1
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Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pučeková N, Abad MA, Spanos C, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. Science 2025; 388:eadq1709. [PMID: 40208986 PMCID: PMC12118822 DOI: 10.1126/science.adq1709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 12/25/2024] [Indexed: 04/12/2025]
Abstract
We used Hi-C, imaging, proteomics, and polymer modeling to define rules of engagement for SMC (structural maintenance of chromosomes) complexes as cells refold interphase chromatin into rod-shaped mitotic chromosomes. First, condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. Second, condensin bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion as sisters separate. Studies of mitotic chromosomes formed by cohesin, condensin II, and condensin I alone or in combination lead to refined models of mitotic chromosome conformation. In these models, loops are consecutive and not overlapping, implying that condensins stall upon encountering each other. The dynamics of Hi-C interactions and chromosome morphology reveal that during prophase, loops are extruded in vivo at ∼1 to 3 kilobases per second by condensins as they form a disordered discontinuous helical scaffold within individual chromatids.
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Affiliation(s)
- Kumiko Samejima
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Johan H. Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
| | - Sameer Abraham
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | | | - Itaru Samejima
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Alison J. Beckett
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool; Liverpool, UK
| | - Nina Pučeková
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Maria Alba Abad
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - Bethan Medina-Pritchard
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
| | - James R. Paulson
- Department of Chemistry, University of Wisconsin-Oshkosh; Oshkosh, USA
| | - Linfeng Xie
- Department of Chemistry, University of Wisconsin-Oshkosh; Oshkosh, USA
| | - A. Arockia Jeyaprakash
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
- Gene Center Munich, Ludwig-Maximilians-Universität München; Munich, Germany
| | - Ian A. Prior
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool; Liverpool, UK
| | - Leonid A. Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| | | | - William C. Earnshaw
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh; Edinburgh, UK
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2
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Zhao H, Shu L, Qin S, Lyu F, Liu F, Lin E, Xia S, Wang B, Wang M, Shan F, Lin Y, Zhang L, Gu Y, Blobel GA, Huang K, Zhang H. Extensive mutual influences of SMC complexes shape 3D genome folding. Nature 2025; 640:543-553. [PMID: 40011778 DOI: 10.1038/s41586-025-08638-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 01/13/2025] [Indexed: 02/28/2025]
Abstract
Mammalian genomes are folded through the distinct actions of structural maintenance of chromosome (SMC) complexes, which include the chromatin loop-extruding cohesin (extrusive cohesin), the sister chromatid cohesive cohesin and the mitotic chromosome-associated condensins1-3. Although these complexes function at different stages of the cell cycle, they exist together on chromatin during the G2-to-M phase transition, when the genome structure undergoes substantial reorganization1,2. Yet, how the different SMC complexes affect each other and how their interactions orchestrate the dynamic folding of the three-dimensional genome remain unclear. Here we engineered all possible cohesin and condensin configurations on mitotic chromosomes to delineate the concerted, mutually influential action of SMC complexes. We show that condensin disrupts the binding of extrusive cohesin at CCCTC-binding factor (CTCF) sites, thereby promoting the disassembly of interphase topologically associating domains (TADs) and loops during mitotic progression. Conversely, extrusive cohesin impedes condensin-mediated mitotic chromosome spiralization. Condensin reduces peaks of cohesive cohesin, whereas cohesive cohesin antagonizes condensin-mediated longitudinal shortening of mitotic chromosomes. The presence of both extrusive and cohesive cohesin synergizes these effects and inhibits mitotic chromosome condensation. Extrusive cohesin positions cohesive cohesin at CTCF-binding sites. However, cohesive cohesin by itself cannot be arrested by CTCF molecules and is insufficient to establish TADs or loops. Moreover, it lacks loop-extrusion capacity, which indicates that cohesive cohesin has nonoverlapping functions with extrusive cohesin. Finally, cohesive cohesin restricts chromatin loop expansion mediated by extrusive cohesin. Collectively, our data describe a three-way interaction among major SMC complexes that dynamically modulates chromatin architecture during cell cycle progression.
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Affiliation(s)
- Han Zhao
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Lirong Shu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Shenzhen Medical Academy of Research and Translation, Shenzhen, China
| | - Shiyi Qin
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Fangxuan Lyu
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Fuhai Liu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - En Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Sijian Xia
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Capital Medical University, Beijing, China
| | - Baiyue Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Manzhu Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Capital Medical University, Beijing, China
| | - Fengnian Shan
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- South China University of Technology, Guangzhou, China
| | - Yinzhi Lin
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Shenzhen Medical Academy of Research and Translation, Shenzhen, China
| | - Lin Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Biological Science, Hong Kong University, Hong Kong, China
| | - Yufei Gu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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3
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Selivanovskiy AV, Molodova MN, Khrameeva EE, Ulianov SV, Razin SV. Liquid condensates: a new barrier to loop extrusion? Cell Mol Life Sci 2025; 82:80. [PMID: 39976773 PMCID: PMC11842697 DOI: 10.1007/s00018-024-05559-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 12/04/2024] [Accepted: 12/20/2024] [Indexed: 02/23/2025]
Abstract
Liquid-liquid phase separation (LLPS), driven by dynamic, low-affinity multivalent interactions of proteins and RNA, results in the formation of macromolecular condensates on chromatin. These structures are likely to provide high local concentrations of effector factors responsible for various processes including transcriptional regulation and DNA repair. In particular, enhancers, super-enhancers, and promoters serve as platforms for condensate assembly. In the current paradigm, enhancer-promoter (EP) interaction could be interpreted as a result of enhancer- and promoter-based condensate contact/fusion. There is increasing evidence that the spatial juxtaposition of enhancers and promoters could be provided by loop extrusion (LE) by SMC complexes. Here, we propose that condensates may act as barriers to LE, thereby contributing to various nuclear processes including spatial contacts between regulatory genomic elements.
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Affiliation(s)
- Arseniy V Selivanovskiy
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Maria N Molodova
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia.
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4
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Meneu L, Chapard C, Serizay J, Westbrook A, Routhier E, Ruault M, Perrot M, Minakakis A, Girard F, Bignaud A, Even A, Gourgues G, Libri D, Lartigue C, Piazza A, Thierry A, Taddei A, Beckouët F, Mozziconacci J, Koszul R. Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus. Science 2025; 387:eadm9466. [PMID: 39913590 DOI: 10.1126/science.adm9466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 09/26/2024] [Accepted: 11/21/2024] [Indexed: 04/23/2025]
Abstract
In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of coevolution. Using bacterial genomes integrated into Saccharomyces cerevisiae, which diverged from yeast more than 2 billion years ago, we show that nucleosomes, cohesins, and associated transcriptional machinery can lead to the formation of two different chromatin archetypes, one transcribed and the other silent, independently of heterochromatin formation. These two archetypes also form on eukaryotic exogenous sequences, depend on sequence composition, and can be predicted using neural networks trained on the native genome. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalization, reminiscent of the organization of vertebrate nuclei.
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Affiliation(s)
- Léa Meneu
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, College Doctoral
| | - Christophe Chapard
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Jacques Serizay
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Alex Westbrook
- Sorbonne Université, College Doctoral
- Laboratoire Structure et Instabilité des génomes, UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
| | - Etienne Routhier
- Sorbonne Université, College Doctoral
- Laboratoire Structure et Instabilité des génomes, UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
- Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université, CNRS, Paris, France
| | - Myriam Ruault
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR 3664 Nuclear Dynamics, Paris, France
| | - Manon Perrot
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, College Doctoral
| | - Alexandros Minakakis
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Fabien Girard
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Amaury Bignaud
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
- Sorbonne Université, College Doctoral
| | - Antoine Even
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR 3664 Nuclear Dynamics, Paris, France
| | - Géraldine Gourgues
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
| | - Domenico Libri
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Carole Lartigue
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
| | - Aurèle Piazza
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
| | - Angela Taddei
- Institut Curie, PSL University, Sorbonne Université, CNRS UMR 3664 Nuclear Dynamics, Paris, France
| | - Frédéric Beckouët
- Molecular, Cellular and Developmental biology unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Mozziconacci
- Laboratoire Structure et Instabilité des génomes, UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
- Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université, CNRS, Paris, France
- UAR 2700 2AD, Muséum National d'Histoire Naturelle, Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, Paris, France
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5
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Barth R, Davidson IF, van der Torre J, Taschner M, Gruber S, Peters JM, Dekker C. SMC motor proteins extrude DNA asymmetrically and can switch directions. Cell 2025; 188:749-763.e21. [PMID: 39824185 DOI: 10.1016/j.cell.2024.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 09/13/2024] [Accepted: 12/13/2024] [Indexed: 01/20/2025]
Abstract
Structural maintenance of chromosomes (SMC) complexes organize the genome via DNA loop extrusion. Although some SMCs were reported to do so symmetrically, reeling DNA from both sides into the extruded DNA loop simultaneously, others perform loop extrusion asymmetrically toward one direction only. The mechanism underlying this variability remains unclear. Here, we examine the directionality of DNA loop extrusion by SMCs using in vitro single-molecule experiments. We find that cohesin and SMC5/6 do not reel in DNA from both sides, as reported before, but instead extrude DNA asymmetrically, although the direction can switch over time. Asymmetric DNA loop extrusion thus is the shared mechanism across all eukaryotic SMC complexes. For cohesin, direction switches strongly correlate with the turnover of the subunit NIPBL, during which DNA strand switching may occur. Apart from expanding by extrusion, loops frequently diffuse and shrink. The findings reveal that SMCs, surprisingly, can switch directions.
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Affiliation(s)
- Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Michael Taschner
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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6
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Zhegalova I, Ulianov S, Galitsyna A, Pletenev I, Tsoy O, Luzhin A, Vasiluev P, Bulavko E, Ivankov D, Gavrilov A, Khrameeva E, Gelfand M, Razin S. Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum. Nucleic Acids Res 2025; 53:gkaf006. [PMID: 39844457 PMCID: PMC11754127 DOI: 10.1093/nar/gkaf006] [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: 07/10/2024] [Revised: 12/25/2024] [Accepted: 01/06/2025] [Indexed: 01/24/2025] Open
Abstract
Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into positionally conserved, largely consecutive, non-hierarchical and weakly insulated loops at the onset of multicellular development. The transcription level within the loop interior tends to be higher than in adjacent regions. Loop interiors frequently contain functionally linked genes and genes which coherently change expression level during development. Loop anchors are predominantly positioned by the genes in convergent orientation. Results of polymer simulations and Hi-C-based observations suggest that the loop profile may arise from the interplay between transcription and extrusion-driven chromatin folding. In this scenario, a convergent gene pair serves as a bidirectional extrusion barrier or a 'diode' that controls passage of the cohesin extruder by relative transcription level of paired genes.
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Affiliation(s)
- Irina V Zhegalova
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
| | - Sergey V Ulianov
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie gory, 1, bld. 12, 119991 Moscow, Russia
| | - Aleksandra A Galitsyna
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
| | - Ilya A Pletenev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
| | - Olga V Tsoy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
| | - Artem V Luzhin
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Petr A Vasiluev
- Research Centre for Medical Genetics, 1 Moskvorechye St., 115522 Moscow, Russia
| | - Egor S Bulavko
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Dmitry N Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
| | - Alexey A Gavrilov
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Ekaterina E Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
| | - Mikhail S Gelfand
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard, 30, bld. 1, 121205 Moscow, Russia
| | - Sergey V Razin
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Department of Molecular Biology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie gory, 1, bld. 12, 119991 Moscow, Russia
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7
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Dekker J, Mirny LA. The chromosome folding problem and how cells solve it. Cell 2024; 187:6424-6450. [PMID: 39547207 PMCID: PMC11569382 DOI: 10.1016/j.cell.2024.10.026] [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: 08/11/2024] [Revised: 10/15/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
Abstract
Every cell must solve the problem of how to fold its genome. We describe how the folded state of chromosomes is the result of the combined activity of multiple conserved mechanisms. Homotypic affinity-driven interactions lead to spatial partitioning of active and inactive loci. Molecular motors fold chromosomes through loop extrusion. Topological features such as supercoiling and entanglements contribute to chromosome folding and its dynamics, and tethering loci to sub-nuclear structures adds additional constraints. Dramatically diverse chromosome conformations observed throughout the cell cycle and across the tree of life can be explained through differential regulation and implementation of these basic mechanisms. We propose that the first functions of chromosome folding are to mediate genome replication, compaction, and segregation and that mechanisms of folding have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, cell types, and species.
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Affiliation(s)
- Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Dumont A, Mendiboure N, Savocco J, Anani L, Moreau P, Thierry A, Modolo L, Jost D, Piazza A. Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae. Mol Cell 2024; 84:3237-3253.e6. [PMID: 39178861 DOI: 10.1016/j.molcel.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/26/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
Abstract
Homology search is a central step of DNA double-strand break (DSB) repair by homologous recombination (HR). How it operates in cells remains elusive. We developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection drives this transition from local to genome-wide search by increasing the probability of assembling extensive NPFs. DSB end-tethering promotes coordinated search by opposite NPFs. Finally, an autonomous genetic element on chromosome III engages the NPF, which stimulates homology search in its vicinity. This work reveals the mechanism of the progressive expansion of homology search that is orchestrated by chromatin organizers, long-range resection, end-tethering, and specialized genetic elements and that exploits the stiff NPF structure conferred by Rad51 oligomerization.
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Affiliation(s)
- Agnès Dumont
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Nicolas Mendiboure
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Jérôme Savocco
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Loqmen Anani
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Pierrick Moreau
- Unité Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525, 75015 Paris, France
| | - Agnès Thierry
- Unité Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525, 75015 Paris, France
| | - Laurent Modolo
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Aurèle Piazza
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France.
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