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Segura J, Díaz-Ingelmo O, Martínez-García B, Ayats-Fraile A, Nikolaou C, Roca J. Nucleosomal DNA has topological memory. Nat Commun 2024; 15:4526. [PMID: 38806488 PMCID: PMC11133463 DOI: 10.1038/s41467-024-49023-4] [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: 06/22/2023] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
One elusive aspect of the chromosome architecture is how it constrains the DNA topology. Nucleosomes stabilise negative DNA supercoils by restraining a DNA linking number difference (∆Lk) of about -1.26. However, whether this capacity is uniform across the genome is unknown. Here, we calculate the ∆Lk restrained by over 4000 nucleosomes in yeast cells. To achieve this, we insert each nucleosome in a circular minichromosome and perform Topo-seq, a high-throughput procedure to inspect the topology of circular DNA libraries in one gel electrophoresis. We show that nucleosomes inherently restrain distinct ∆Lk values depending on their genomic origin. Nucleosome DNA topologies differ at gene bodies (∆Lk = -1.29), intergenic regions (∆Lk = -1.23), rDNA genes (∆Lk = -1.24) and telomeric regions (∆Lk = -1.07). Nucleosomes near the transcription start and termination sites also exhibit singular DNA topologies. Our findings demonstrate that nucleosome DNA topology is imprinted by its native chromatin context and persists when the nucleosome is relocated.
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Affiliation(s)
- Joana Segura
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Madrid, Spain
| | - Ofelia Díaz-Ingelmo
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Belén Martínez-García
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Alba Ayats-Fraile
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | | | - Joaquim Roca
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain.
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2
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Murayama Y, Endo S, Kurokawa Y, Kurita A, Iwasaki S, Araki H. Coordination of cohesin and DNA replication observed with purified proteins. Nature 2024; 626:653-660. [PMID: 38267580 DOI: 10.1038/s41586-023-07003-6] [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: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/26/2024]
Abstract
Two newly duplicated copies of genomic DNA are held together by the ring-shaped cohesin complex to ensure faithful inheritance of the genome during cell division1-3. Cohesin mediates sister chromatid cohesion by topologically entrapping two sister DNAs during DNA replication4,5, but how cohesion is established at the replication fork is poorly understood. Here, we studied the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins. Once DNA is encircled before replication, the cohesin ring accommodates replication in its entirety, from initiation to termination, leading to topological capture of newly synthesized DNA. This suggests that topological cohesin loading is a critical molecular prerequisite to cope with replication. Paradoxically, topological loading per se is highly rate limiting and hardly occurs under the replication-competent physiological salt concentration. This inconsistency is resolved by the replisome-associated cohesion establishment factors Chl1 helicase and Ctf4 (refs. 6,7), which promote cohesin loading specifically during continuing replication. Accordingly, we found that bubble DNA, which mimics the state of DNA unwinding, induces topological cohesin loading and this is further promoted by Chl1. Thus, we propose that cohesin converts the initial electrostatic DNA-binding mode to a topological embrace when it encounters unwound DNA structures driven by enzymatic activities including replication. Together, our results show how cohesin initially responds to replication, and provide a molecular model for the establishment of sister chromatid cohesion.
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Affiliation(s)
- Yasuto Murayama
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan.
- Department of Genetics, Graduate University for Advanced Studies (SOUKENDAI), Mishima, Japan.
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Japan.
| | - Shizuko Endo
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Yumiko Kurokawa
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOUKENDAI), Mishima, Japan
| | - Ayako Kurita
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Sanae Iwasaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Hiroyuki Araki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
- Joint Support-Centre for Data Science Research, Research Organisation of Information and Systems, Tachikawa, Japan
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3
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Warecki B, Sullivan W. The Cell Biology of Heterochromatin. Cells 2022; 11:cells11071247. [PMID: 35406810 PMCID: PMC8997597 DOI: 10.3390/cells11071247] [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: 11/23/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 12/10/2022] Open
Abstract
A conserved feature of virtually all higher eukaryotes is that the centromeres are embedded in heterochromatin. Here we provide evidence that this tight association between pericentric heterochromatin and the centromere is essential for proper metaphase exit and progression into telophase. Analysis of chromosome rearrangements that separate pericentric heterochromatin and centromeres indicates that they must remain associated in order to balance Cohesin/DNA catenation-based binding forces and centromere-based pulling forces during the metaphase–anaphase transition. In addition, a centromere embedded in heterochromatin facilitates nuclear envelope assembly around the entire complement of segregating chromosomes. Because the nuclear envelope initially forms on pericentric heterochromatin, nuclear envelope formation proceeds from the pole, thus providing time for incorporation of lagging and trailing chromosome arms into the newly formed nucleus. Additional analysis of noncanonical mitoses provides further insights into the functional significance of the tight association between heterochromatin and centromeres.
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4
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Conin B, Billault-Chaumartin I, El Sayyed H, Quenech'Du N, Cockram C, Koszul R, Espéli O. Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome. Nucleic Acids Res 2022; 50:2635-2650. [PMID: 35212387 PMCID: PMC8934667 DOI: 10.1093/nar/gkac105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/07/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022] Open
Abstract
In bacteria, chromosome segregation occurs progressively from the origin to terminus within minutes of replication of each locus. Between replication and segregation, sister loci are held in an apparent cohesive state by topological links. The decatenation activity of topoisomerase IV (Topo IV) is required for segregation of replicated loci, yet little is known about the structuring of the chromosome maintained in a cohesive state. In this work, we investigated chromosome folding in cells with altered decatenation activities. Within minutes after Topo IV inactivation, massive chromosome reorganization occurs, associated with increased in contacts between nearby loci, likely trans-contacts between sister chromatids, and in long-range contacts between the terminus and distant loci. We deciphered the respective roles of Topo III, MatP and MukB when TopoIV activity becomes limiting. Topo III reduces short-range inter-sister contacts suggesting its activity near replication forks. MatP, the terminus macrodomain organizing system, and MukB, the Escherichia coli SMC, promote long-range contacts with the terminus. We propose that the large-scale conformational changes observed under these conditions reveal defective decatenation attempts involving the terminus area. Our results support a model of spatial and temporal partitioning of the tasks required for sister chromosome segregation.
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Affiliation(s)
- Brenna Conin
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France.,Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France.,Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Ingrid Billault-Chaumartin
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Hafez El Sayyed
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Nicole Quenech'Du
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Charlotte Cockram
- Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France
| | - Romain Koszul
- Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France
| | - Olivier Espéli
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
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5
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Heintzman DR, Campos LV, Byl JAW, Osheroff N, Dewar JM. Topoisomerase II Is Crucial for Fork Convergence during Vertebrate Replication Termination. Cell Rep 2020; 29:422-436.e5. [PMID: 31597101 PMCID: PMC6919565 DOI: 10.1016/j.celrep.2019.08.097] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/27/2019] [Accepted: 08/28/2019] [Indexed: 11/28/2022] Open
Abstract
Termination of DNA replication occurs when two replication forks converge upon the same stretch of DNA. Resolution of topological stress by topoisomerases is crucial for fork convergence in bacteria and viruses, but it is unclear whether similar mechanisms operate during vertebrate termination. Using Xenopus egg extracts, we show that topoisomerase II (Top2) resolves topological stress to prevent converging forks from stalling during termination. Under these conditions, stalling arises due to an inability to unwind the final stretch of DNA ahead of each fork. By promoting fork convergence, Top2 facilitates all downstream events of termination. Converging forks ultimately overcome stalling independently of Top2, indicating that additional mechanisms support fork convergence. Top2 acts throughout replication to prevent the accumulation of topological stress that would otherwise stall converging forks. Thus, termination poses evolutionarily conserved topological problems that can be mitigated by careful execution of the earlier stages of replication.
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Affiliation(s)
- Darren R Heintzman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lillian V Campos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Medicine (Hematology, Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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6
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Finardi A, Massari LF, Visintin R. Anaphase Bridges: Not All Natural Fibers Are Healthy. Genes (Basel) 2020; 11:genes11080902. [PMID: 32784550 PMCID: PMC7464157 DOI: 10.3390/genes11080902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
At each round of cell division, the DNA must be correctly duplicated and distributed between the two daughter cells to maintain genome identity. In order to achieve proper chromosome replication and segregation, sister chromatids must be recognized as such and kept together until their separation. This process of cohesion is mainly achieved through proteinaceous linkages of cohesin complexes, which are loaded on the sister chromatids as they are generated during S phase. Cohesion between sister chromatids must be fully removed at anaphase to allow chromosome segregation. Other (non-proteinaceous) sources of cohesion between sister chromatids consist of DNA linkages or sister chromatid intertwines. DNA linkages are a natural consequence of DNA replication, but must be timely resolved before chromosome segregation to avoid the arising of DNA lesions and genome instability, a hallmark of cancer development. As complete resolution of sister chromatid intertwines only occurs during chromosome segregation, it is not clear whether DNA linkages that persist in mitosis are simply an unwanted leftover or whether they have a functional role. In this review, we provide an overview of DNA linkages between sister chromatids, from their origin to their resolution, and we discuss the consequences of a failure in their detection and processing and speculate on their potential role.
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Affiliation(s)
- Alice Finardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Lucia F. Massari
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK;
| | - Rosella Visintin
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Correspondence: ; Tel.: +39-02-5748-9859; Fax: +39-02-9437-5991
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7
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Martínez V, Schaerer C, Hernández P, Krimer DB, Schvartzman JB, Fernández-Nestosa MJ. Distribution of torsional stress between the un-replicated and replicated regions in partially replicated molecules. J Biomol Struct Dyn 2020; 39:2266-2277. [DOI: 10.1080/07391102.2020.1751294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Víctor Martínez
- Polytechnic School, National University of Asunción, San Lorenzo, Paraguay
| | - Christian Schaerer
- Polytechnic School, National University of Asunción, San Lorenzo, Paraguay
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Dora B. Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Jorge B. Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
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Schvartzman JB, Hernández P, Krimer DB. Replication Fork Barriers and Topological Barriers: Progression of DNA Replication Relies on DNA Topology Ahead of Forks. Bioessays 2020; 42:e1900204. [PMID: 32115727 DOI: 10.1002/bies.201900204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/05/2020] [Indexed: 11/09/2022]
Abstract
During replication, the topology of DNA changes continuously in response to well-known activities of DNA helicases, polymerases, and topoisomerases. However, replisomes do not always progress at a constant speed and can slow-down and even stall at precise sites. The way these changes in the rate of replisome progression affect DNA topology is not yet well understood. The interplay of DNA topology and replication in several cases where progression of replication forks reacts differently to changes in DNA topology ahead is discussed here. It is proposed, there are at least two types of replication fork barriers: those that behave also as topological barriers and those that do not. Two-Dimensional (2D) agarose gel electrophoresis is the method of choice to distinguish between these two different types of replication fork barriers.
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Affiliation(s)
- Jorge B Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Dora B Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, Madrid, 28040, Spain
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10
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Forte G, Caraglio M, Marenduzzo D, Orlandini E. Plectoneme dynamics and statistics in braided polymers. Phys Rev E 2019; 99:052503. [PMID: 31212427 DOI: 10.1103/physreve.99.052503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Braids composed of two interwoven polymer chains exhibit a "buckling" transition whose origin has been explained through the onset of plectonemic structures. Here we study, by a combination of simulation and analytics, the dynamics of plectoneme formation and their statistics in steady state. The introduction of an order parameter-the plectonemic fraction-allows us to map out the phase boundary between the straight-braid phase and the plectonemic one. We then monitor the formation and the growth of plectonemes, observing events typical of phase separation kinetics for liquid-gas systems (fusion, fission, and one-dimensional Ostwald ripening) but also of DNA supercoiling dynamics (plectonemic hopping). Finally, we propose a stochastic field theory for the coupled dynamics of twist and local writhe which explains the phenomenology found with Brownian dynamics simulations as well as the power laws underlying the coarsening of plectonemes.
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Affiliation(s)
- Giada Forte
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
| | - Michele Caraglio
- Soft Matter and Biophysics section, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
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