1
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Luo J, Vale-Silva LA, Raghavan AR, Mercy G, Heldrich J, Sun X, Li MK, Zhang W, Agmon N, Yang K, Cai J, Stracquadanio G, Thierry A, Zhao Y, Coelho C, McCulloch LH, Lauer S, Kaback DB, Bader JS, Mitchell LA, Mozziconacci J, Koszul R, Hochwagen A, Boeke JD. Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function. CELL GENOMICS 2023; 3:100439. [PMID: 38020967 PMCID: PMC10667551 DOI: 10.1016/j.xgen.2023.100439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.
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Affiliation(s)
- Jingchuan Luo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Biochemistry, Cellular and Molecular Biology Graduate program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | - Guillaume Mercy
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
- Collège Doctoral, Sorbonne Université, 75005 Paris, France
| | - Jonna Heldrich
- Department of Biology, New York University, New York, NY 10003, USA
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mingyu Kenneth Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Kun Yang
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
| | - Jitong Cai
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
| | - Giovanni Stracquadanio
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Camila Coelho
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Laura H. McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Stephanie Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David B. Kaback
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, International Center for Public Health, Newark, NJ 07101-1709, USA
| | - Joel S. Bader
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leslie A. Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Julien Mozziconacci
- Structure and instability of Genomes Lab, UMR 7196, Muséum National d'Histoire Naturelle (MNHN), 75005 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | | | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, Tandon School of Engineering, Brooklyn, NY 11201, USA
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2
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Matthey-Doret C, Baudry L, Mortaza S, Moreau P, Koszul R, Cournac A. Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization. Methods Mol Biol 2022; 2301:1-15. [PMID: 34415528 DOI: 10.1007/978-1-0716-1390-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation digestion, ligation…) to detect pairs of genomic positions in close proximity. The most common way to represent these data is a matrix, or contact map, which allows visualizing the different chromatin structures (compartments, loops, etc.) that can be associated to other signals such as transcription, protein occupancy, etc. as well as, in some instances, to biological functions.In this chapter we present and discuss the filtering of the events recovered in proximity ligation experiments as well as the application of the balancing normalization procedure on the resulting contact map. We also describe a computational tool for visualizing normalized contact data dubbed Scalogram.The different processes described here are illustrated and supported by the laboratory custom-made scripts pooled into "hicstuff," an open-access python package accessible on github ( https://github.com/koszullab/hicstuff ).
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Affiliation(s)
- Cyril Matthey-Doret
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Shogofa Mortaza
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Pierrick Moreau
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France
| | - Axel Cournac
- Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France.
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3
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Lioy VS, Lorenzi JN, Najah S, Poinsignon T, Leh H, Saulnier C, Aigle B, Lautru S, Thibessard A, Lespinet O, Leblond P, Jaszczyszyn Y, Gorrichon K, Varoquaux N, Junier I, Boccard F, Pernodet JL, Bury-Moné S. Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation. Nat Commun 2021; 12:5221. [PMID: 34471117 PMCID: PMC8410849 DOI: 10.1038/s41467-021-25462-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria of the genus Streptomyces are prolific producers of specialized metabolites, including antibiotics. The linear chromosome includes a central region harboring core genes, as well as extremities enriched in specialized metabolite biosynthetic gene clusters. Here, we show that chromosome structure in Streptomyces ambofaciens correlates with genetic compartmentalization during exponential phase. Conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends tend to be transcriptionally quiescent compartments with different structural features. The onset of metabolic differentiation is accompanied by a rearrangement of chromosome architecture, from a rather 'open' to a 'closed' conformation, in which highly expressed specialized metabolite biosynthetic genes form new boundaries. Thus, our results indicate that the linear chromosome of S. ambofaciens is partitioned into structurally distinct entities, suggesting a link between chromosome folding, gene expression and genome evolution.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
| | - Jean-Noël Lorenzi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Soumaya Najah
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Thibault Poinsignon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Hervé Leh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Corinne Saulnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Sylvie Lautru
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Olivier Lespinet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Kevin Gorrichon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nelle Varoquaux
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Ivan Junier
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean-Luc Pernodet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphanie Bury-Moné
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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4
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Abstract
Since the nucleoid was isolated from bacteria in the 1970s, two fundamental questions emerged and are still in the spotlight: how bacteria organize their chromosomes to fit inside the cell and how nucleoid organization enables essential biological processes. During the last decades, knowledge of bacterial chromosome organization has advanced considerably, and today, such chromosomes are considered to be highly organized and dynamic structures that are shaped by multiple factors in a multiscale manner. Here we review not only the classical well-known factors involved in chromosome organization but also novel components that have recently been shown to dynamically shape the 3D structuring of the bacterial genome. We focus on the different functional elements that control short-range organization and describe how they collaborate in the establishment of the higher-order folding and disposition of the chromosome. Recent advances have opened new avenues for a deeper understanding of the principles and mechanisms of chromosome organization in bacteria. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
| | - Ivan Junier
- Université Grenoble Alpes, CNRS, TIMC-IMAG, 38000 Grenoble, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
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5
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Moreau P, Cournac A, Palumbo GA, Marbouty M, Mortaza S, Thierry A, Cairo S, Lavigne M, Koszul R, Neuveut C. Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin. Nat Commun 2018; 9:4268. [PMID: 30323189 PMCID: PMC6189100 DOI: 10.1038/s41467-018-06739-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/19/2018] [Indexed: 01/05/2023] Open
Abstract
Whether non-integrated viral DNAs distribute randomly or target specific positions within the higher-order architecture of mammalian genomes remains largely unknown. Here we use Hi-C and viral DNA capture (CHi-C) in primary human hepatocytes infected by either hepatitis B virus (HBV) or adenovirus type 5 (Ad5) virus to show that they adopt different strategies in their respective positioning at active chromatin. HBV contacts preferentially CpG islands (CGIs) enriched in Cfp1 a factor required for its transcription. These CGIs are often associated with highly expressed genes (HEG) and genes deregulated during infection. Ad5 DNA interacts preferentially with transcription start sites (TSSs) and enhancers of HEG, as well as genes upregulated during infection. These results show that DNA viruses use different strategies to infiltrate genomic 3D networks and target specific regions. This targeting may facilitate the recruitment of transcription factors necessary for their own replication and contribute to the deregulation of cellular gene expression.
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Affiliation(s)
- Pierrick Moreau
- Institut Pasteur, Unité Hepacivirus et Immunité Innée, 75015, Paris, France.,CNRS, UMR 3569, 75015, Paris, France.,Institut Pasteur, Département de Virologie, Paris, France
| | - Axel Cournac
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Gianna Aurora Palumbo
- Institut Pasteur, Unité Hepacivirus et Immunité Innée, 75015, Paris, France.,CNRS, UMR 3569, 75015, Paris, France.,Institut Pasteur, Département de Virologie, Paris, France
| | - Martial Marbouty
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Shogofa Mortaza
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Agnes Thierry
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France.,CNRS, UMR 3525, 75015, Paris, France
| | - Stefano Cairo
- XenTech, Research and Development Department, 91000, Evry, France
| | - Marc Lavigne
- Institut Pasteur, Département de Virologie, Paris, France.,Institut Cochin-INSERM U1016-CNRS UMR8104, Université Paris Descartes, Paris, France
| | - Romain Koszul
- Institut Pasteur, Département Génomes et Génétique, Groupe Régulation spatiale des génomes, 75015, Paris, France. .,CNRS, UMR 3525, 75015, Paris, France.
| | - Christine Neuveut
- Institut Pasteur, Unité Hepacivirus et Immunité Innée, 75015, Paris, France. .,CNRS, UMR 3569, 75015, Paris, France. .,Institut Pasteur, Département de Virologie, Paris, France.
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6
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Lioy VS, Boccard F. Conformational Studies of Bacterial Chromosomes by High-Throughput Sequencing Methods. Methods Enzymol 2018; 612:25-45. [PMID: 30502944 DOI: 10.1016/bs.mie.2018.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The development of next-generation sequencing technologies has allowed the application of different methods dedicated to the study of DNA-protein interactions and chromosome conformation to entire bacterial genome. By combining these approaches, the role of various parameters and factors involved in gene expression and chromosome organization can be disclosed at the molecular level over the full genome. Here we describe two methods that profoundly revolutionized our vision of DNA-protein interactions and spatial organization of chromosomes. Chromosome conformation capture (3C) coupled to deep sequencing (3C-seq) enables studies of the genome-wide chromosome folding and its control by different parameters and structural factors. Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) revealed the extent and regulation of DNA-protein interactions in vivo and highlight the role of structural factors in the control of chromosome organization. In this chapter, we describe a detailed protocol of 3C-seq and ChIP-seq experiments that, when combined, allows the spatial study of the chromosome and the factors that promote specific folding. Data processing and analysis for both experiments are also discussed.
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Affiliation(s)
- Virginia S Lioy
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Frédéric Boccard
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.
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7
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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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8
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Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R. 3D organization of synthetic and scrambled chromosomes. Science 2017; 355:355/6329/eaaf4597. [PMID: 28280150 DOI: 10.1126/science.aaf4597] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/01/2017] [Indexed: 11/02/2022]
Abstract
Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.
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Affiliation(s)
- Guillaume Mercy
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.,Sorbonne Universités, Université Pierre et Marie Curie (Université Paris 6), Paris 75005, France
| | - Julien Mozziconacci
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR7600, Université Pierre et Marie Curie (Université Paris 6), Sorbonne Universités, Paris, France
| | - Vittore F Scolari
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
| | - Kun Yang
- Department of Biomedical Engineering and High-Throughput Biology Center, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Guanghou Zhao
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Agnès Thierry
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
| | - Yisha Luo
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Michael Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, Qingdao 266555, China.,School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Roy Walker
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Weimin Zhang
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yi Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ze-Xiong Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhouqing Luo
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yizhi Cai
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Junbiao Dai
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huanming Yang
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Joel S Bader
- Department of Biomedical Engineering and High-Throughput Biology Center, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Héloïse Muller
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France. .,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
| | - Romain Koszul
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France. .,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
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9
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Lazar-Stefanita L, Scolari VF, Mercy G, Muller H, Guérin TM, Thierry A, Mozziconacci J, Koszul R. Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle. EMBO J 2017; 36:2684-2697. [PMID: 28729434 PMCID: PMC5599795 DOI: 10.15252/embj.201797342] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions. During replication, cohesion establishment promotes numerous long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. In anaphase, mitotic chromosomes are abruptly reorganized depending on mechanical forces exerted by the mitotic spindle. Formation of a condensin-dependent loop bridging the centromere cluster with the rDNA loci suggests that condensin-mediated forces may also directly facilitate segregation. This work therefore comprehensively recapitulates cell cycle-dependent chromosome dynamics in a unicellular eukaryote, but also unveils new features of chromosome structural reorganization during highly conserved stages of cell division.
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Affiliation(s)
- Luciana Lazar-Stefanita
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, Complexité du Vivant, Paris, France
| | - Vittore F Scolari
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Guillaume Mercy
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, Complexité du Vivant, Paris, France
| | - Héloise Muller
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Thomas M Guérin
- Laboratoire Télomères et Réparation du Chromosome, CEA, INSERM, UMR 967, IRCM, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Agnès Thierry
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Julien Mozziconacci
- Sorbonne Universités, Theoretical Physics for Condensed Matter Lab, UPMC Université Paris 06, Paris, France
- CNRS, UMR 7600, Paris, France
| | - Romain Koszul
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
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10
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Abstract
This methods article described a protocol aiming at generating chromosome contact maps of bacterial species using a genome-wide derivative of the chromosome conformation capture (3C) technique. The approach is readily applicable on a broad variety of gram + and gram-bacterial species. It describes and addresses known caveats and technicalities associated with the technique, and should be of interest to any laboratory interested to perform a multiscale analysis of the genome structure of its species of interest.
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Affiliation(s)
- Martial Marbouty
- Groupe Régulation Spatiale des Génomes, Département Génomes et Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France. .,CNRS, UMR 3525, 75724, Paris Cedex 15, France. .,Centre de Bioinformatique, Biostatistique et Biologie Intégrative, USR 3756, Institut Pasteur, Paris Cedex 15, 75724, Paris Cedex 15, France.
| | - Romain Koszul
- Groupe Régulation Spatiale des Génomes, Département Génomes et Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France. .,CNRS, UMR 3525, 75724, Paris Cedex 15, France. .,Centre de Bioinformatique, Biostatistique et Biologie Intégrative, USR 3756, Institut Pasteur, Paris Cedex 15, 75724, Paris Cedex 15, France.
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