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Chriss A, Börner GV, Ryan SD. Agent-based modeling of nuclear chromosome ensembles identifies determinants of homolog pairing during meiosis. PLoS Comput Biol 2024; 20:e1011416. [PMID: 38739641 PMCID: PMC11115365 DOI: 10.1371/journal.pcbi.1011416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 05/23/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
During meiosis, pairing of homologous chromosomes (homologs) ensures the formation of haploid gametes from diploid precursor cells, a prerequisite for sexual reproduction. Pairing during meiotic prophase I facilitates crossover recombination and homolog segregation during the ensuing reductional cell division. Mechanisms that ensure stable homolog alignment in the presence of an excess of non-homologous chromosomes have remained elusive, but rapid chromosome movements appear to play a role in the process. Apart from homolog attraction, provided by early intermediates of homologous recombination, dissociation of non-homologous associations also appears to contribute to homolog pairing, as suggested by the detection of stable non-homologous chromosome associations in pairing-defective mutants. Here, we have developed an agent-based model for homolog pairing derived from the dynamics of a naturally occurring chromosome ensemble. The model simulates unidirectional chromosome movements, as well as collision dynamics determined by attractive and repulsive forces arising from close-range physical interactions. Chromosome number and size as well as movement velocity and repulsive forces are identified as key factors in the kinetics and efficiency of homologous pairing in addition to homolog attraction. Dissociation of interactions between non-homologous chromosomes may contribute to pairing by crowding homologs into a limited nuclear area thus creating preconditions for close-range homolog attraction. Incorporating natural chromosome lengths, the model accurately recapitulates efficiency and kinetics of homolog pairing observed for wild-type and mutant meiosis in budding yeast, and can be adapted to nuclear dimensions and chromosome sets of other organisms.
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Affiliation(s)
- Ariana Chriss
- Department of Mathematics and Statistics, Cleveland State University, Cleveland, Ohio, United States of America
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - G. Valentin Börner
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, United States of America
| | - Shawn D. Ryan
- Department of Mathematics and Statistics, Cleveland State University, Cleveland, Ohio, United States of America
- Center for Applied Data Analysis and Modeling, Cleveland State University, Cleveland, Ohio, United States of America
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Chriss A, Börner GV, Ryan SD. Agent-based modeling of nuclear chromosome ensemble identifies determinants of homolog pairing during meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.09.552574. [PMID: 38260664 PMCID: PMC10802385 DOI: 10.1101/2023.08.09.552574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
During meiosis, pairing of homologous chromosomes (homologs) ensures the formation of haploid gametes from diploid precursor cells, a prerequisite for sexual reproduction. Pairing during meiotic prophase I facilitates crossover recombination and homolog segregation during the ensuing reductional cell division. Mechanisms that ensure stable homolog alignment in the presence of an excess of non-homologous chromosomes have remained elusive, but rapid chromosome movements during prophase I appear to play a role in the process. Apart from homolog attraction, provided by early intermediates of homologous recombination, dissociation of non-homologous associations also appears to contribute to homolog pairing, as suggested by the detection of stable non-homologous chromosome associations in pairing-defective mutants. Here, we have developed an agent-based model for homolog pairing derived from the dynamics of a naturally occurring chromosome ensemble. The model simulates unidirectional chromosome movements, as well as collision dynamics determined by attractive and repulsive forces arising from close-range physical interactions. In addition to homolog attraction, chromosome number and size as well as movement velocity and repulsive forces are identified as key factors in the kinetics and efficiency of homologous pairing. Dissociation of interactions between non-homologous chromosomes may contribute to pairing by crowding homologs into a limited nuclear area thus creating preconditions for close-range homolog attraction. Predictions from the model are readily compared to experimental data from budding yeast, parameters can be adjusted to other cellular systems and predictions from the model can be tested via experimental manipulation of the relevant chromosomal features.
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Affiliation(s)
- Ariana Chriss
- Department of Mathematics and Statistics, Cleveland State University, Cleveland, OH 44115
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH 44115
| | - G. Valentin Börner
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH 44115
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115
| | - Shawn D. Ryan
- Department of Mathematics and Statistics, Cleveland State University, Cleveland, OH 44115
- Center for Applied Data Analysis and Modeling, Cleveland State University, Cleveland, OH 44115
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3
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Vasquez PA, Walker B, Bloom K, Kolbin D, Caughman N, Freeman R, Lysy M, Hult C, Newhall KA, Papanikolas M, Edelmaier C, Forest MG. The power of weak, transient interactions across biology: A paradigm of emergent behavior. PHYSICA D. NONLINEAR PHENOMENA 2023; 454:133866. [PMID: 38274029 PMCID: PMC10806540 DOI: 10.1016/j.physd.2023.133866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
A growing list of diverse biological systems and their equally diverse functionalities provides realizations of a paradigm of emergent behavior. In each of these biological systems, pervasive ensembles of weak, short-lived, spatially local interactions act autonomously to convey functionalities at larger spatial and temporal scales. In this article, a range of diverse systems and functionalities are presented in a cursory manner with literature citations for further details. Then two systems and their properties are discussed in more detail: yeast chromosome biology and human respiratory mucus.
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Affiliation(s)
- Paula A. Vasquez
- Department of Mathematics, University of South Carolina, United States of America
| | - Ben Walker
- Department of Mathematics, University of California at Irvine, United States of America
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Neall Caughman
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Martin Lysy
- Department of Statistics and Actuarial Science, University of Waterloo, Canada
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, United States of America
| | - Katherine A. Newhall
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Christopher Edelmaier
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
- Center for Computational Biology, Flatiron Institute, United States of America
| | - M. Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
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4
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Dauban L, Kamgoué A, Wang R, Léger-Silvestre I, Beckouët F, Cantaloube S, Gadal O. Quantification of the dynamic behaviour of ribosomal DNA genes and nucleolus during yeast Saccharomyces cerevisiae cell cycle. J Struct Biol 2019; 208:152-164. [PMID: 31449968 DOI: 10.1016/j.jsb.2019.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/19/2022]
Abstract
Spatial organisation of chromosomes is a determinant of genome stability and is required for proper mitotic segregation. However, visualization of individual chromatids in living cells and quantification of their geometry, remains technically challenging. Here, we used live cell imaging to quantitate the three-dimensional conformation of yeast Saccharomyces cerevisiae ribosomal DNA (rDNA). rDNA is confined within the nucleolus and is composed of about 200 copies representing about 10% of the yeast genome. To fluorescently label rDNA in living cells, we generated a set of nucleolar proteins fused to GFP or made use of a tagged rDNA, in which lacO repetitions were inserted in each repeat unit. We could show that nucleolus is not modified in appearance, shape or size during interphase while rDNA is highly reorganized. Computationally tracing 3D rDNA paths allowed us to quantitatively assess rDNA size, shape and geometry. During interphase, rDNA was progressively reorganized from a zig-zag segmented line of small size (5,5 µm) to a long, homogeneous, line-like structure of 8,7 µm in metaphase. Most importantly, whatever the cell-cycle stage considered, rDNA fibre could be decomposed in subdomains, as previously suggested for 3D chromatin organisation. Finally, we could determine that spatial reorganisation of these subdomains and establishment of rDNA mitotic organisation is under the control of the cohesin complex.
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Affiliation(s)
- Lise Dauban
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Alain Kamgoué
- Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Frédéric Beckouët
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Sylvain Cantaloube
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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Abstract
Maintaining the integrity of the genome in the face of DNA damage is crucial to ensure the survival of the cell and normal development. DNA lesions and repair occur in the context of the chromatin fiber, whose 3D organization and movements in the restricted volume of the nucleus are under intense scrutiny. Here, we highlight work from our and other labs that addresses how the dynamic organization of the chromatin fiber affects the repair of damaged DNA and how, conversely, DNA damage and repair affect the structure and dynamics of chromatin in the budding yeast nucleus.
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Affiliation(s)
- Emmanuelle Fabre
- a Equipe Biologie et Dynamique des Chromosomes , Institut Universitaire d'Hématologie, Hôpital St. Louis , Paris , France.,b CNRS, UMR 7212 INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité , Paris , France
| | - Christophe Zimmer
- c Institut Pasteur, Unité Imagerie et Modélisation , 25 rue du Docteur Roux, 75015 , Paris , France.,d UMR 3691, CNRS; C3BI, USR 3756, IP CNRS , Paris , France
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6
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Walker B, Taylor D, Lawrimore J, Hult C, Adalsteinsson D, Bloom K, Forest MG. Transient crosslinking kinetics optimize gene cluster interactions. PLoS Comput Biol 2019; 15:e1007124. [PMID: 31433796 PMCID: PMC6730938 DOI: 10.1371/journal.pcbi.1007124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/06/2019] [Accepted: 07/18/2019] [Indexed: 02/05/2023] Open
Abstract
Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and cohesin that stochastically generate loops within and between chains, and entrap proximal strands of sister chromatids. In this paper, we explore the ability of transient, protein-mediated, gene-gene crosslinks to induce clusters of genes, thereby dynamic architecture, within the highly repeated ribosomal DNA that comprises the nucleolus of budding yeast. We implement three approaches: live cell microscopy; computational modeling of the full genome during G1 in budding yeast, exploring four decades of timescales for transient crosslinks between 5kbp domains (genes) in the nucleolus on Chromosome XII; and, temporal network models with automated community (cluster) detection algorithms applied to the full range of 4D modeling datasets. The data analysis tools detect and track gene clusters, their size, number, persistence time, and their plasticity (deformation). Of biological significance, our analysis reveals an optimal mean crosslink lifetime that promotes pairwise and cluster gene interactions through "flexible" clustering. In this state, large gene clusters self-assemble yet frequently interact (merge and separate), marked by gene exchanges between clusters, which in turn maximizes global gene interactions in the nucleolus. This regime stands between two limiting cases each with far less global gene interactions: with shorter crosslink lifetimes, "rigid" clustering emerges with clusters that interact infrequently; with longer crosslink lifetimes, there is a dissolution of clusters. These observations are compared with imaging experiments on a normal yeast strain and two condensin-modified mutant cell strains. We apply the same image analysis pipeline to the experimental and simulated datasets, providing support for the modeling predictions.
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Affiliation(s)
- Benjamin Walker
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dane Taylor
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Computational and Data Enabled Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Caitlin Hult
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - M. Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Departments of Applied Physical Sciences and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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7
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Miné-Hattab J, Taddei A. Physical principles and functional consequences of nuclear compartmentalization in budding yeast. Curr Opin Cell Biol 2019; 58:105-113. [PMID: 30928833 DOI: 10.1016/j.ceb.2019.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/28/2019] [Accepted: 02/20/2019] [Indexed: 12/19/2022]
Abstract
One striking feature of eukaryotic nuclei is the existence of discrete regions, in which specific factors concentrate while others are excluded, thus forming microenvironments with different molecular compositions and biological functions. These domains are often referred to as subcompartments even though they are not membrane enclosed. Despite their functional importance the physical nature of these structures remains largely unknown. Here, we describe how the Saccharomyces cerevisiae nucleus is compartmentalized and discuss possible physical models underlying the formation and maintenance of chromatin associated subcompartments. Focusing on three particular examples, the nucleolus, silencing foci, and repair foci, we discuss the biological implications of these different models as well as possible approaches to challenge them in living cells.
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France
| | - Angela Taddei
- Institut Curi-PSL Research University, CNRS, Sorbonne Université, UMR3664, F-75005, Paris, France.
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8
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Sharakhov IV, Bondarenko SM, Artemov GN, Onufriev AV. The Role of Chromosome–Nuclear Envelope Attachments in 3D Genome Organization. BIOCHEMISTRY (MOSCOW) 2018; 83:350-358. [DOI: 10.1134/s0006297918040065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Hult C, Adalsteinsson D, Vasquez PA, Lawrimore J, Bennett M, York A, Cook D, Yeh E, Forest MG, Bloom K. Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus. Nucleic Acids Res 2017; 45:11159-11173. [PMID: 28977453 PMCID: PMC5737219 DOI: 10.1093/nar/gkx741] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 01/24/2023] Open
Abstract
Regions of highly repetitive DNA, such as those found in the nucleolus, show a self-organization that is marked by spatial segregation and frequent self-interaction. The mechanisms that underlie the sequestration of these sub-domains are largely unknown. Using a stochastic, bead-spring representation of chromatin in budding yeast, we find enrichment of protein-mediated, dynamic chromosomal cross-links recapitulates the segregation, morphology and self-interaction of the nucleolus. Rates and enrichment of dynamic crosslinking have profound consequences on domain morphology. Our model demonstrates the nucleolus is phase separated from other chromatin in the nucleus and predicts that multiple rDNA loci will form a single nucleolus independent of their location within the genome. Fluorescent labeling of budding yeast nucleoli with CDC14-GFP revealed that a split rDNA locus indeed forms a single nucleolus. We propose that nuclear sub-domains, such as the nucleolus, result from phase separations within the nucleus, which are driven by the enrichment of protein-mediated, dynamic chromosomal crosslinks.
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Affiliation(s)
- Caitlin Hult
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paula A. Vasquez
- Department of Mathematics, University of South Carolina, Columbia, SC 29808, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Maggie Bennett
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alyssa York
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Diana Cook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elaine Yeh
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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Herbert S, Brion A, Arbona JM, Lelek M, Veillet A, Lelandais B, Parmar J, Fernández FG, Almayrac E, Khalil Y, Birgy E, Fabre E, Zimmer C. Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast. EMBO J 2017; 36:2595-2608. [PMID: 28694242 PMCID: PMC5579376 DOI: 10.15252/embj.201695842] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 12/31/2022] Open
Abstract
DNA double-strand breaks (DSBs) induce a cellular response that involves histone modifications and chromatin remodeling at the damaged site and increases chromosome dynamics both locally at the damaged site and globally in the nucleus. In parallel, it has become clear that the spatial organization and dynamics of chromosomes can be largely explained by the statistical properties of tethered, but randomly moving, polymer chains, characterized mainly by their rigidity and compaction. How these properties of chromatin are affected during DNA damage remains, however, unclear. Here, we use live cell microscopy to track chromatin loci and measure distances between loci on yeast chromosome IV in thousands of cells, in the presence or absence of genotoxic stress. We confirm that DSBs result in enhanced chromatin subdiffusion and show that intrachromosomal distances increase with DNA damage all along the chromosome. Our data can be explained by an increase in chromatin rigidity, but not by chromatin decondensation or centromeric untethering only. We provide evidence that chromatin stiffening is mediated in part by histone H2A phosphorylation. Our results support a genome-wide stiffening of the chromatin fiber as a consequence of DNA damage and as a novel mechanism underlying increased chromatin mobility.
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Affiliation(s)
- Sébastien Herbert
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Alice Brion
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Jean-Michel Arbona
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mickaël Lelek
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Adeline Veillet
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Benoît Lelandais
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jyotsana Parmar
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Fabiola García Fernández
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Etienne Almayrac
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Yasmine Khalil
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Eleonore Birgy
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Christophe Zimmer
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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11
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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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12
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Vasquez PA, Hult C, Adalsteinsson D, Lawrimore J, Forest MG, Bloom K. Entropy gives rise to topologically associating domains. Nucleic Acids Res 2016; 44:5540-9. [PMID: 27257057 PMCID: PMC4937343 DOI: 10.1093/nar/gkw510] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/06/2016] [Accepted: 05/25/2016] [Indexed: 12/15/2022] Open
Abstract
We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains.
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Affiliation(s)
- Paula A Vasquez
- Department of Mathematics, University of South Carolina, Columbia, SC 29808, USA
| | - Caitlin Hult
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David Adalsteinsson
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mark G Forest
- Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
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13
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Kinney NA, Onufriev AV, Sharakhov IV. Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes. Nucleus 2016; 6:212-24. [PMID: 26068134 DOI: 10.1080/19491034.2015.1056441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We use a combined experimental and computational approach to study the effects of chromosome-nuclear envelope (Chr-NE) attachments on the 3D genome organization of Drosophila melanogaster (fruit fly) salivary gland nuclei. We consider 3 distinct models: a Null model - without specific Chr-NE attachments, a 15-attachment model - with 15 previously known Chr-NE attachments, and a 48-attachment model - with 15 original and 33 recently identified Chr-NE attachments. The radial densities of chromosomes in the models are compared to the densities observed in 100 experimental images of optically sectioned salivary gland nuclei forming "z-stacks." Most of the experimental z-stacks support the Chr-NE 48-attachment model suggesting that as many as 48 chromosome loci with appreciable affinity for the NE are necessary to reproduce the experimentally observed distribution of chromosome density in fruit fly nuclei. Next, we investigate if and how the presence and the number of Chr-NE attachments affect several key characteristics of 3D genome organization: chromosome territories and gene-gene contacts. This analysis leads to novel insight about the possible role of Chr-NE attachments in regulating the genome architecture. Specifically, we find that model nuclei with more numerous Chr-NE attachments form more distinct chromosome territories and their chromosomes intertwine less frequently. Intra-chromosome and intra-arm contacts are more common in model nuclei with Chr-NE attachments compared to the Null model (no specific attachments), while inter-chromosome and inter-arm contacts are less common in nuclei with Chr-NE attachments. We demonstrate that Chr-NE attachments increase the specificity of long-range inter-chromosome and inter-arm contacts. The predicted effects of Chr-NE attachments are rationalized by intuitive volume vs. surface accessibility arguments.
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Affiliation(s)
- Nicholas Allen Kinney
- a Genomics Bioinformatics and Computational Biology; Virginia Tech ; Blacksburg , VA , USA
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14
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Chromosome position determines the success of double-strand break repair. Proc Natl Acad Sci U S A 2015; 113:E146-54. [PMID: 26715752 DOI: 10.1073/pnas.1523660113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repair of a chromosomal double-strand break (DSB) by gene conversion depends on the ability of the broken ends to encounter a donor sequence. To understand how chromosomal location of a target sequence affects DSB repair, we took advantage of genome-wide Hi-C analysis of yeast chromosomes to create a series of strains in which an induced site-specific DSB in budding yeast is repaired by a 2-kb donor sequence inserted at different locations. The efficiency of repair, measured by cell viability or competition between each donor and a reference site, showed a strong correlation (r = 0.85 and 0.79) with the contact frequencies of each donor with the DSB repair site. Repair efficiency depends on the distance between donor and recipient rather than any intrinsic limitation of a particular donor site. These results further demonstrate that the search for homology is the rate-limiting step in DSB repair and suggest that cells often fail to repair a DSB because they cannot locate a donor before other, apparently lethal, processes arise. The repair efficiency of a donor locus can be improved by four factors: slower 5' to 3' resection of the DSB ends, increased abundance of replication protein factor A (RPA), longer shared homology, or presence of a recombination enhancer element adjacent to a donor.
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15
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Ay F, Noble WS. Analysis methods for studying the 3D architecture of the genome. Genome Biol 2015; 16:183. [PMID: 26328929 PMCID: PMC4556012 DOI: 10.1186/s13059-015-0745-7] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/10/2015] [Indexed: 11/10/2022] Open
Abstract
The rapidly increasing quantity of genome-wide chromosome conformation capture data presents great opportunities and challenges in the computational modeling and interpretation of the three-dimensional genome. In particular, with recent trends towards higher-resolution high-throughput chromosome conformation capture (Hi-C) data, the diversity and complexity of biological hypotheses that can be tested necessitates rigorous computational and statistical methods as well as scalable pipelines to interpret these datasets. Here we review computational tools to interpret Hi-C data, including pipelines for mapping, filtering, and normalization, and methods for confidence estimation, domain calling, visualization, and three-dimensional modeling.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. .,Feinberg School of Medicine, Northwestern University, Chicago, 60661, IL, USA.
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. .,Department of Computer Science and Engineering, University of Washington, Seattle, 98195, WA, USA.
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16
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Mozziconacci J, Koszul R. Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution. Genome Biol 2015; 16:169. [PMID: 26294274 PMCID: PMC4546249 DOI: 10.1186/s13059-015-0744-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The fine three-dimensional structure of the nucleosomal fiber has remained elusive to genome-wide chromosome conformation capture (3C) approaches. A new study mapping contacts at the single nucleosome level (Micro-C) reveals topological interacting domains along budding yeast chromosomes. These domains encompass one to five consecutive genes and are delimited by highly active promoters.
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Affiliation(s)
- Julien Mozziconacci
- Theoretical Physics for Condensed Matter Laboratory, UPMC, CNRS UMR 7600, Sorbonne Universités, Place Jussieu, 75005, Paris, France.
| | - Romain Koszul
- Institut Pasteur, Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, 75015, Paris, France. .,CNRS, UMR 3525, 75015, Paris, France.
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17
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Renkawitz J, Lademann CA, Jentsch S. Mechanisms and principles of homology search during recombination. Nat Rev Mol Cell Biol 2014; 15:369-83. [PMID: 24824069 DOI: 10.1038/nrm3805] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events.
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Affiliation(s)
- Jörg Renkawitz
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2] Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria. [3]
| | - Claudio A Lademann
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2]
| | - Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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18
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Kinney NA, Sharakhov IV, Onufriev AV. Investigation of the chromosome regions with significant affinity for the nuclear envelope in fruit fly--a model based approach. PLoS One 2014; 9:e91943. [PMID: 24651400 PMCID: PMC3961273 DOI: 10.1371/journal.pone.0091943] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/18/2014] [Indexed: 12/16/2022] Open
Abstract
Three dimensional nuclear architecture is important for genome function, but is still poorly understood. In particular, little is known about the role of the “boundary conditions” – points of attachment between chromosomes and the nuclear envelope. We describe a method for modeling the 3D organization of the interphase nucleus, and its application to analysis of chromosome-nuclear envelope (Chr-NE) attachments of polytene (giant) chromosomes in Drosophila melanogaster salivary glands. The model represents chromosomes as self-avoiding polymer chains confined within the nucleus; parameters of the model are taken directly from experiment, no fitting parameters are introduced. Methods are developed to objectively quantify chromosome territories and intertwining, which are discussed in the context of corresponding experimental observations. In particular, a mathematically rigorous definition of a territory based on convex hull is proposed. The self-avoiding polymer model is used to re-analyze previous experimental data; the analysis suggests 33 additional Chr-NE attachments in addition to the 15 already explored Chr-NE attachments. Most of these new Chr-NE attachments correspond to intercalary heterochromatin – gene poor, dark staining, late replicating regions of the genome; however, three correspond to euchromatin – gene rich, light staining, early replicating regions of the genome. The analysis also suggests 5 regions of anti-contact, characterized by aversion for the NE, only two of these correspond to euchromatin. This composition of chromatin suggests that heterochromatin may not be necessary or sufficient for the formation of a Chr-NE attachment. To the extent that the proposed model represents reality, the confinement of the polytene chromosomes in a spherical nucleus alone does not favor the positioning of specific chromosome regions at the NE as seen in experiment; consequently, the 15 experimentally known Chr-NE attachment positions do not appear to arise due to non-specific (entropic) forces. Robustness of the key conclusions to model assumptions is thoroughly checked.
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Affiliation(s)
- Nicholas Allen Kinney
- Genomics Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail: (IVS); (AVO)
| | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail: (IVS); (AVO)
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