1
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Liu S, Miné-Hattab J, Villemeur M, Guerois R, Pinholt HD, Mirny LA, Taddei A. Author Correction: In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search. Nat Struct Mol Biol 2023:10.1038/s41594-023-01180-8. [PMID: 37993685 DOI: 10.1038/s41594-023-01180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Affiliation(s)
- Siyu Liu
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Judith Miné-Hattab
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Marie Villemeur
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), University of Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Henrik Dahl Pinholt
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonid A Mirny
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela Taddei
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France.
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2
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García Fernández F, Huet S, Miné-Hattab J. Multi-Scale Imaging of the Dynamic Organization of Chromatin. Int J Mol Sci 2023; 24:15975. [PMID: 37958958 PMCID: PMC10649806 DOI: 10.3390/ijms242115975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution imaging, among other new technologies developed in the last decade. In addition to challenging early assumptions of chromatin being regular and static, high spatiotemporal resolution imaging made it possible to visualize and characterize different chromatin structures such as clutches, domains and compartments. More specifically, super-resolution microscopy facilitates the study of different cellular processes at a nucleosome scale, providing a multi-scale view of chromatin behavior within the nucleus in different environments. In this review, we describe recent imaging techniques to study the dynamic organization of chromatin at high spatiotemporal resolution. We also discuss recent findings, elucidated by these techniques, on the chromatin landscape during different cellular processes, with an emphasis on the DNA damage response.
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Affiliation(s)
- Fabiola García Fernández
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, 35000 Rennes, France;
- Institut Universitaire de France, 75231 Paris, France
| | - Judith Miné-Hattab
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
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3
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Liu S, Miné-Hattab J, Villemeur M, Guerois R, Pinholt HD, Mirny LA, Taddei A. In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search. Nat Struct Mol Biol 2023; 30:1582-1591. [PMID: 37605042 DOI: 10.1038/s41594-023-01065-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 07/12/2023] [Indexed: 08/23/2023]
Abstract
Homologous recombination (HR) is a major pathway to repair DNA double-strand breaks (DSB). HR uses an undamaged homologous DNA sequence as a template for copying the missing information, which requires identifying a homologous sequence among megabases of DNA within the crowded nucleus. In eukaryotes, the conserved Rad51-single-stranded DNA nucleoprotein filament (NPF) performs this homology search. Although NPFs have been extensively studied in vitro by molecular and genetic approaches, their in vivo formation and dynamics could not thus far be assessed due to the lack of functional tagged versions of Rad51. Here we develop and characterize in budding yeast the first fully functional, tagged version of Rad51. Following induction of a unique DSB, we observe Rad51-ssDNA forming exceedingly long filaments, spanning the whole nucleus and eventually contacting the donor sequence. Emerging filaments adopt a variety of shapes not seen in vitro and are modulated by Rad54 and Srs2, shedding new light on the function of these factors. The filaments are also dynamic, undergoing rounds of compaction and extension. Our biophysical models demonstrate that formation of extended filaments, and particularly their compaction-extension dynamics, constitute a robust search strategy, allowing DSB to rapidly explore the nuclear volume and thus enable efficient HR.
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Affiliation(s)
- Siyu Liu
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Judith Miné-Hattab
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Marie Villemeur
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), University of Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Henrik Dahl Pinholt
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonid A Mirny
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela Taddei
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France.
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4
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Liu S, Miné-Hattab J, Villemeur M, Guerois R, Pinholt HD, Mirny LA, Taddei A. Publisher Correction: In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search. Nat Struct Mol Biol 2023; 30:1607. [PMID: 37679566 DOI: 10.1038/s41594-023-01114-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Affiliation(s)
- Siyu Liu
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Judith Miné-Hattab
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Marie Villemeur
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), University of Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Henrik Dahl Pinholt
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonid A Mirny
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela Taddei
- Institut Curie, Université PSL, Sorbonne University, CNRS, Nuclear Dynamics, Paris, France.
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5
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Abstract
A chemical regularly used to image cells can dramatically alter the way cellular compartments called condensates look under the microscope.
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Affiliation(s)
- Judith Miné-Hattab
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne UniversitéParisFrance
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6
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Miné-Hattab J, Liu S, Taddei A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes (Basel) 2022; 13:1846. [PMID: 36292731 PMCID: PMC9602295 DOI: 10.3390/genes13101846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 07/26/2023] Open
Abstract
In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.
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7
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Heltberg ML, Miné-Hattab J, Taddei A, Walczak AM, Mora T. Physical observables to determine the nature of membrane-less cellular sub-compartments. eLife 2021; 10:69181. [PMID: 34677123 PMCID: PMC8598233 DOI: 10.7554/elife.69181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of contexts, but the mechanism of their formation is not fully understood. Several competing mechanisms exist that are difficult to distinguish empirically, including liquid-liquid phase separation, and the trapping of molecules by multiple binding sites. Here, we propose a theoretical framework and outline observables to differentiate between these scenarios from single molecule tracking experiments. In the binding site model, we derive relations between the distribution of proteins, their diffusion properties, and their radial displacement. We predict that protein search times can be reduced for targets inside a liquid droplet, but not in an aggregate of slowly moving binding sites. We use our results to reject the multiple binding site model for Rad52 foci, and find a picture consistent with a liquid-liquid phase separation. These results are applicable to future experiments and suggest different biological roles for liquid droplet and binding site foci.
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Affiliation(s)
- Mathias L Heltberg
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France.,Institut Curie, CNRS, PSL University, Sorbonne Université, Paris, France
| | - Judith Miné-Hattab
- Institut Curie, CNRS, PSL University, Sorbonne Université, Paris, France
| | - Angela Taddei
- Institut Curie, CNRS, PSL University, Sorbonne Université, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Thierry Mora
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
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8
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Miné-Hattab J, Heltberg M, Villemeur M, Guedj C, Mora T, Walczak AM, Dahan M, Taddei A. Single molecule microscopy reveals key physical features of repair foci in living cells. eLife 2021; 10:60577. [PMID: 33543712 PMCID: PMC7924958 DOI: 10.7554/elife.60577] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/26/2021] [Indexed: 12/20/2022] Open
Abstract
In response to double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less sub-compartments or foci. Here we explored the physical nature of these foci, using single molecule microscopy in living cells. Rad52, the functional homolog of BRCA2 in yeast, accumulates at DSB sites and diffuses ~6 times faster within repair foci than the focus itself, exhibiting confined motion. The Rad52 confinement radius coincides with the focus size: foci resulting from 2 DSBs are twice larger in volume that the ones induced by a unique DSB and the Rad52 confinement radius scales accordingly. In contrast, molecules of the single strand binding protein Rfa1 follow anomalous diffusion similar to the focus itself or damaged chromatin. We conclude that while most Rfa1 molecules are bound to the ssDNA, Rad52 molecules are free to explore the entire focus reflecting the existence of a liquid droplet around damaged DNA.
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Mathias Heltberg
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Marie Villemeur
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Chloé Guedj
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Maxime Dahan
- Institut Curie, PSL University, Sorbonne Université, CNRS, Physico Chimie Curie, Paris, France
| | - Angela Taddei
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Cogitamus Laboratory, Paris, France
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9
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Abstract
A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.
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Affiliation(s)
- Judith Miné-Hattab
- UMR 3664, CNRS, Institut Curie, PSL Research University, Paris, France
- UMR 3664, CNRS, Institut Curie, Sorbonne Université, Paris, France
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
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10
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Alberman G, Gagez JM, Miné-Hattab J. [When science and music meet]. Med Sci (Paris) 2019; 35:881-885. [PMID: 31845880 DOI: 10.1051/medsci/2019169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Musique et sciences ont souvent été liées dans l’histoire de la musique. Cependant, rares sont les compositeurs qui ont eu l’occasion d’interagir avec un scientifique pour s’imprégner de son travail et l’utiliser comme source d’inspiration. Le projet Muse-IC se propose de donner cette opportunité à des compositeurs d’aujourd’hui, en leur commandant une œuvre inspirée par une découverte scientifique récente. À la suite d’un double appel réalisé auprès de chercheurs et de compositeurs, des compositeurs se sont immergés dans l’univers scientifique de chercheurs afin de repousser les limites de leur démarche créative. Entre 2017 et 2019, six compositeurs ont écrit une pièce inspirée de la découverte d’un chercheur avec lequel ils ont interagit directement. L’aboutissement de ce projet a donné lieu à une conférence-concert à la salle Cortot, à Paris, une occasion unique de sensibiliser le public à l’importance de la recherche fondamentale au travers d’une rencontre originale entre compositeurs, musiciens et chercheurs.
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Affiliation(s)
| | | | - Judith Miné-Hattab
- Institut Curie-PSL Research University, CNRS, Sorbonne Université, UMR3664, 26 rue d'Ulm, 75005 Paris, France
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Klein HL, Bačinskaja G, Che J, Cheblal A, Elango R, Epshtein A, Fitzgerald DM, Gómez-González B, Khan SR, Kumar S, Leland BA, Marie L, Mei Q, Miné-Hattab J, Piotrowska A, Polleys EJ, Putnam CD, Radchenko EA, Saada AA, Sakofsky CJ, Shim EY, Stracy M, Xia J, Yan Z, Yin Y, Aguilera A, Argueso JL, Freudenreich CH, Gasser SM, Gordenin DA, Haber JE, Ira G, Jinks-Robertson S, King MC, Kolodner RD, Kuzminov A, Lambert SA, Lee SE, Miller KM, Mirkin SM, Petes TD, Rosenberg SM, Rothstein R, Symington LS, Zawadzki P, Kim N, Lisby M, Malkova A. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microb Cell 2019; 6:1-64. [PMID: 30652105 PMCID: PMC6334234 DOI: 10.15698/mic2019.01.664] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Giedrė Bačinskaja
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jun Che
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Anais Cheblal
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Rajula Elango
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Anastasiya Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Devon M Fitzgerald
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Belén Gómez-González
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Sharik R Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Léa Marie
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Qian Mei
- Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Judith Miné-Hattab
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France
| | - Alicja Piotrowska
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | | | - Christopher D Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA.,Department of Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
| | | | - Anissia Ait Saada
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405, Orsay, France
| | - Cynthia J Sakofsky
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Mathew Stracy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jun Xia
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Zhenxin Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yi Yin
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA
| | - Andrés Aguilera
- Centro Andaluz de BIología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, Seville, Spain
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA USA.,Program in Genetics, Tufts University, Boston, MA, USA
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC USA
| | | | - Richard D Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA.,Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, La Jolla, CA, USA.,Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, CA, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sarah Ae Lambert
- Institut Curie, PSL Research University, CNRS, UMR3348 F-91405, Orsay, France.,University Paris Sud, Paris-Saclay University, CNRS, UMR3348, F-91405, Orsay, France
| | - Sang Eun Lee
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Kyle M Miller
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Thomas D Petes
- Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, NC USA
| | - Susan M Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Systems, Synthetic and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Pawel Zawadzki
- NanoBioMedical Centre, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA, USA
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13
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curie, PSL research university, CNRS, UMR3664, 75005 Paris, France - Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France
| | - Xavier Darzacq
- Division of genetics, genomics and development, Department of molecular and cell biology, University of California, Berkeley, Berkeley, CA 947201 États-Unis
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Clément C, Orsi GA, Gatto A, Boyarchuk E, Forest A, Hajj B, Miné-Hattab J, Garnier M, Gurard-Levin ZA, Quivy JP, Almouzni G. High-resolution visualization of H3 variants during replication reveals their controlled recycling. Nat Commun 2018; 9:3181. [PMID: 30093638 PMCID: PMC6085313 DOI: 10.1038/s41467-018-05697-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/05/2018] [Indexed: 12/11/2022] Open
Abstract
DNA replication is a challenge for the faithful transmission of parental information to daughter cells, as both DNA and chromatin organization must be duplicated. Replication stress further complicates the safeguard of epigenome integrity. Here, we investigate the transmission of the histone variants H3.3 and H3.1 during replication. We follow their distribution relative to replication timing, first in the genome and, second, in 3D using super-resolution microscopy. We find that H3.3 and H3.1 mark early- and late-replicating chromatin, respectively. In the nucleus, H3.3 forms domains, which decrease in density throughout replication, while H3.1 domains increase in density. Hydroxyurea impairs local recycling of parental histones at replication sites. Similarly, depleting the histone chaperone ASF1 affects recycling, leading to an impaired histone variant landscape. We discuss how faithful transmission of histone variants involves ASF1 and can be impacted by replication stress, with ensuing consequences for cell fate and tumorigenesis. Epigenetic modifications are a key contributor to cell identity, and their propagation is crucial for proper development. Here the authors use a super-resolution microscopy approach to reveal how histone variants are faithfully transmitted during genome duplication, and reveal an important role for the histone chaperone ASF1 in the redistribution of parental histones.
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Affiliation(s)
- Camille Clément
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Guillermo A Orsi
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Alberto Gatto
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Ekaterina Boyarchuk
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Audrey Forest
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Bassam Hajj
- Institut Curie, PSL Research University, CNRS, UMR168, Laboratoire Physico-Chimie, F-75005, Paris, France
| | - Judith Miné-Hattab
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR3664, F-75005, Paris, France
| | - Mickaël Garnier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR3664, F-75005, Paris, France
| | - Zachary A Gurard-Levin
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,SAMDI Tech, Inc., Chicago, IL, 60657, USA
| | - Jean-Pierre Quivy
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.
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Miné-Hattab J, Recamier V, Izeddin I, Rothstein R, Darzacq X. Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage. Mol Biol Cell 2017; 28:mbc.E17-05-0317. [PMID: 28794266 PMCID: PMC5687033 DOI: 10.1091/mbc.e17-05-0317] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/21/2017] [Accepted: 08/02/2017] [Indexed: 12/19/2022] Open
Abstract
The dynamic organization of genes inside the nucleus is an important determinant for their function. Using fast DNA tracking microscopy in S. cerevisiae cells and improved analysis of mean square displacements, we quantified DNA motion at time scales ranging from 10 milliseconds to minute and found that following DNA damage, DNA exhibits distinct sub-diffusive regimes. In response to double-strand breaks, chromatin is more mobile at large time scales but, surprisingly, its mobility is reduced at short time scales. This effect is even more pronounced at the site of damage. Such a pattern of dynamics is consistent with a global increase in chromatin persistence length in response to DNA damage. Scale-dependent nuclear exploration is regulated by the Rad51 repair protein, both at the break and throughout the genome. We propose a model in which stiffening of the damaged ends by the repair complex, combined with global increased stiffness, act like a "needle in a ball of yarn", enhancing the ability of the break to traverse the chromatin meshwork.
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Affiliation(s)
- Judith Miné-Hattab
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
- Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA
- Nuclear Dynamics, CNRS UMR 3664, Institut Curie, Paris 75005, France
| | - Vincent Recamier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
| | - Ignacio Izeddin
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
- Institut Langevin, CNRS, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xavier Darzacq
- Division of Genetics, Genomics & Development, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
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Kepten E, Miné-Hattab J. [Lamin A: a key protein in chromatin motion]. Med Sci (Paris) 2017; 33:126-130. [PMID: 28240200 DOI: 10.1051/medsci/20173302004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Eldad Kepten
- Institut Curie, PSL Research University, CNRS, Génétique et biologie du développement, UMR 3215, 26, rue d'Ulm, F-75005, Paris, France
| | - Judith Miné-Hattab
- Institut Curie, PSL Research University, CNRS, Dynamique du noyau, UMR 3664, 26, rue d'Ulm, F-75005, Paris, France
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Pierobon P, Miné-Hattab J, Cappello G, Viovy JL, Lagomarsino MC. Separation of time scales in one-dimensional directed nucleation-growth processes. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 82:061904. [PMID: 21230687 DOI: 10.1103/physreve.82.061904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 10/11/2010] [Indexed: 05/30/2023]
Abstract
Proteins involved in homologous recombination such as RecA and hRad51 polymerize on single- and double-stranded DNA according to a nucleation-growth kinetics, which can be monitored by single-molecule in vitro assays. The basic models currently used to extract biochemical rates rely on ensemble averages and are typically based on an underlying process of bidirectional polymerization, in contrast with the often observed anisotropic polymerization of similar proteins. For these reasons, if one considers single-molecule experiments, the available models are useful to understand observations only in some regimes. In particular, recent experiments have highlighted a steplike polymerization kinetics. The classical model of one-dimensional nucleation growth, the Kolmogorov-Avrami-Mehl-Johnson (KAMJ) model, predicts the correct polymerization kinetics only in some regimes and fails to predict the steplike behavior. This work illustrates by simulations and analytical arguments the limitation of applicability of the KAMJ description and proposes a minimal model for the statistics of the steps based on the so-called stick-breaking stochastic process. We argue that this insight might be useful to extract information on the time and length scales involved in the polymerization kinetics.
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Affiliation(s)
- Paolo Pierobon
- Institut Curie, Centre de recherche, INSERM U932 Immunité et cancer, 12 rue Lhomond, 75005 Paris, France.
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