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Gu C, Takada S, Brandani GB, Terakawa T. Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion. PLoS Comput Biol 2025; 21:e1012493. [PMID: 40184420 PMCID: PMC11970657 DOI: 10.1371/journal.pcbi.1012493] [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: 09/13/2024] [Accepted: 02/19/2025] [Indexed: 04/06/2025] Open
Abstract
The SMC complex cohesin mediates interphase chromatin structural formation in eukaryotic cells through DNA loop extrusion. Here, we sought to investigate its mechanism using molecular dynamics simulations. To achieve this, we first constructed the amino-acid-residue-resolution structural models of the cohesin subunits, SMC1, SMC3, STAG1, and NIPBL. By simulating these subunits with double-stranded DNA molecules, we predicted DNA binding patches on each subunit and quantified the affinities of these patches to DNA using their dissociation rate constants as a proxy. Then, we constructed the structural model of the whole cohesin complex and mapped the predicted high-affinity DNA binding patches on the structure. From the spatial relations of the predicted patches, we identified that multiple patches on the SMC1, SMC3, STAG1, and NIPBL subunits form a DNA clamping patch group. The simulations of the whole complex with double-stranded DNA molecules suggest that this patch group facilitates DNA bending and helps capture a DNA segment in the cohesin ring formed by the SMC1 and SMC3 subunits. In previous studies, these have been identified as critical steps in DNA loop extrusion. Therefore, this study provides experimentally testable predictions of DNA binding sites implicated in previously proposed DNA loop extrusion mechanisms and highlights the essential roles of the accessory subunits STAG1 and NIPBL in the mechanism.
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Affiliation(s)
- Chenyang Gu
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Giovanni B. Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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2
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Yu R, Roseman S, Siegenfeld AP, Gardner Z, Nguyen SC, Tran KA, Joyce EF, Jain R, Liau BB, Krantz ID, Alexander KA, Berger SL. CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association. Nat Struct Mol Biol 2025:10.1038/s41594-024-01465-6. [PMID: 39984730 DOI: 10.1038/s41594-024-01465-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/03/2024] [Indexed: 02/23/2025]
Abstract
Recent findings indicate that nuclear speckles, a distinct type of nuclear body, interact with certain chromatin regions in a ground state. Here, we report that the chromatin structural factors CTCF and cohesin are required for full ground-state association between DNA and nuclear speckles. We identified a putative speckle-targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association, disruption of which also impaired induction of speckle-associated genes. Depletion of the cohesin-releasing factor WAPL, which stabilizes cohesin on chromatin, resulted in reinforcement of DNA-speckle contacts and enhanced inducibility of speckle-associated genes. Additionally, we observed disruption of chromatin-nuclear speckle association in patient-derived cells with Cornelia de Lange syndrome, a congenital neurodevelopmental disorder involving defective cohesin pathways. In summary, our findings reveal a mechanism for establishing the ground state of chromatin-speckle association and promoting gene inducibility, with relevance to human disease.
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Affiliation(s)
- Ruofan Yu
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Cell and Developmental Biology; Genetics; Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelby Roseman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Allison P Siegenfeld
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zachary Gardner
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Cell and Developmental Biology; Genetics; Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Son C Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Khoa A Tran
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Cell and Developmental Biology; Genetics; Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Eric F Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Cell and Developmental Biology; Genetics; Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Penn Cardiovascular Institute and Institute of Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ian D Krantz
- Roberts Individualized Medical Genetics Center, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katherine A Alexander
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Cell and Developmental Biology; Genetics; Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Cold Spring Harbor Laboratories, Cold Spring Harbor, New York, NY, USA.
| | - Shelley L Berger
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Cell and Developmental Biology; Genetics; Biology, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Tang W, Costantino L, Stocsits R, Wutz G, Ladurner R, Hudecz O, Mechtler K, Peters JM. Cohesin positions the epigenetic reader Phf2 within the genome. EMBO J 2025; 44:736-766. [PMID: 39748119 PMCID: PMC11790891 DOI: 10.1038/s44318-024-00348-2] [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: 09/13/2024] [Revised: 12/11/2024] [Accepted: 12/12/2024] [Indexed: 01/04/2025] Open
Abstract
Genomic DNA is assembled into chromatin by histones, and extruded into loops by cohesin. These mechanisms control important genomic functions, but whether histones and cohesin cooperate in genome regulation is poorly understood. Here we identify Phf2, a member of the Jumonji-C family of histone demethylases, as a cohesin-interacting protein. Phf2 binds to H3K4me3 nucleosomes at active transcription start sites (TSSs), but also co-localizes with cohesin. Cohesin depletion reduces Phf2 binding at sites lacking H3K4me3, and depletion of Wapl and CTCF re-positions Phf2 together with cohesin in the genome, resulting in the accumulation of both proteins in chromosomal regions called vermicelli and cohesin islands. Conversely, Phf2 depletion reduces cohesin binding at TSSs lacking CTCF and decreases the number of short cohesin loops, while increasing the length of heterochromatic B compartments. These results suggest that Phf2 is an 'epigenetic reader', which is translocated through the genome by cohesin-mediated DNA loop extrusion, and which recruits cohesin to active TSSs and limits the size of B compartments. These findings reveal an unexpected degree of cooperativity between epigenetic and architectural mechanisms of eukaryotic genome regulation.
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Affiliation(s)
- Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Lorenzo Costantino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Roman Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Otto Hudecz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.
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Zhu Q, Chen X, Lin Z. Discovery of KPT-6566 as STAG1/2 Inhibitor sensitizing PARP and NHEJ Inhibitors to suppress tumor cells growth in vitro. DNA Repair (Amst) 2024; 144:103784. [PMID: 39541712 DOI: 10.1016/j.dnarep.2024.103784] [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: 09/02/2024] [Revised: 10/30/2024] [Accepted: 11/03/2024] [Indexed: 11/16/2024]
Abstract
Stromal antigen 1 and 2 (STAG1 and STAG2) are two mutually exclusive components of the cohesin complex that is crucial for centromeric and telomeric cohesion. Beyond its structural role, STAG2 also plays a pivotal role in homologous recombination (HR) repair and has emerged as a promising therapeutic target in cancer treatment. Here, we employed a fluorescence polarization (FP)-based high-throughput screening and identified KPT-6566 as a dual inhibitor of STAG1 and STAG2. Biochemical and biophysical analyses demonstrated that KPT-6566 directly binds to STAG1 and STAG2, disrupting their interactions with SCC1 and double-stranded DNA. A metaphase chromosome spread assay showed that KPT-6566 causes premature chromosome separation and induces chromosome damages in HeLa cells. Furthermore, KPT-6566 also impairs DNA damage repair, leading to the accumulation of double-strand breaks and cell apoptosis. Finally, KPT-6566 can sensitize HeLa and HepG2 cells to PARP inhibitor Olaparib and the NHEJ inhibitor UMI-77, exhibiting a synergistic effect in suppressing cell proliferation. Our findings highlight the potential of STAG1/2 as promising therapeutic targets in cancer treatment, particularly when they are targeted in combination with other DNA damage response inhibitors.
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Affiliation(s)
- Qinwei Zhu
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Xuening Chen
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou 350108, China.
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5
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Hellmuth S, Stemmann O. Requirement of Nek2a and cyclin A2 for Wapl-dependent removal of cohesin from prophase chromatin. EMBO J 2024; 43:5237-5259. [PMID: 39271794 PMCID: PMC11535040 DOI: 10.1038/s44318-024-00228-9] [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: 03/08/2024] [Revised: 08/14/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Sister chromatid cohesion is mediated by the cohesin complex. In mitotic prophase cohesin is removed from chromosome arms in a Wapl- and phosphorylation-dependent manner. Sgo1-PP2A protects pericentromeric cohesion by dephosphorylation of cohesin and its associated Wapl antagonist sororin. However, Sgo1-PP2A relocates to inner kinetochores well before sister chromatids are separated by separase, leaving pericentromeric regions unprotected. Why deprotected cohesin is not removed by Wapl remains enigmatic. By reconstituting Wapl-dependent cohesin removal from chromatin in vitro, we discovered a requirement for Nek2a and Cdk1/2-cyclin A2. These kinases phosphorylate cohesin-bound Pds5b, thereby converting it from a sororin- to a Wapl-interactor. Replacement of endogenous Pds5b by a phosphorylation mimetic variant causes premature sister chromatid separation (PCS). Conversely, phosphorylation-resistant Pds5b impairs chromosome arm separation in prometaphase-arrested cells and suppresses PCS in the absence of Sgo1. Early mitotic degradation of Nek2a and cyclin A2 may therefore explain why only separase, but not Wapl, can trigger anaphase.
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Affiliation(s)
- Susanne Hellmuth
- Chair of Genetics, University of Bayreuth, 95440, Bayreuth, Germany.
| | - Olaf Stemmann
- Chair of Genetics, University of Bayreuth, 95440, Bayreuth, Germany
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Vitoria Gomes M, Landwerlin P, Diebold-Durand ML, Shaik TB, Durand A, Troesch E, Weber C, Brillet K, Lemée MV, Decroos C, Dulac L, Antony P, Watrin E, Ennifar E, Golzio C, Romier C. The cohesin ATPase cycle is mediated by specific conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase domains. Cell Rep 2024; 43:114656. [PMID: 39240714 DOI: 10.1016/j.celrep.2024.114656] [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: 12/15/2023] [Revised: 06/17/2024] [Accepted: 08/02/2024] [Indexed: 09/08/2024] Open
Abstract
Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we characterize distinct steps of the human cohesin ATPase cycle and show that the SMC1A and SMC3 ATPase domains undergo specific but concerted structural rearrangements along this cycle. Specifically, whereas the proximal coiled coil of the SMC1A ATPase domain remains conformationally stable, that of the SMC3 displays an intrinsic flexibility. The ATP-dependent formation of the heterodimeric SMC1A/SMC3 ATPase module (engaged state) favors this flexibility, which is counteracted by NIPBL and DNA binding (clamped state). Opening of the SMC3/RAD21 interface (open-engaged state) stiffens the SMC3 proximal coiled coil, thus constricting together with that of SMC1A the ATPase module DNA-binding chamber. The plasticity of the ATP-dependent interface between the SMC1A and SMC3 ATPase domains enables these structural rearrangements while keeping the ATP gate shut. VIDEO ABSTRACT.
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Affiliation(s)
- Marina Vitoria Gomes
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Pauline Landwerlin
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Marie-Laure Diebold-Durand
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Tajith B Shaik
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Alexandre Durand
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Edouard Troesch
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Chantal Weber
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Karl Brillet
- Architecture et Réactivité de l'ARN, IBMC CNRS UPR 9002, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Marianne Victoria Lemée
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Christophe Decroos
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Ludivine Dulac
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Pierre Antony
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Erwan Watrin
- CNRS, Université de Rennes, IGDR UMR 6290, 35000 Rennes, France
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, IBMC CNRS UPR 9002, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Christelle Golzio
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Christophe Romier
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France.
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Tortora MMC, Fudenberg G. The physical chemistry of interphase loop extrusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609419. [PMID: 39229088 PMCID: PMC11370536 DOI: 10.1101/2024.08.23.609419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Loop extrusion constitutes a universal mechanism of genome organization, whereby structural maintenance of chromosomes (SMC) protein complexes load onto the chromatin fiber and generate DNA loops of increasingly-larger sizes until their eventual release. In mammalian interphase cells, loop extrusion is mediated by the cohesin complex, which is dynamically regulated by the interchange of multiple accessory proteins. Although these regulators bind the core cohesin complex only transiently, their disruption can dramatically alter cohesin dynamics, gene expression, chromosome morphology and contact patterns. Still, a theory of how cohesin regulators and their molecular interplay with the core complex modulate genome folding remains at large. Here we derive a model of cohesin loop extrusion from first principles, based on in vivo measurements of the abundance and dynamics of cohesin regulators. We systematically evaluate potential chemical reaction networks that describe the association of cohesin with its regulators and with the chromatin fiber. Remarkably, experimental observations are consistent with only a single biochemical reaction cycle, which results in a unique minimal model that may be fully parameterized by quantitative protein measurements. We demonstrate how distinct roles for cohesin regulators emerge simply from the structure of the reaction network, and how their dynamic exchange can regulate loop extrusion kinetics over time-scales that far exceed their own chromatin residence times. By embedding our cohesin biochemical reaction network within biophysical chromatin simulations, we evidence how variations in regulatory protein abundance can alter chromatin architecture across multiple length- and time-scales. Predictions from our model are corroborated by biophysical and biochemical assays, optical microscopy observations, and Hi-C conformation capture techniques. More broadly, our theoretical and numerical framework bridges the gap between in vitro observations of extrusion motor dynamics at the molecular scale and their structural consequences at the genome-wide level.
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Affiliation(s)
- Maxime M C Tortora
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Geoffrey Fudenberg
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
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8
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Yuan X, Yan L, Chen Q, Zhu S, Zhou X, Zeng LH, Liu M, He X, Huang J, Lu W, Zhang L, Yan H, Wang F. Molecular mechanism and functional significance of Wapl interaction with the Cohesin complex. Proc Natl Acad Sci U S A 2024; 121:e2405177121. [PMID: 39110738 PMCID: PMC11331136 DOI: 10.1073/pnas.2405177121] [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: 03/12/2024] [Accepted: 07/01/2024] [Indexed: 08/21/2024] Open
Abstract
The ring-shaped Cohesin complex, consisting of core subunits Smc1, Smc3, Scc1, and SA2 (or its paralog SA1), topologically entraps two duplicated sister DNA molecules to establish sister chromatid cohesion in S-phase. It remains largely elusive how the Cohesin release factor Wapl binds the Cohesin complex, thereby inducing Cohesin disassociation from mitotic chromosomes to allow proper resolution and separation of sister chromatids. Here, we show that Wapl uses two structural modules containing the FGF motif and the YNARHWN motif, respectively, to simultaneously bind distinct pockets in the extensive composite interface between Scc1 and SA2. Strikingly, only when both docking modules are mutated, Wapl completely loses the ability to bind the Scc1-SA2 interface and release Cohesin, leading to erroneous chromosome segregation in mitosis. Surprisingly, Sororin, which contains a conserved FGF motif and functions as a master antagonist of Wapl in S-phase and G2-phase, does not bind the Scc1-SA2 interface. Moreover, Sgo1, the major protector of Cohesin at mitotic centromeres, can only compete with the FGF motif but not the YNARHWN motif of Wapl for binding Scc1-SA2 interface. Our data uncover the molecular mechanism by which Wapl binds Cohesin to ensure precise chromosome segregation.
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Affiliation(s)
- Xueying Yuan
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lu Yan
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qinfu Chen
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shukai Zhu
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xinyu Zhou
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ling-Hui Zeng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Mingjie Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojing He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute and MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Weiguo Lu
- Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital of Zhejiang University School of Medicine, and Cancer Center of Zhejiang University, Hangzhou, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute and MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Haiyan Yan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Fangwei Wang
- Department of Gynecologic Oncology of Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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9
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Labudina AA, Meier M, Gimenez G, Tatarakis D, Ketharnathan S, Mackie B, Schilling TF, Antony J, Horsfield JA. Cohesin composition and dosage independently affect early development in zebrafish. Development 2024; 151:dev202593. [PMID: 38975838 DOI: 10.1242/dev.202593] [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: 12/07/2023] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Cohesin, a chromatin-associated protein complex with four core subunits (Smc1a, Smc3, Rad21 and either Stag1 or 2), has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed 'cohesinopathies' are characterized by germline variants of cohesin or its regulators that do not entirely eliminate cohesin function. However, it is not clear whether mutations in individual cohesin subunits have independent developmental consequences. Here, we show that zebrafish rad21 or stag2b mutants independently influence embryonic tailbud development. Both mutants have altered mesoderm induction, but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2b mutants have narrower notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single-cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2b, but not rad21, mutants. Our results suggest that mutations altering the quantity versus composition of cohesin have independent developmental consequences, with implications for the understanding and management of cohesinopathies.
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Affiliation(s)
- Anastasia A Labudina
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Michael Meier
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - David Tatarakis
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Sarada Ketharnathan
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Bridget Mackie
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Thomas F Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin 9016, New Zealand
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10
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Grothusen GP, Chang R, Cao Z, Zhou N, Mittal M, Datta A, Wulfridge P, Beer T, Wang B, Zheng N, Tang HY, Sarma K, Greenberg RA, Shi J, Busino L. DCAF15 control of cohesin dynamics sustains acute myeloid leukemia. Nat Commun 2024; 15:5604. [PMID: 38961054 PMCID: PMC11222469 DOI: 10.1038/s41467-024-49882-x] [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: 08/03/2023] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The CRL4-DCAF15 E3 ubiquitin ligase complex is targeted by the aryl-sulfonamide molecular glues, leading to neo-substrate recruitment, ubiquitination, and proteasomal degradation. However, the physiological function of DCAF15 remains unknown. Using a domain-focused genetic screening approach, we reveal DCAF15 as an acute myeloid leukemia (AML)-biased dependency. Loss of DCAF15 results in suppression of AML through compromised replication fork integrity and consequent accumulation of DNA damage. Accordingly, DCAF15 loss sensitizes AML to replication stress-inducing therapeutics. Mechanistically, we discover that DCAF15 directly interacts with the SMC1A protein of the cohesin complex and destabilizes the cohesin regulatory factors PDS5A and CDCA5. Loss of PDS5A and CDCA5 removal precludes cohesin acetylation on chromatin, resulting in uncontrolled chromatin loop extrusion, defective DNA replication, and apoptosis. Collectively, our findings uncover an endogenous, cell autonomous function of DCAF15 in sustaining AML proliferation through post-translational control of cohesin dynamics.
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Affiliation(s)
- Grant P Grothusen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renxu Chang
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhendong Cao
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nan Zhou
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monika Mittal
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arindam Datta
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip Wulfridge
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Thomas Beer
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Baiyun Wang
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Kavitha Sarma
- Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Prusén Mota I, Galova M, Schleiffer A, Nguyen TT, Kovacikova I, Farias Saad C, Litos G, Nishiyama T, Gregan J, Peters JM, Schlögelhofer P. Sororin is an evolutionary conserved antagonist of WAPL. Nat Commun 2024; 15:4729. [PMID: 38830897 PMCID: PMC11148194 DOI: 10.1038/s41467-024-49178-0] [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: 10/24/2022] [Accepted: 05/26/2024] [Indexed: 06/05/2024] Open
Abstract
Cohesin mediates sister chromatid cohesion to enable chromosome segregation and DNA damage repair. To perform these functions, cohesin needs to be protected from WAPL, which otherwise releases cohesin from DNA. It has been proposed that cohesin is protected from WAPL by SORORIN. However, in vivo evidence for this antagonism is missing and SORORIN is only known to exist in vertebrates and insects. It is therefore unknown how important and widespread SORORIN's functions are. Here we report the identification of SORORIN orthologs in Schizosaccharomyces pombe (Sor1) and Arabidopsis thaliana (AtSORORIN). sor1Δ mutants display cohesion defects, which are partially alleviated by wpl1Δ. Atsororin mutant plants display dwarfism, tissue specific cohesion defects and chromosome mis-segregation. Furthermore, Atsororin mutant plants are sterile and separate sister chromatids prematurely at anaphase I. The somatic, but not the meiotic deficiencies can be alleviated by loss of WAPL. These results provide in vivo evidence for SORORIN antagonizing WAPL, reveal that SORORIN is present in organisms beyond the animal kingdom and indicate that it has acquired tissue specific functions in plants.
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Affiliation(s)
- Ignacio Prusén Mota
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Marta Galova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tan-Trung Nguyen
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
| | - Ines Kovacikova
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
| | - Carolina Farias Saad
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tomoko Nishiyama
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Juraj Gregan
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria.
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Tulln an der Donau, Austria.
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
| | - Peter Schlögelhofer
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Chromosome Biology, Vienna, Austria.
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12
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Golov AK, Gavrilov AA. Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:601-625. [PMID: 38831499 DOI: 10.1134/s0006297924040023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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13
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Golov AK, Gavrilov AA. Cohesin Complex: Structure and Principles of Interaction with DNA. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:585-600. [PMID: 38831498 DOI: 10.1134/s0006297924040011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 06/05/2024]
Abstract
Accurate duplication and separation of long linear genomic DNA molecules is associated with a number of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decatenation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eukaryotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be threaded. Capacity of cohesin for such topological entrapment of DNA is crucial for the phenomenon of post-replicative association of sister chromatids better known as cohesion. Recently, it became apparent that cohesin and other SMC complexes are, in fact, motor proteins with a very peculiar movement pattern leading to formation of DNA loops. This specific process has been called loop extrusion. Extrusion underlies multiple functions of cohesin beyond cohesion, but molecular mechanism of the process remains a mystery. In this review, we summarized the data on molecular architecture of cohesin, effect of ATP hydrolysis cycle on this architecture, and known modes of cohesin-DNA interactions. Many of the seemingly disparate facts presented here will probably be incorporated in a unified mechanistic model of loop extrusion in the not-so-distant future.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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14
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Richeldi M, Pobegalov G, Higashi TL, Gmurczyk K, Uhlmann F, Molodtsov MI. Mechanical disengagement of the cohesin ring. Nat Struct Mol Biol 2024; 31:23-31. [PMID: 37872232 PMCID: PMC11377297 DOI: 10.1038/s41594-023-01122-4] [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: 11/11/2022] [Accepted: 09/11/2023] [Indexed: 10/25/2023]
Abstract
Cohesin forms a proteinaceous ring that is thought to link sister chromatids by entrapping DNA and counteracting the forces generated by the mitotic spindle. Whether individual cohesins encircle both sister DNAs and how cohesin opposes spindle-generated forces remains unknown. Here we perform force measurements on individual yeast cohesin complexes either bound to DNA or holding together two DNAs. By covalently closing the hinge and Smc3Psm3-kleisin interfaces we find that the mechanical stability of the cohesin ring entrapping DNA is determined by the hinge domain. Forces of ~20 pN disengage cohesin at the hinge and release DNA, indicating that ~40 cohesin molecules are sufficient to counteract known spindle forces. Our findings provide a mechanical framework for understanding how cohesin interacts with sister chromatids and opposes the spindle-generated tension during mitosis, with implications for other force-generating chromosomal processes including transcription and DNA replication.
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Affiliation(s)
- Martina Richeldi
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Georgii Pobegalov
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Kamakura Research Laboratories, Chugai Pharmaceutical Co., Kamakura City, Japan
| | - Karolina Gmurczyk
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
| | - Maxim I Molodtsov
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics and Astronomy, University College London, London, UK.
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15
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Bsteh D, Moussa HF, Michlits G, Yelagandula R, Wang J, Elling U, Bell O. Loss of cohesin regulator PDS5A reveals repressive role of Polycomb loops. Nat Commun 2023; 14:8160. [PMID: 38071364 PMCID: PMC10710464 DOI: 10.1038/s41467-023-43869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) are conserved epigenetic regulators that promote transcriptional gene silencing. PRC1 and PRC2 converge on shared targets, catalyzing repressive histone modifications. Additionally, a subset of PRC1/PRC2 targets engage in long-range interactions whose functions in gene silencing are poorly understood. Using a CRISPR screen in mouse embryonic stem cells, we found that the cohesin regulator PDS5A links transcriptional silencing by Polycomb and 3D genome organization. PDS5A deletion impairs cohesin unloading and results in derepression of a subset of endogenous PRC1/PRC2 target genes. Importantly, derepression is not linked to loss of Polycomb chromatin domains. Instead, PDS5A removal causes aberrant cohesin activity leading to ectopic insulation sites, which disrupt the formation of ultra-long Polycomb loops. We show that these loops are important for robust silencing at a subset of PRC1/PRC2 target genes and that maintenance of cohesin-dependent genome architecture is critical for Polycomb regulation.
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Affiliation(s)
- Daniel Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Medical Oncology, Department of Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hagar F Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- JLP Health GmbH, Himmelhofgasse 62, 1130, Vienna, Austria
| | - Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, 500039, India
| | - Jingkui Wang
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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16
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Yu R, Roseman S, Siegenfeld AP, Nguyen SC, Joyce EF, Liau BB, Krantz ID, Alexander KA, Berger SL. CTCF/cohesin organize the ground state of chromatin-nuclear speckle association. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550178. [PMID: 37961560 PMCID: PMC10634669 DOI: 10.1101/2023.07.22.550178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The interchromatin space in the cell nucleus contains various membrane-less nuclear bodies. Recent findings indicate that nuclear speckles, comprising a distinct nuclear body, exhibit interactions with certain chromatin regions in a ground state. Key questions are how this ground state of chromatin-nuclear speckle association is established and what are the gene regulatory roles of this layer of nuclear organization. We report here that chromatin structural factors CTCF and cohesin are required for full ground state association between DNA and nuclear speckles. Disruption of ground state DNA-speckle contacts via either CTCF depletion or cohesin depletion had minor effects on basal level expression of speckle-associated genes, however we show strong negative effects on stimulus-dependent induction of speckle-associated genes. We identified a putative speckle targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association. In contrast to reduction of CTCF or RAD21, depletion of the cohesin releasing factor WAPL stabilized cohesin on chromatin and DNA-speckle contacts, resulting in enhanced inducibility of speckle-associated genes. In addition, we observed disruption of chromatin-nuclear speckle association in patient derived cells with Cornelia de Lange syndrome (CdLS), a congenital neurodevelopmental diagnosis involving defective cohesin pathways, thus revealing nuclear speckles as an avenue for therapeutic inquiry. In summary, our findings reveal a mechanism to establish the ground organizational state of chromatin-speckle association, to promote gene inducibility, and with relevance to human disease.
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17
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Rosa C, Singh P, Chen P, Sinha A, Claës A, Preiser PR, Dedon PC, Baumgarten S, Scherf A, Bryant JM. Cohesin contributes to transcriptional repression of stage-specific genes in the human malaria parasite. EMBO Rep 2023; 24:e57090. [PMID: 37592911 PMCID: PMC10561359 DOI: 10.15252/embr.202357090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
The complex life cycle of the human malaria parasite, Plasmodium falciparum, is driven by specific transcriptional programs, but it is unclear how most genes are activated or silenced at specific times. There is an association between transcription and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks key genome-organizing proteins found in metazoans, it has all core components of the cohesin complex. To investigate the role of cohesin in P. falciparum, we functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown during early stages of the intraerythrocytic developmental cycle (IDC) upregulates a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq analyses reveal that during the IDC, SMC3 enrichment at the promoter regions of these genes inversely correlates with gene expression and chromatin accessibility. These data suggest that SMC3 binding contributes to the repression of specific genes until their appropriate time of expression, revealing a new mode of stage-specific gene repression in P. falciparum.
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Affiliation(s)
- Catarina Rosa
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
- Sorbonne Université, Collège Doctoral Complexité du Vivant ED515ParisFrance
| | - Parul Singh
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Patty Chen
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Ameya Sinha
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Aurélie Claës
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Peter R Preiser
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore‐MIT Alliance for Research and TechnologySingaporeSingapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | | | - Artur Scherf
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
| | - Jessica M Bryant
- Institut Pasteur, Université Paris Cité, INSERM U1201, CNRS EMR9195, Biology of Host‐Parasite Interactions UnitParisFrance
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18
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Agarwal A, Korsak S, Choudhury A, Plewczynski D. The dynamic role of cohesin in maintaining human genome architecture. Bioessays 2023; 45:e2200240. [PMID: 37603403 DOI: 10.1002/bies.202200240] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers. Cohesin plays a fundamental role in chromatin organization, gene expression and regulation. This review aims to describe the current understanding of the dynamic nature of the cohesin-DNA complex and its dependence on cohesin for genome maintenance. We discuss the current 3C technique and numerous bioinformatics pipelines used to comprehend structural genomics and epigenetics focusing on the analysis of Cohesin-centred interactions. We also incorporate our present comprehension of Loop Extrusion (LE) and insights from stochastic modelling.
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Affiliation(s)
- Abhishek Agarwal
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sevastianos Korsak
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | | | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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19
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Wu D, Zhang K, Khan FA, Wu Q, Pandupuspitasari NS, Tang Y, Guan K, Sun F, Huang C. The emerging era of lactate: A rising star in cellular signaling and its regulatory mechanisms. J Cell Biochem 2023; 124:1067-1081. [PMID: 37566665 DOI: 10.1002/jcb.30458] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Cellular metabolites are ancient molecules with pleiotropic implications in health and disease. Beyond their cognate roles, they have signaling functions as the ligands for specific receptors and the precursors for epigenetic or posttranslational modifications. Lactate has long been recognized as a metabolic waste and fatigue product mainly produced from glycolytic metabolism. Recent evidence however suggests lactate is an unique molecule with diverse signaling attributes in orchestration of numerous biological processes, including tumor immunity and neuronal survival. The copious metabolic and non-metabolic functions of lactate mediated by its bidirectional shuttle between cells or intracellular organelles lead to a phenotype called "lactormone." Importantly, the mechanisms of lactate signaling, via acting as a molecular sensor and a regulator of NAD+ metabolism and AMP-activated protein kinase signaling, and via the newly identified lactate-driven lactylation, have been discovered. Further, we include a brief discussion about the autocrine regulation of efferocytosis by lactate in Sertoli cells which favoraerobic glycolysis. By emphasizing a repertoire of the most recent discovered mechanisms of lactate signaling, this review will open tantalizing avenues for future investigations cracking the regulatory topology of lactate signaling covered in the veil of mystery.
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Affiliation(s)
- Di Wu
- School of Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Kejia Zhang
- School of Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, Ministry of Research and Technology National Research and Innovation Agency, Jakarta, Indonesia
| | - Qin Wu
- Jinan Second People's Hospital & The Ophthalmologic Hospital of Jinan, Jinan, China
| | | | - Yuan Tang
- School of Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Kaifeng Guan
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Fei Sun
- School of Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Chunjie Huang
- School of Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
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20
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Pobegalov G, Chu LY, Peters JM, Molodtsov MI. Single cohesin molecules generate force by two distinct mechanisms. Nat Commun 2023; 14:3946. [PMID: 37402740 DOI: 10.1038/s41467-023-39696-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Spatial organization of DNA is facilitated by cohesin protein complexes that move on DNA and extrude DNA loops. How cohesin works mechanistically as a molecular machine is poorly understood. Here, we measure mechanical forces generated by conformational changes in single cohesin molecules. We show that bending of SMC coiled coils is driven by random thermal fluctuations leading to a ~32 nm head-hinge displacement that resists forces up to 1 pN; ATPase head engagement occurs in a single step of ~10 nm and is driven by an ATP dependent head-head movement, resisting forces up to 15 pN. Our molecular dynamic simulations show that the energy of head engagement can be stored in a mechanically strained conformation of NIPBL and released during disengagement. These findings reveal how single cohesin molecules generate force by two distinct mechanisms. We present a model, which proposes how this ability may power different aspects of cohesin-DNA interaction.
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Affiliation(s)
- Georgii Pobegalov
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Lee-Ya Chu
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria
| | - Maxim I Molodtsov
- The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria.
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21
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González-Martín E, Jiménez J, Tallada VA. BiFCo: visualizing cohesin assembly/disassembly cycle in living cells. Life Sci Alliance 2023; 6:e202301945. [PMID: 37160310 PMCID: PMC10172768 DOI: 10.26508/lsa.202301945] [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: 01/24/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/11/2023] Open
Abstract
Cohesin is a highly conserved, ring-shaped protein complex found in all eukaryotes. It consists of at least two structural maintenance of chromosomes (SMC) proteins, SMC1 and SMC3 in humans (Psm1 and Psm3 in fission yeast), and the kleisin RAD21 (Rad21 in fission yeast). Mutations in its components or regulators can lead to genetic syndromes, known as cohesinopathies, and various types of cancer. Studies in several organisms have shown that only a small fraction of each subunit assembles into complexes, making it difficult to investigate dynamic chromatin loading and unloading using fluorescent fusions in vivo because of excess soluble components. In this study, we introduce bimolecular fluorescent cohesin (BiFCo), based on bimolecular fluorescent complementation in the fission yeast Schizosaccharomyces pombe BiFCo selectively excludes signals from individual proteins, enabling the monitoring of complex assembly and disassembly within a physiological context throughout the entire cell cycle in living cells. This versatile system can be expanded and adapted for various genetic backgrounds and other eukaryotic models, including human cells.
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Affiliation(s)
- Emilio González-Martín
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
| | - Juan Jiménez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
| | - Víctor A Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Seville, Spain
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22
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Shin H, Kim Y. Regulation of loop extrusion on the interphase genome. Crit Rev Biochem Mol Biol 2023; 58:1-18. [PMID: 36921088 DOI: 10.1080/10409238.2023.2182273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
In the human cell nucleus, dynamically organized chromatin is the substrate for gene regulation, DNA replication, and repair. A central mechanism of DNA loop formation is an ATPase motor cohesin-mediated loop extrusion. The cohesin complexes load and unload onto the chromosome under the control of other regulators that physically interact and affect motor activity. Regulation of the dynamic loading cycle of cohesin influences not only the chromatin structure but also genome-associated human disorders and aging. This review focuses on the recently spotlighted genome organizing factors and the mechanism by which their dynamic interactions shape the genome architecture in interphase.
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Affiliation(s)
- Hyogyung Shin
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Yoori Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea.,New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
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23
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Xu X, Yanagida M. Cohesin organization, dynamics, and subdomain functions revealed by genetic suppressor screening. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:61-74. [PMID: 36908173 PMCID: PMC10170060 DOI: 10.2183/pjab.99.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cohesin is a heteropentameric protein complex that contributes to various aspects of chromosome structure and function, such as sister chromatid cohesion, genome compaction, and DNA damage response. Previous studies have provided abundant information on architecture and regional structures of the cohesin complex, but the configuration and structural dynamics of the whole cohesin complex are still largely unknown, partly due to flexibility of its coiled coils. We studied cohesin organization and dynamics using in vivo functional mutation compensation. Specifically, we developed and applied genetic suppressor screening methods to identify second mutations in cohesin complex genes that rescue lethality caused by various site-specific abnormalities in the cohesin complex. Functional analysis of these missense suppressor mutations revealed novel features of cohesin. Here, we summarize recent genetic suppressor screening results and insights into: 1) cohesin's structural organization when holding chromosomal DNAs; 2) interaction between cohesin head-kleisin and hinge; 3) ATP-driven cohesin conformational changes for genome packaging.
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Affiliation(s)
- Xingya Xu
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
- Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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24
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Freitag M, Jaklin S, Padovani F, Radzichevici E, Zernia S, Schmoller KM, Stigler J. Single-molecule experiments reveal the elbow as an essential folding guide in SMC coiled-coil arms. Biophys J 2022; 121:4702-4713. [PMID: 36242515 PMCID: PMC9748247 DOI: 10.1016/j.bpj.2022.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/16/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022] Open
Abstract
Structural maintenance of chromosome (SMC) complexes form ring-like structures through exceptional elongated coiled-coils (CCs). Recent studies found that variable CC conformations, including open and collapsed forms, which might result from discontinuities in the CC, facilitate the diverse functions of SMCs in DNA organization. However, a detailed description of the SMC CC architecture is still missing. Here, we study the structural composition and mechanical properties of SMC proteins with optical tweezers unfolding experiments using the isolated Psm3 CC as a model system. We find a comparatively unstable protein with three unzipping intermediates, which we could directly assign to CC features by crosslinking experiments and state-of-the-art prediction software. Particularly, the CC elbow is shown to be a flexible, potentially non-structured feature, which divides the CC into sections, induces a pairing shift from one CC strand to the other and could facilitate large-scale conformational changes, most likely via thermal fluctuations of the flanking CC sections. A replacement of the elbow amino acids hinders folding of the consecutive CC region and frequently leads to non-native misalignments, revealing the elbow as a guide for proper folding. Additional in vivo manipulation of the elbow flexibility resulted in impaired cohesin complexes, which directly link the sensitive CC architecture to the biological function of cohesin.
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Affiliation(s)
- Marvin Freitag
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sigrun Jaklin
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Francesco Padovani
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Sarah Zernia
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.
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25
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Cohesin ATPase activities regulate DNA binding and coiled-coil configuration. Proc Natl Acad Sci U S A 2022; 119:e2208004119. [PMID: 35939705 PMCID: PMC9388089 DOI: 10.1073/pnas.2208004119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cohesin is a heteropentameric protein complex consisting of two structural maintenance of chromosomes (SMC) subunits and three non-SMC subunits. The two SMC subunits form a heterodimer with an ATPase head and hinge that are connected by long coiled coils. Isolation of ATPase mutants followed by comprehensive identification of suppressor mutations in SMC subunits that can bypass ATPase defects was performed. Locations and properties of mutant alleles reflect how ATPase activities could be compromised by structural adaptation. ATP-driven conformational changes may enhance DNA anchoring by the head, alter interactions of coiled coils at the head with other subunits for DNA to go through, and fold/extend coiled coils near break sites around midpoint to bring together DNA elements far from each other. The cohesin complex is required for sister chromatid cohesion and genome compaction. Cohesin coiled coils (CCs) can fold at break sites near midpoints to bring head and hinge domains, located at opposite ends of coiled coils, into proximity. Whether ATPase activities in the head play a role in this conformational change is yet to be known. Here, we dissected functions of cohesin ATPase activities in cohesin dynamics in Schizosaccharomyces pombe. Isolation and characterization of cohesin ATPase temperature-sensitive (ts) mutants indicate that both ATPase domains are required for proper chromosome segregation. Unbiased screening of spontaneous suppressor mutations rescuing the temperature lethality of cohesin ATPase mutants identified several suppressor hotspots in cohesin that located outside of ATPase domains. Then, we performed comprehensive saturation mutagenesis targeted to these suppressor hotspots. Large numbers of the identified suppressor mutations indicated several different ways to compensate for the ATPase mutants: 1) Substitutions to amino acids with smaller side chains in coiled coils at break sites around midpoints may enable folding and extension of coiled coils more easily; 2) substitutions to arginine in the DNA binding region of the head may enhance DNA binding; or 3) substitutions to hydrophobic amino acids in coiled coils, connecting the head and interacting with other subunits, may alter conformation of coiled coils close to the head. These results reflect serial structural changes in cohesin driven by its ATPase activities potentially for packaging DNAs.
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26
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Mattingly M, Seidel C, Muñoz S, Hao Y, Zhang Y, Wen Z, Florens L, Uhlmann F, Gerton JL. Mediator recruits the cohesin loader Scc2 to RNA Pol II-transcribed genes and promotes sister chromatid cohesion. Curr Biol 2022; 32:2884-2896.e6. [PMID: 35654035 PMCID: PMC9286023 DOI: 10.1016/j.cub.2022.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/07/2022] [Accepted: 05/09/2022] [Indexed: 11/25/2022]
Abstract
The ring-like cohesin complex plays an essential role in chromosome segregation, organization, and double-strand break repair through its ability to bring two DNA double helices together. Scc2 (NIPBL in humans) together with Scc4 functions as the loader of cohesin onto chromosomes. Chromatin adapters such as the RSC complex facilitate the localization of the Scc2-Scc4 cohesin loader. Here, we identify a broad range of Scc2-chromatin protein interactions that are evolutionarily conserved and reveal a role for one complex, Mediator, in the recruitment of the cohesin loader. We identified budding yeast Med14, a subunit of the Mediator complex, as a high copy suppressor of poor growth in Scc2 mutant strains. Physical and genetic interactions between Scc2 and Mediator are functionally substantiated in direct recruitment and cohesion assays. Depletion of Med14 results in defective sister chromatid cohesion and the decreased binding of Scc2 at RNA Pol II-transcribed genes. Previous work has suggested that Mediator, Nipbl, and cohesin connect enhancers and promoters of active mammalian genes. Our studies suggest an evolutionarily conserved fundamental role for Mediator in the direct recruitment of Scc2 to RNA Pol II-transcribed genes.
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Affiliation(s)
- Mark Mattingly
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chris Seidel
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Zhihui Wen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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27
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Justice M, Bryan AF, Limas JC, Cook JG, Dowen JM. Chromosomal localization of cohesin is differentially regulated by WIZ, WAPL, and G9a. BMC Genomics 2022; 23:337. [PMID: 35501690 PMCID: PMC9063240 DOI: 10.1186/s12864-022-08574-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cohesin complex is essential for proper chromosome structure and gene expression. Defects in cohesin subunits and regulators cause changes in cohesin complex dynamics and thereby alter three-dimensional genome organization. However, the molecular mechanisms that drive cohesin localization and function remain poorly understood. RESULTS In this study, we observe that loss of WIZ causes changes to cohesin localization that are distinct from loss of the known WIZ binding partner G9a. Whereas loss of WIZ uniformly increases cohesin levels on chromatin at known binding sites and leads to new, ectopic cohesin binding sites, loss of G9a does not. Ectopic cohesin binding on chromatin after the loss of WIZ occurs at regions that are enriched for activating histone modifications and transcription factors motifs. Furthermore, loss of WIZ causes changes in cohesin localization that are distinct from those observed by loss of WAPL, the canonical cohesin unloading factor. CONCLUSIONS The evidence presented here suggests that WIZ can function independently from its previously identified role with G9a and GLP in heterochromatin formation. Furthermore, while WIZ limits the levels and localization pattern of cohesin across the genome, it appears to function independently of WAPL-mediated cohesin unloading.
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Affiliation(s)
- Megan Justice
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Audra F Bryan
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Juanita C Limas
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jill M Dowen
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.
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28
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A walk through the SMC cycle: From catching DNAs to shaping the genome. Mol Cell 2022; 82:1616-1630. [PMID: 35477004 DOI: 10.1016/j.molcel.2022.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 02/02/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
SMC protein complexes are molecular machines that provide structure to chromosomes. These complexes bridge DNA elements and by doing so build DNA loops in cis and hold together the sister chromatids in trans. We discuss how drastic conformational changes allow SMC complexes to build such intricate DNA structures. The tight regulation of these complexes controls fundamental chromosomal processes such as transcription, recombination, repair, and mitosis.
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29
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Xu X, Kanai R, Wang L, Yanagida M. Single amino acid substitutions in hydrophobic cores at a head-coiled coil junction region of cohesin facilitate its release of DNA during anaphase. Open Biol 2022; 12:210275. [PMID: 35472286 PMCID: PMC9042573 DOI: 10.1098/rsob.210275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023] Open
Abstract
Cohesin holds sister chromatids together and is cleaved by separase/Cut1 to release DNA during the transition from mitotic metaphase to anaphase. The cohesin complex consists of heterodimeric structural maintenance of chromosomes (SMC) subunits (Psm1 and Psm3), which possess a head and a hinge, separated by long coiled coils. Non-SMC subunits (Rad21, Psc3 and Mis4) bind to the SMC heads. Kleisin/Rad21's N-terminal domain (Rad21-NTD) interacts with Psm3's head-coiled coil junction (Psm3-HCJ). Spontaneous mutations that rescued the cleavage defects in temperature-sensitive (ts) separase mutants were identified in the interaction interface, but the underlying mechanism is yet to be understood. Here, we performed site-directed random mutagenesis to introduce single amino acid substitutions in Psm3-HCJ and Rad21-NTD, and then identified 300 mutations that rescued the cohesin-releasing defects in a separase ts mutant. Mutational analysis indicated that the amino acids involved in hydrophobic cores (which may be in close contact) in Psm3-HCJ and Rad21-NTD are hotspots, since 80 mutations (approx. 27%) were mapped in these locations. Properties of these substitutions indicate that they destabilize the interaction between the Psm3 head and Rad21-NTD. Thus, they may facilitate sister chromatid separation in a cleavage-independent way through cohesin structural re-arrangement.
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Affiliation(s)
- Xingya Xu
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Ryuta Kanai
- Institute of Quantitative Biosciences, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Li Wang
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
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30
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van Schie JJM, de Lange J. The Interplay of Cohesin and the Replisome at Processive and Stressed DNA Replication Forks. Cells 2021; 10:3455. [PMID: 34943967 PMCID: PMC8700348 DOI: 10.3390/cells10123455] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex facilitates faithful chromosome segregation by pairing the sister chromatids after DNA replication until mitosis. In addition, cohesin contributes to proficient and error-free DNA replication. Replisome progression and establishment of sister chromatid cohesion are intimately intertwined processes. Here, we review how the key factors in DNA replication and cohesion establishment cooperate in unperturbed conditions and during DNA replication stress. We discuss the detailed molecular mechanisms of cohesin recruitment and the entrapment of replicated sister chromatids at the replisome, the subsequent stabilization of sister chromatid cohesion via SMC3 acetylation, as well as the role and regulation of cohesin in the response to DNA replication stress.
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Affiliation(s)
- Janne J. M. van Schie
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Job de Lange
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
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31
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Houlard M, Cutts EE, Shamim MS, Godwin J, Weisz D, Presser Aiden A, Lieberman Aiden E, Schermelleh L, Vannini A, Nasmyth K. MCPH1 inhibits Condensin II during interphase by regulating its SMC2-Kleisin interface. eLife 2021; 10:e73348. [PMID: 34850681 PMCID: PMC8673838 DOI: 10.7554/elife.73348] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Dramatic change in chromosomal DNA morphology between interphase and mitosis is a defining features of the eukaryotic cell cycle. Two types of enzymes, namely cohesin and condensin confer the topology of chromosomal DNA by extruding DNA loops. While condensin normally configures chromosomes exclusively during mitosis, cohesin does so during interphase. The processivity of cohesin's loop extrusion during interphase is limited by a regulatory factor called WAPL, which induces cohesin to dissociate from chromosomes via a mechanism that requires dissociation of its kleisin from the neck of SMC3. We show here that a related mechanism may be responsible for blocking condensin II from acting during interphase. Cells derived from patients affected by microcephaly caused by mutations in the MCPH1 gene undergo premature chromosome condensation. We show that deletion of Mcph1 in mouse embryonic stem cells unleashes an activity of condensin II that triggers formation of compact chromosomes in G1 and G2 phases, accompanied by enhanced mixing of A and B chromatin compartments, and this occurs even in the absence of CDK1 activity. Crucially, inhibition of condensin II by MCPH1 depends on the binding of a short linear motif within MCPH1 to condensin II's NCAPG2 subunit. MCPH1's ability to block condensin II's association with chromatin is abrogated by the fusion of SMC2 with NCAPH2, hence may work by a mechanism similar to cohesin. Remarkably, in the absence of both WAPL and MCPH1, cohesin and condensin II transform chromosomal DNAs of G2 cells into chromosomes with a solenoidal axis.
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Affiliation(s)
- Martin Houlard
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Erin E Cutts
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Muhammad S Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Medical Scientist Training Program, Baylor College of Medicine, Department of Bioengineering, Rice UniversityHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Jonathan Godwin
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Aviva Presser Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | | | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer ResearchLondonUnited Kingdom
- Human TechnopoleMilanItaly
| | - Kim Nasmyth
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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32
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The Cohesin Complex and Its Interplay with Non-Coding RNAs. Noncoding RNA 2021; 7:ncrna7040067. [PMID: 34707078 PMCID: PMC8552073 DOI: 10.3390/ncrna7040067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
The cohesin complex is a multi-subunit protein complex initially discovered for its role in sister chromatid cohesion. However, cohesin also has several other functions and plays important roles in transcriptional regulation, DNA double strand break repair, and chromosome architecture thereby influencing gene expression and development in organisms from yeast to man. While most of these functions rely on protein–protein interactions, post-translational protein, as well as DNA modifications, non-coding RNAs are emerging as additional players that facilitate and modulate the function or expression of cohesin and its individual components. This review provides a condensed overview about the architecture as well as the function of the cohesin complex and highlights its multifaceted interplay with both short and long non-coding RNAs.
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33
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Bauer BW, Davidson IF, Canena D, Wutz G, Tang W, Litos G, Horn S, Hinterdorfer P, Peters JM. Cohesin mediates DNA loop extrusion by a "swing and clamp" mechanism. Cell 2021; 184:5448-5464.e22. [PMID: 34624221 PMCID: PMC8563363 DOI: 10.1016/j.cell.2021.09.016] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/02/2021] [Accepted: 09/09/2021] [Indexed: 10/28/2022]
Abstract
Structural maintenance of chromosomes (SMC) complexes organize genome topology in all kingdoms of life and have been proposed to perform this function by DNA loop extrusion. How this process works is unknown. Here, we have analyzed how loop extrusion is mediated by human cohesin-NIPBL complexes, which enable chromatin folding in interphase cells. We have identified DNA binding sites and large-scale conformational changes that are required for loop extrusion and have determined how these are coordinated. Our results suggest that DNA is translocated by a spontaneous 50 nm-swing of cohesin's hinge, which hands DNA over to the ATPase head of SMC3, where upon binding of ATP, DNA is clamped by NIPBL. During this process, NIPBL "jumps ship" from the hinge toward the SMC3 head and might thereby couple the spontaneous hinge swing to ATP-dependent DNA clamping. These results reveal mechanistic principles of how cohesin-NIPBL and possibly other SMC complexes mediate loop extrusion.
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Affiliation(s)
- Benedikt W Bauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Daniel Canena
- Insitute for Biophysics, Johannes Kepler University Linz, Life Science Center, Gruberstrasse 40, 4020 Linz, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Gabriele Litos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Sabrina Horn
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Peter Hinterdorfer
- Insitute for Biophysics, Johannes Kepler University Linz, Life Science Center, Gruberstrasse 40, 4020 Linz, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC) Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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34
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Kawasumi R, Abe T, Psakhye I, Miyata K, Hirota K, Branzei D. Vertebrate CTF18 and DDX11 essential function in cohesion is bypassed by preventing WAPL-mediated cohesin release. Genes Dev 2021; 35:1368-1382. [PMID: 34503989 PMCID: PMC8494208 DOI: 10.1101/gad.348581.121] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/16/2021] [Indexed: 01/26/2023]
Abstract
The alternative PCNA loader containing CTF18-DCC1-CTF8 facilitates sister chromatid cohesion (SCC) by poorly defined mechanisms. Here we found that in DT40 cells, CTF18 acts complementarily with the Warsaw breakage syndrome DDX11 helicase in mediating SCC and proliferation. We uncover that the lethality and cohesion defects of ctf18 ddx11 mutants are associated with reduced levels of chromatin-bound cohesin and rescued by depletion of WAPL, a cohesin-removal factor. On the contrary, high levels of ESCO1/2 acetyltransferases that acetylate cohesin to establish SCC do not rescue ctf18 ddx11 phenotypes. Notably, the tight proximity of sister centromeres and increased anaphase bridges characteristic of WAPL-depleted cells are abrogated by loss of both CTF18 and DDX11 The results reveal that vertebrate CTF18 and DDX11 collaborate to provide sufficient amounts of chromatin-loaded cohesin available for SCC generation in the presence of WAPL-mediated cohesin-unloading activity. This process modulates chromosome structure and is essential for cellular proliferation in vertebrates.
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Affiliation(s)
- Ryotaro Kawasumi
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
| | - Takuya Abe
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ivan Psakhye
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
| | - Keiji Miyata
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Dana Branzei
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
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35
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Golov AK, Golova AV, Gavrilov AA, Razin SV. Sensitivity of cohesin-chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion. Epigenetics Chromatin 2021; 14:36. [PMID: 34321070 PMCID: PMC8320178 DOI: 10.1186/s13072-021-00411-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/19/2021] [Indexed: 12/18/2022] Open
Abstract
Cohesin is a key organizer of chromatin folding in eukaryotic cells. The two main activities of this ring-shaped protein complex are the maintenance of sister chromatid cohesion and the establishment of long-range DNA-DNA interactions through the process of loop extrusion. Although the basic principles of both cohesion and loop extrusion have been described, we still do not understand several crucial mechanistic details. One of such unresolved issues is the question of whether a cohesin ring topologically embraces DNA string(s) during loop extrusion. Here, we show that cohesin complexes residing on CTCF-occupied genomic sites in mammalian cells do not interact with DNA topologically. We assessed the stability of cohesin-dependent loops and cohesin association with chromatin in high-ionic-strength conditions in G1-synchronized HeLa cells. We found that increased salt concentration completely displaces cohesin from those genomic regions that correspond to CTCF-defined loop anchors. Unsurprisingly, CTCF-anchored cohesin loops also dissipate in these conditions. Because topologically engaged cohesin is considered to be salt resistant, our data corroborate a non-topological model of loop extrusion. We also propose a model of cohesin activity throughout the interphase, which essentially equates the termination of non-topological loop extrusion with topological loading of cohesin. This theoretical framework enables a parsimonious explanation of various seemingly contradictory experimental findings.
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Affiliation(s)
- Arkadiy K. Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Mental Health Research Center, Moscow, Russia
| | - Anastasia V. Golova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey A. Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V. Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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36
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Higashi TL, Pobegalov G, Tang M, Molodtsov MI, Uhlmann F. A Brownian ratchet model for DNA loop extrusion by the cohesin complex. eLife 2021; 10:e67530. [PMID: 34309513 PMCID: PMC8313234 DOI: 10.7554/elife.67530] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin's heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function.
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Affiliation(s)
- Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Georgii Pobegalov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Minzhe Tang
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Maxim I Molodtsov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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37
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Petela NJ, Gonzalez Llamazares A, Dixon S, Hu B, Lee BG, Metson J, Seo H, Ferrer-Harding A, Voulgaris M, Gligoris T, Collier J, Oh BH, Löwe J, Nasmyth KA. Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes. eLife 2021; 10:e67268. [PMID: 34259632 PMCID: PMC8279761 DOI: 10.7554/elife.67268] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/21/2021] [Indexed: 01/01/2023] Open
Abstract
Cohesin's association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being 'clamped' by Scc2 and ATP-dependent engagement of cohesin's Smc1 and Smc3 head domains. Scc2's replacement by Pds5 abrogates cohesin's ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1's ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin's coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1's hinge that alters how Scc2 and Pds5 interact with Smc1's hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin's hinge, which in turn requires coiled coil folding.
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Affiliation(s)
- Naomi J Petela
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | | | - Sarah Dixon
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Bin Hu
- Institute of Medical Sciences, University of AberdeenAberdeenUnited Kingdom
| | - Byung-Gil Lee
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Jean Metson
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Heekyo Seo
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and TechnologyDaejeonRepublic of Korea
| | | | | | - Thomas Gligoris
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - James Collier
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and TechnologyDaejeonRepublic of Korea
| | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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38
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Davidson IF, Peters JM. Genome folding through loop extrusion by SMC complexes. Nat Rev Mol Cell Biol 2021; 22:445-464. [PMID: 33767413 DOI: 10.1038/s41580-021-00349-7] [Citation(s) in RCA: 281] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 02/02/2023]
Abstract
Genomic DNA is folded into loops and topologically associating domains (TADs), which serve important structural and regulatory roles. It has been proposed that these genomic structures are formed by a loop extrusion process, which is mediated by structural maintenance of chromosomes (SMC) protein complexes. Recent single-molecule studies have shown that the SMC complexes condensin and cohesin are indeed able to extrude DNA into loops. In this Review, we discuss how the loop extrusion hypothesis can explain key features of genome architecture; cellular functions of loop extrusion, such as separation of replicated DNA molecules, facilitation of enhancer-promoter interactions and immunoglobulin gene recombination; and what is known about the mechanism of loop extrusion and its regulation, for example, by chromatin boundaries that depend on the DNA binding protein CTCF. We also discuss how the loop extrusion hypothesis has led to a paradigm shift in our understanding of both genome architecture and the functions of SMC complexes.
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Affiliation(s)
- Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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39
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Li J, Pertsinidis A. New insights into promoter-enhancer communication mechanisms revealed by dynamic single-molecule imaging. Biochem Soc Trans 2021; 49:1299-1309. [PMID: 34060610 PMCID: PMC8325597 DOI: 10.1042/bst20200963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/10/2023]
Abstract
Establishing cell-type-specific gene expression programs relies on the action of distal enhancers, cis-regulatory elements that can activate target genes over large genomic distances - up to Mega-bases away. How distal enhancers physically relay regulatory information to target promoters has remained a mystery. Here, we review the latest developments and insights into promoter-enhancer communication mechanisms revealed by live-cell, real-time single-molecule imaging approaches.
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Affiliation(s)
- Jieru Li
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, NY 10065, USA
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40
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Henrikus SS, Costa A. Towards a Structural Mechanism for Sister Chromatid Cohesion Establishment at the Eukaryotic Replication Fork. BIOLOGY 2021; 10:466. [PMID: 34073213 PMCID: PMC8229022 DOI: 10.3390/biology10060466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022]
Abstract
Cohesion between replicated chromosomes is essential for chromatin dynamics and equal segregation of duplicated genetic material. In the G1 phase, the ring-shaped cohesin complex is loaded onto duplex DNA, enriching at replication start sites, or "origins". During the same phase of the cell cycle, and also at the origin sites, two MCM helicases are loaded as symmetric double hexamers around duplex DNA. During the S phase, and through the action of replication factors, cohesin switches from encircling one parental duplex DNA to topologically enclosing the two duplicated DNA filaments, which are known as sister chromatids. Despite its vital importance, the structural mechanism leading to sister chromatid cohesion establishment at the replication fork is mostly elusive. Here we review the current understanding of the molecular interactions between the replication machinery and cohesin, which support sister chromatid cohesion establishment and cohesin function. In particular, we discuss how cryo-EM is shedding light on the mechanisms of DNA replication and cohesin loading processes. We further expound how frontier cryo-EM approaches, combined with biochemistry and single-molecule fluorescence assays, can lead to understanding the molecular basis of sister chromatid cohesion establishment at the replication fork.
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Affiliation(s)
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
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41
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Kriz AJ, Colognori D, Sunwoo H, Nabet B, Lee JT. Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation. Mol Cell 2021; 81:1970-1987.e9. [PMID: 33725485 PMCID: PMC8106664 DOI: 10.1016/j.molcel.2021.02.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022]
Abstract
Depletion of architectural factors globally alters chromatin structure but only modestly affects gene expression. We revisit the structure-function relationship using the inactive X chromosome (Xi) as a model. We investigate cohesin imbalances by forcing its depletion or retention using degron-tagged RAD21 (cohesin subunit) or WAPL (cohesin release factor). Cohesin loss disrupts the Xi superstructure, unveiling superloops between escapee genes with minimal effect on gene repression. By contrast, forced cohesin retention markedly affects Xi superstructure, compromises spreading of Xist RNA-Polycomb complexes, and attenuates Xi silencing. Effects are greatest at distal chromosomal ends, where looping contacts with the Xist locus are weakened. Surprisingly, cohesin loss creates an Xi superloop, and cohesin retention creates Xi megadomains on the active X chromosome. Across the genome, a proper cohesin balance protects against aberrant inter-chromosomal interactions and tempers Polycomb-mediated repression. We conclude that a balance of cohesin eviction and retention regulates X inactivation and inter-chromosomal interactions across the genome.
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Affiliation(s)
- Andrea J Kriz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - David Colognori
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hongjae Sunwoo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Behnam Nabet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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42
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Sakata R, Niwa K, Ugarte La Torre D, Gu C, Tahara E, Takada S, Nishiyama T. Opening of cohesin's SMC ring is essential for timely DNA replication and DNA loop formation. Cell Rep 2021; 35:108999. [PMID: 33909997 DOI: 10.1016/j.celrep.2021.108999] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/16/2021] [Accepted: 03/24/2021] [Indexed: 11/15/2022] Open
Abstract
The ring-shaped cohesin complex topologically binds to DNA to establish sister chromatid cohesion. This topological binding creates a structural obstacle to genome-wide chromosomal events, such as replication. Here, we examine how conformational changes in cohesin circumvent being an obstacle in human cells. We show that ATP hydrolysis-driven head disengagement, leading to the structural maintenance of chromosome (SMC) ring opening, is essential for the progression of DNA replication. Closure of the SMC ring stalls replication in a checkpoint-independent manner. The SMC ring opening also facilitates sister chromatid resolution and chromosome segregation in mitosis. Single-molecule analyses reveal that forced closure of the SMC ring suppresses the translocation of cohesin on DNA as well as the formation of stable DNA loops. Our results suggest that the ATP hydrolysis-driven SMC ring opening makes topologically bound cohesin dynamic on DNA to achieve replication-dependent cohesion in the S phase and to resolve cohesion in mitosis. Thus, the SMC ring opening could be a fundamental mechanism to modulate both cohesion and higher-order genome structure.
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Affiliation(s)
- Ryota Sakata
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kyoma Niwa
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Diego Ugarte La Torre
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8501, Japan
| | - Chenyang Gu
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8501, Japan
| | - Eri Tahara
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8501, Japan
| | - Tomoko Nishiyama
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
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43
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Pongubala JMR, Murre C. Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development. Front Immunol 2021; 12:633825. [PMID: 33854505 PMCID: PMC8039525 DOI: 10.3389/fimmu.2021.633825] [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: 11/26/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Higher-order spatial organization of the genome into chromatin compartments (permissive and repressive), self-associating domains (TADs), and regulatory loops provides structural integrity and offers diverse gene regulatory controls. In particular, chromatin regulatory loops, which bring enhancer and associated transcription factors in close spatial proximity to target gene promoters, play essential roles in regulating gene expression. The establishment and maintenance of such chromatin loops are predominantly mediated involving CTCF and the cohesin machinery. In recent years, significant progress has been made in revealing how loops are assembled and how they modulate patterns of gene expression. Here we will discuss the mechanistic principles that underpin the establishment of three-dimensional (3D) chromatin structure and how changes in chromatin structure relate to alterations in gene programs that establish immune cell fate.
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Affiliation(s)
| | - Cornelis Murre
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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44
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Carico ZM, Stefan HC, Justice M, Yimit A, Dowen JM. A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression. PLoS Genet 2021; 17:e1009435. [PMID: 33760811 PMCID: PMC7990204 DOI: 10.1371/journal.pgen.1009435] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/20/2021] [Indexed: 12/21/2022] Open
Abstract
The cohesin complex spatially organizes interphase chromatin by bringing distal genomic loci into close physical proximity, looping out the intervening DNA. Mutation of cohesin complex subunits is observed in cancer and developmental disorders, but the mechanisms through which these mutations may contribute to disease remain poorly understood. Here, we investigate a recurrent missense mutation to the hinge domain of the cohesin subunit SMC1A, observed in acute myeloid leukemia. Engineering this mutation into murine embryonic stem cells caused widespread changes in gene expression, including dysregulation of the pluripotency gene expression program. This mutation reduced cohesin levels at promoters and enhancers, decreased DNA loops and interactions across short genomic distances, and weakened insulation at CTCF-mediated DNA loops. These findings provide insight into how altered cohesin function contributes to disease and identify a requirement for the cohesin hinge domain in three-dimensional chromatin structure.
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Affiliation(s)
- Zachary M. Carico
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Holden C. Stefan
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Megan Justice
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Askar Yimit
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jill M. Dowen
- Cancer Epigenetics Training Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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45
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Liu NQ, Maresca M, van den Brand T, Braccioli L, Schijns MMGA, Teunissen H, Bruneau BG, Nora EP, de Wit E. WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation. Nat Genet 2021; 53:100-109. [PMID: 33318687 PMCID: PMC7610352 DOI: 10.1038/s41588-020-00744-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/27/2020] [Indexed: 01/28/2023]
Abstract
The cohesin complex has an essential role in maintaining genome organization. However, its role in gene regulation remains largely unresolved. Here we report that the cohesin release factor WAPL creates a pool of free cohesin, in a process known as cohesin turnover, which reloads it to cell-type-specific binding sites. Paradoxically, stabilization of cohesin binding, following WAPL ablation, results in depletion of cohesin from these cell-type-specific regions, loss of gene expression and differentiation. Chromosome conformation capture experiments show that cohesin turnover is important for maintaining promoter-enhancer loops. Binding of cohesin to cell-type-specific sites is dependent on the pioneer transcription factors OCT4 (POU5F1) and SOX2, but not NANOG. We show the importance of cohesin turnover in controlling transcription and propose that a cycle of cohesin loading and off-loading, instead of static cohesin binding, mediates promoter and enhancer interactions critical for gene regulation.
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Affiliation(s)
- Ning Qing Liu
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michela Maresca
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Teun van den Brand
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Luca Braccioli
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marijne M G A Schijns
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Elphѐge P Nora
- Gladstone Institutes, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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46
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Cutts EE, Vannini A. Condensin complexes: understanding loop extrusion one conformational change at a time. Biochem Soc Trans 2020; 48:2089-2100. [PMID: 33005926 PMCID: PMC7609036 DOI: 10.1042/bst20200241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Condensin and cohesin, both members of the structural maintenance of chromosome (SMC) family, contribute to the regulation and structure of chromatin. Recent work has shown both condensin and cohesin extrude DNA loops and most likely work via a conserved mechanism. This review focuses on condensin complexes, highlighting recent in vitro work characterising DNA loop formation and protein structure. We discuss similarities between condensin and cohesin complexes to derive a possible mechanistic model, as well as discuss differences that exist between the different condensin isoforms found in higher eukaryotes.
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Affiliation(s)
- Erin E. Cutts
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, U.K
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, U.K
- Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy
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Zuilkoski CM, Skibbens RV. PCNA promotes context-specific sister chromatid cohesion establishment separate from that of chromatin condensation. Cell Cycle 2020; 19:2436-2450. [PMID: 32926661 PMCID: PMC7553509 DOI: 10.1080/15384101.2020.1804221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022] Open
Abstract
Cellular genomes undergo various structural changes that include cis tethering (the tethering together of two loci within a single DNA molecule), which promotes chromosome condensation and transcriptional activation, and trans tethering (the tethering together of two DNA molecules), which promotes sister chromatid cohesion and DNA repair. The protein complex termed cohesin promotes both cis and trans forms of DNA tethering, but the extent to which these cohesin functions occur in temporally or spatially defined contexts remains largely unknown. Prior studies indicate that DNA polymerase sliding clamp PCNA recruits cohesin acetyltransferase Eco1, suggesting that sister chromatid cohesion is established in the context of the DNA replication fork. In support of this model, elevated levels of PCNA rescue the temperature growth and cohesion defects exhibited by eco1 mutant cells. Here, we test whether Eco1-dependent chromatin condensation is also promoted in the context of this DNA replication fork component. Our results reveal that overexpressed PCNA does not promote DNA condensation in eco1 mutant cells, even though Smc3 acetylation levels are increased. We further provide evidence that replication fork-associated E3 ligase impacts on Eco1 are more complex that previously described. In combination, the data suggests that Eco1 acetylates Smc3 and thus promotes sister chromatid cohesion in context of the DNA replication fork, whereas a distinct cohesin population participates in chromatin condensation outside the context of the DNA replication fork.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, 18015, Bethlehem, Pennsylvania, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, 18015, Bethlehem, Pennsylvania, USA
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48
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Kong M, Cutts EE, Pan D, Beuron F, Kaliyappan T, Xue C, Morris EP, Musacchio A, Vannini A, Greene EC. Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA. Mol Cell 2020; 79:99-114.e9. [PMID: 32445620 PMCID: PMC7335352 DOI: 10.1016/j.molcel.2020.04.026] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/08/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022]
Abstract
Structural maintenance of chromosomes (SMC) complexes are essential for genome organization from bacteria to humans, but their mechanisms of action remain poorly understood. Here, we characterize human SMC complexes condensin I and II and unveil the architecture of the human condensin II complex, revealing two putative DNA-entrapment sites. Using single-molecule imaging, we demonstrate that both condensin I and II exhibit ATP-dependent motor activity and promote extensive and reversible compaction of double-stranded DNA. Nucleosomes are incorporated into DNA loops during compaction without being displaced from the DNA, indicating that condensin complexes can readily act upon nucleosome-bound DNA molecules. These observations shed light on critical processes involved in genome organization in human cells.
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Affiliation(s)
- Muwen Kong
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Erin E Cutts
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Dongqing Pan
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Thangavelu Kaliyappan
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK; Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Shi Z, Gao H, Bai XC, Yu H. Cryo-EM structure of the human cohesin-NIPBL-DNA complex. Science 2020; 368:1454-1459. [PMID: 32409525 DOI: 10.1126/science.abb0981] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2023]
Abstract
As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo-electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72-base pair DNA. NIPBL and DNA promote the engagement of cohesin's ATPase head domains and ATP binding. The hinge domains of cohesin adopt an "open washer" conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin.
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Affiliation(s)
- Zhubing Shi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Haishan Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongtao Yu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
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Abstract
Structural Maintenance of Chromosomes (SMCs) are part of a large family of ring complexes that participates in a number of DNA transactions. Among SMCs, SMC1A gene is unique. It encodes a subunit of the cohesin-core complex that tethers sister chromatids together to ensure correct chromosome segregation in both mitosis and meiosis. As a member of the cohesin ring, SMC1A takes part in gene transcription regulation and genome organization; and it participates in the DNA Damage Repair (DDR) pathway, being phosphorylated by Ataxia Telangiectasia Mutated (ATM) and Ataxia Telangiectasia and Rad3 Related (ATR) threonine/serine kinases. It is also a component of the Recombination protein complex (RC-1) involved in DNA repair by recombination. SMC1A pathogenic variants have been described in Cornelia de Lange syndrome (CdLS), a human rare disease, and recently SMC1A variants have been associated with epilepsy or resembling Rett syndrome phenotype. Finally, SMC1A variants have been identified in several human cancers. In this review, our current knowledge of the SMC1A gene has been summarized.
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Affiliation(s)
- Antonio Musio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Pisa, Italy.
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