2020] [Indexed: 12/29/2022]
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Ohyama T. New Aspects of Magnesium Function: A Key Regulator in Nucleosome Self-Assembly, Chromatin Folding and Phase Separation. Int J Mol Sci 2019; 20:ijms20174232. [PMID: 31470631 PMCID: PMC6747271 DOI: 10.3390/ijms20174232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023] Open
Abstract
Metal cations are associated with many biological processes. The effects of these cations on nucleic acids and chromatin were extensively studied in the early stages of nucleic acid and chromatin research. The results revealed that some monovalent and divalent metal cations, including Mg2+, profoundly affect the conformations and stabilities of nucleic acids, the folding of chromatin fibers, and the extent of chromosome condensation. Apart from these effects, there have only been a few reports on the functions of these cations. In 2007 and 2013, however, Mg2+-implicated novel phenomena were found: Mg2+ facilitates or enables both self-assembly of identical double-stranded (ds) DNA molecules and self-assembly of identical nucleosomes in vitro. These phenomena may be deeply implicated in the heterochromatin domain formation and chromatin-based phase separation. Furthermore, a recent study showed that elevation of the intranuclear Mg2+ concentration causes unusual differentiation of mouse ES (embryonic stem) cells. All of these phenomena seem to be closely related to one another. Mg2+ seems to be a key regulator of chromatin dynamics and chromatin-based biological processes.
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Affiliation(s)
- Takashi Ohyama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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8
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Portillo-Ledesma S, Schlick T. Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019; 10. [PMID: 34046090 DOI: 10.1002/wcms.1434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chromatin structure, dynamics, and function are being intensely investigated by a variety of methods, including microscopy, X-ray diffraction, nuclear magnetic resonance, biochemical crosslinking, chromosome conformation capture, and computation. A range of experimental techniques combined with modeling is clearly valuable to help interpret experimental data and, importantly, generate configurations and mechanisms related to the 3D organization and function of the genome. Contact maps, in particular, as obtained by a variety of chromosome conformation capture methods, are of increasing interest due to their implications on genome structure and regulation on many levels. In this perspective, using seven examples from our group's studies, we illustrate how molecular modeling can help interpret such experimental data. Specifically, we show how computed contact maps related to experimental systems can be used to explain structures of nucleosomes, chromatin higher-order folding, domain segregation mechanisms, gene organization, and the effect on chromatin structure of external and internal fiber parameters, such as nucleosome positioning, presence of nucleosome free regions, histone posttranslational modifications, and linker histone binding. We argue that such computations on multiple spatial and temporal scales will be increasingly important for the integration of genomic, epigenomic, and biophysical data on chromatin structure and related cellular processes.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, New York, 10003, USA.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, New York, 10012, USA.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200062, China
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Socol M, Wang R, Jost D, Carrivain P, Vaillant C, Le Cam E, Dahirel V, Normand C, Bystricky K, Victor JM, Gadal O, Bancaud A. Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes. Nucleic Acids Res 2019; 47:6195-6207. [PMID: 31114898 PMCID: PMC6614813 DOI: 10.1093/nar/gkz374] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/25/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023] Open
Abstract
DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of -0.3 to -0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in 'theta' conditions, in which they are poised for compartmentalization and phase separation.
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Affiliation(s)
- Marius Socol
- LAAS-CNRS, Université de Toulouse, CNRS, F-31400 Toulouse, France
- IRIM, CNRS, University of Montpellier, France
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
- Material Science & Engineering School, Henan University of Technology, 450001 Zhengzhou, P.R. China
| | - Daniel Jost
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Pascal Carrivain
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Cédric Vaillant
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR8126, CNRS, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex France
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Physicochimie des Electrolytes et Nanosystèmes interfaciaux, laboratoire PHENIX, F-75005 Paris, France
| | - Christophe Normand
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Jean-Marc Victor
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, F-75005 Paris, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Aurélien Bancaud
- LAAS-CNRS, Université de Toulouse, CNRS, F-31400 Toulouse, France
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10
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Miura O, Ogake T, Yoneyama H, Kikuchi Y, Ohyama T. A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats. Curr Genet 2018; 65:575-590. [PMID: 30498953 PMCID: PMC6420913 DOI: 10.1007/s00294-018-0907-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 11/22/2022]
Abstract
DNA sequences that read the same from 5′ to 3′ in either strand are called inverted repeat sequences or simply IRs. They are found throughout a wide variety of genomes, from prokaryotes to eukaryotes. Despite extensive research, their in vivo functions, if any, remain unclear. Using Saccharomyces cerevisiae, we performed genome-wide analyses for the distribution, occurrence frequency, sequence characteristics and relevance to chromatin structure, for the IRs that reportedly have a cruciform-forming potential. Here, we provide the first comprehensive map of these IRs in the S. cerevisiae genome. The statistically significant enrichment of the IRs was found in the close vicinity of the DNA positions corresponding to polyadenylation [poly(A)] sites and ~ 30 to ~ 60 bp downstream of start codon-coding sites (referred to as ‘start codons’). In the former, ApT- or TpA-rich IRs and A-tract- or T-tract-rich IRs are enriched, while in the latter, different IRs are enriched. Furthermore, we found a strong structural correlation between the former IRs and the poly(A) signal. In the chromatin formed on the gene end regions, the majority of the IRs causes low nucleosome occupancy. The IRs in the region ~ 30 to ~ 60 bp downstream of start codons are located in the + 1 nucleosomes. In contrast, fewer IRs are present in the adjacent region downstream of start codons. The current study suggests that the IRs play similar roles in Escherichia coli and S. cerevisiae to regulate or complete transcription at the RNA level.
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Affiliation(s)
- Osamu Miura
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Toshihiro Ogake
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Hiroki Yoneyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Yo Kikuchi
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Takashi Ohyama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. .,Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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11
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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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12
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Arbona JM, Herbert S, Fabre E, Zimmer C. Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations. Genome Biol 2017; 18:81. [PMID: 28468672 PMCID: PMC5414205 DOI: 10.1186/s13059-017-1199-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/23/2017] [Indexed: 01/06/2023] Open
Abstract
Background The structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constraints and a small number of structural parameters can explain diverse experimental data on nuclear architecture. However, how assumed chromatin properties affect model predictions was not previously systematically investigated. Results We used hundreds of dynamic chromosome simulations and Bayesian inference to determine chromatin properties consistent with an extensive dataset that includes hundreds of measurements from imaging in fixed and live cells and two Hi-C studies. We place new constraints on average chromatin fiber properties, narrowing down the chromatin compaction to ~53–65 bp/nm and persistence length to ~52–85 nm. These constraints argue against a 20–30 nm fiber as the exclusive chromatin structure in the genome. Our best model provides a much better match to experimental measurements of nuclear architecture and also recapitulates chromatin dynamics measured on multiple loci over long timescales. Conclusion This work substantially improves our understanding of yeast chromatin mechanics and chromosome architecture and provides a new analytic framework to infer chromosome properties in other organisms. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1199-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean-Michel Arbona
- Unité Imagerie et Modélisation, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France.,UMR 3691, CNRS; C3BI, USR 3756, IP CNRS, Paris, France
| | - Sébastien Herbert
- Unité Imagerie et Modélisation, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France.,UMR 3691, CNRS; C3BI, USR 3756, IP CNRS, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, 75015, Paris, France
| | - Emmanuelle Fabre
- Chromosome Biology and Dynamics, Hôpital Saint Louis, Paris, France
| | - Christophe Zimmer
- Unité Imagerie et Modélisation, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France. .,UMR 3691, CNRS; C3BI, USR 3756, IP CNRS, Paris, France.
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13
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Haddad N, Jost D, Vaillant C. Perspectives: using polymer modeling to understand the formation and function of nuclear compartments. Chromosome Res 2017; 25:35-50. [PMID: 28091870 PMCID: PMC5346151 DOI: 10.1007/s10577-016-9548-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/18/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022]
Abstract
Compartmentalization is a ubiquitous feature of cellular function. In the nucleus, early observations revealed a non-random spatial organization of the genome with a large-scale segregation between transcriptionally active—euchromatin—and silenced—heterochromatin—parts of the genome. Recent advances in genome-wide mapping and imaging techniques have strikingly improved the resolution at which nuclear genome folding can be analyzed and have revealed a multiscale spatial compartmentalization with increasing evidences that such compartment may indeed result from and participate to genome function. Understanding the underlying mechanisms of genome folding and in particular the link to gene regulation requires a cross-disciplinary approach that combines the new high-resolution techniques with computational modeling of chromatin and chromosomes. In this perspective article, we first present how the copolymer theoretical framework can account for the genome compartmentalization. We then suggest, in a second part, that compartments may act as a “nanoreactor,” increasing the robustness of either activation or repression by enhancing the local concentration of regulators. We conclude with the need to develop a new framework, namely the “living chromatin” model that will allow to explicitly investigate the coupling between spatial compartmentalization and gene regulation.
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Affiliation(s)
- N Haddad
- CNRS, Laboratoire de Physique, University of Lyon, ENS de Lyon, University of Claude Bernard, 69007, Lyon, France
| | - D Jost
- University Grenoble-Alpes, CNRS, TIMC-IMAG lab, UMR 5525, Grenoble, France.
| | - C Vaillant
- CNRS, Laboratoire de Physique, University of Lyon, ENS de Lyon, University of Claude Bernard, 69007, Lyon, France.
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Jost D, Vaillant C, Meister P. Coupling 1D modifications and 3D nuclear organization: data, models and function. Curr Opin Cell Biol 2016; 44:20-27. [PMID: 28040646 DOI: 10.1016/j.ceb.2016.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 12/17/2022]
Abstract
Over the past decade, advances in molecular methods have strikingly improved the resolution at which nuclear genome folding can be analyzed. This revealed a wealth of conserved features organizing the one dimensional DNA molecule into tridimensional nuclear domains. In this review, we briefly summarize the main findings and highlight how models based on polymer physics shed light on the principles underlying the formation of these domains. Finally, we discuss the mechanistic similarities allowing self-organization of these structures and the functional importance of these in the maintenance of transcriptional programs.
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Affiliation(s)
- Daniel Jost
- University Grenoble Alpes, CNRS, TIMC-IMAG lab, UMR 5525, Grenoble, F-38706 La Tronche, France
| | - Cédric Vaillant
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69007 Lyon, France
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.
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15
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Chen C, Lim HH, Shi J, Tamura S, Maeshima K, Surana U, Gan L. Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo. Mol Biol Cell 2016; 27:3357-3368. [PMID: 27605704 PMCID: PMC5170867 DOI: 10.1091/mbc.e16-07-0506] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/01/2016] [Indexed: 11/11/2022] Open
Abstract
Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin-nucleosomes-are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an "open" configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome-nucleosome associations.
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Affiliation(s)
- Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Hong Hwa Lim
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Proteos, Singapore 138673, Singapore.,Bioprocessing Technology Institute, Singapore 138668, Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sachiko Tamura
- National Institute of Genetics and Sokendai, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- National Institute of Genetics and Sokendai, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Proteos, Singapore 138673, Singapore.,Bioprocessing Technology Institute, Singapore 138668, Singapore.,Department of Pharmacology, National University of Singapore, Singapore 117543, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
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16
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Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Curr Opin Struct Biol 2016; 37:29-45. [DOI: 10.1016/j.sbi.2015.11.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/05/2023]
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17
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Schwede T. Protein modeling: what happened to the "protein structure gap"? Structure 2014; 21:1531-40. [PMID: 24010712 DOI: 10.1016/j.str.2013.08.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 11/27/2022]
Abstract
Computational modeling of three-dimensional macromolecular structures and complexes from their sequence has been a long-standing vision in structural biology. Over the last 2 decades, a paradigm shift has occurred: starting from a large "structure knowledge gap" between the huge number of protein sequences and small number of known structures, today, some form of structural information, either experimental or template-based models, is available for the majority of amino acids encoded by common model organism genomes. With the scientific focus of interest moving toward larger macromolecular complexes and dynamic networks of interactions, the integration of computational modeling methods with low-resolution experimental techniques allows the study of large and complex molecular machines. One of the open challenges for computational modeling and prediction techniques is to convey the underlying assumptions, as well as the expected accuracy and structural variability of a specific model, which is crucial to understanding its limitations.
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Affiliation(s)
- Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
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