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Kim J, Wang H, Ercan S. Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans. Genome Res 2025; 35:1108-1123. [PMID: 40210441 PMCID: PMC12047539 DOI: 10.1101/gr.279365.124] [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: 03/18/2024] [Accepted: 02/15/2025] [Indexed: 04/12/2025]
Abstract
In mammals, cohesin and CTCF organize the 3D genome into topologically associating domains (TADs) to regulate communication between cis-regulatory elements. Many organisms, including S. cerevisiae, C. elegans, and A. thaliana contain cohesin but lack CTCF. Here, we used C. elegans to investigate the function of cohesin in 3D genome organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features called "fountains," which have also been reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20-40 kb in C. elegans Hi-C analysis upon cohesin and WAPL-1 depletion supports the idea that cohesin is preferentially loaded at sites bound by the C. elegans ortholog of NIPBL and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains suggest that cohesin processivity is unequal on each side, possibly owing to collision with cohesin loaded from surrounding sites. The putative cohesin loading sites are closest to active enhancers, and fountain strength is associated with transcription. Compared with mammals, the average processivity of C. elegans cohesin is about 10-fold shorter, and the binding of NIPBL ortholog does not depend on cohesin. We propose that preferential loading and loop extrusion by cohesin is an evolutionarily conserved mechanism that regulates the 3D interactions of enhancers in animal genomes.
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Affiliation(s)
- Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Haoyu Wang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA
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2
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Buka K, Parteka-Tojek Z, Agarwal A, Denkiewicz M, Korsak S, Chiliński M, Banecki KH, Plewczynski D. Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes. Commun Biol 2025; 8:437. [PMID: 40082674 PMCID: PMC11906747 DOI: 10.1038/s42003-025-07847-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: 06/14/2024] [Accepted: 02/27/2025] [Indexed: 03/16/2025] Open
Abstract
Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step, allowing genome-wide identification of chromatin contacts mediated by a protein of interest. In mammalian cells, cohesin protein complex is one of the major players in the establishment of chromatin loops. We present an improved cohesin HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show that a dual chromatin fixation method compared to the standard formaldehyde-only method, results in a substantially better signal-to-noise ratio, increased ChIP efficiency and improved detection of chromatin loops and architectural stripes. Additionally, we propose an automated pipeline called nf-HiChIP ( https://github.com/SFGLab/hichip-nf-pipeline ) for processing HiChIP samples starting from raw sequencing reads data and ending with a set of significant chromatin interactions (loops), which allows efficient and timely analysis of multiple samples in parallel, without requiring additional ChIP-seq experiments. Finally, using advanced approaches for biophysical modelling and stripe calling we generate accurate loop extrusion polymer models for a region of interest and provide a detailed picture of architectural stripes, respectively.
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Affiliation(s)
- Karolina Buka
- University of Warsaw, Centre of New Technologies, Laboratory of Functional and Structural Genomics, Warsaw, Poland.
| | - Zofia Parteka-Tojek
- University of Warsaw, Centre of New Technologies, Laboratory of Functional and Structural Genomics, Warsaw, Poland
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Laboratory of Bioinformatics and Computational Genomics, Warsaw, Poland
| | - Abhishek Agarwal
- University of Warsaw, Centre of New Technologies, Laboratory of Functional and Structural Genomics, Warsaw, Poland
| | - Michał Denkiewicz
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Laboratory of Bioinformatics and Computational Genomics, Warsaw, Poland
| | - Sevastianos Korsak
- University of Warsaw, Centre of New Technologies, Laboratory of Functional and Structural Genomics, Warsaw, Poland
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Laboratory of Bioinformatics and Computational Genomics, Warsaw, Poland
| | - Mateusz Chiliński
- University of Warsaw, Centre of New Technologies, Laboratory of Functional and Structural Genomics, Warsaw, Poland
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Laboratory of Bioinformatics and Computational Genomics, Warsaw, Poland
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Krzysztof H Banecki
- University of Warsaw, Centre of New Technologies, Laboratory of Functional and Structural Genomics, Warsaw, Poland
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Laboratory of Bioinformatics and Computational Genomics, Warsaw, Poland
| | - Dariusz Plewczynski
- University of Warsaw, Centre of New Technologies, Laboratory of Functional and Structural Genomics, Warsaw, Poland.
- Warsaw University of Technology, Faculty of Mathematics and Information Science, Laboratory of Bioinformatics and Computational Genomics, Warsaw, Poland.
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3
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Wang G, Fang K, Shang Y, Zhou X, Shao Q, Li S, Wang P, Chen CD, Zhang L, Wang S. Testis-Specific PDHA2 Is Required for Proper Meiotic Recombination and Chromosome Organisation During Spermatogenesis. Cell Prolif 2025:e70003. [PMID: 39973374 DOI: 10.1111/cpr.70003] [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: 09/20/2024] [Revised: 01/16/2025] [Accepted: 02/05/2025] [Indexed: 02/21/2025] Open
Abstract
Proper segregation of homologous chromosomes during meiosis requires crossovers that are tightly regulated by the chromosome structure. PDHA2 is the testis-specific paralog of PDHA1, a core subunit of pyruvate dehydrogenase. However, its role during spermatogenesis is unclear. We show that PDHA2 knockout results in male infertility in mice, but meiotic DSBs in spermatocytes occur normally and are efficiently repaired. Detailed analysis reveals that mid/late recombination intermediates are moderately reduced, resulting in fewer crossovers and many chromosomes without a crossover. Furthermore, defective chromosome structure is observed, including aberrant histone modifications, defective chromosome ends, precocious release of REC8 from chromosomes and fragmented chromosome axes after pachytene. These defects contribute to the failure of pyruvate conversion to acetyl-CoA, resulting in decreased acetyl-CoA and precursors for metabolites and energy in the absence of PDHA2. These findings reveal the important functions of PDHA2 in ensuring proper crossover formation and in modulating chromosome structure during spermatogenesis.
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Affiliation(s)
- Guoqiang Wang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Kailun Fang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yongliang Shang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Xu Zhou
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Qiqi Shao
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
| | - Si Li
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Ping Wang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Liangran Zhang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Shunxin Wang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong, China
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4
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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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5
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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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6
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Alonso-Gil D, Losada A. NIPBL and cohesin: new take on a classic tale. Trends Cell Biol 2023; 33:860-871. [PMID: 37062615 DOI: 10.1016/j.tcb.2023.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023]
Abstract
Cohesin folds the genome in dynamic chromatin loops and holds the sister chromatids together. NIPBLScc2 is currently considered the cohesin loader, a role that may need reevaluation. NIPBL activates the cohesin ATPase, which is required for topological entrapment of sister DNAs and to fuel DNA loop extrusion, but is not required for chromatin association. Mechanistic dissection of these processes suggests that both NIPBL and the cohesin STAG subunit bind DNA. NIPBL also regulates conformational switches of the complex. Interactions of NIPBL with chromatin factors, including remodelers, replication proteins, and the transcriptional machinery, affect cohesin loading and distribution. Here, we discuss recent research addressing how NIPBL modulates cohesin activities and how its mutation causes a developmental disorder, Cornelia de Lange Syndrome (CdLS).
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Affiliation(s)
- Dácil Alonso-Gil
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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7
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Elias M, Gani S, Lerner Y, Yamin K, Tor C, Patel A, Matityahu A, Dessau M, Qvit N, Onn I. Developing a peptide to disrupt cohesin head domain interactions. iScience 2023; 26:107498. [PMID: 37664609 PMCID: PMC10470313 DOI: 10.1016/j.isci.2023.107498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
Cohesin mediates the 3-D structure of chromatin and is involved in maintaining genome stability and function. The cohesin core comprises Smc1 and Smc3, elongated-shaped proteins that dimerize through globular domains at their edges, called head and hinge. ATP binding to the Smc heads induces their dimerization and the formation of two active sites, while ATP hydrolysis results in head disengagement. This ATPase cycle is essential for driving cohesin activity. We report on the development of the first cohesin-inhibiting peptide (CIP). The CIP binds Smc3 in vitro and inhibits the ATPase activity of the holocomplex. Treating yeast cells with the CIP prevents cohesin's tethering activity and, interestingly, leads to the accumulation of cohesin on chromatin. CIP3 also affects cohesin activity in human cells. Altogether, we demonstrate the power of peptides to inhibit cohesin in cells and discuss the potential application of CIPs as a therapeutic approach.
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Affiliation(s)
- Maria Elias
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Samar Gani
- Protein-Protein Interactions Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yana Lerner
- Protein-Protein Interactions Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Katreen Yamin
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Chen Tor
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Adarsh Patel
- The Lab for Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Moshe Dessau
- The Lab for Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Nir Qvit
- Protein-Protein Interactions Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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8
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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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9
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Singh AK, Chen Q, Nguyen C, Meerzaman D, Singer DS. Cohesin regulates alternative splicing. SCIENCE ADVANCES 2023; 9:eade3876. [PMID: 36857449 PMCID: PMC9977177 DOI: 10.1126/sciadv.ade3876] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Cohesin, a trimeric complex that establishes sister chromatid cohesion, has additional roles in chromatin organization and transcription. We report that among those roles is the regulation of alternative splicing through direct interactions and in situ colocalization with splicing factors. Degradation of cohesin results in marked changes in splicing, independent of its effects on transcription. Introduction of a single cohesin point mutation in embryonic stem cells alters splicing patterns, demonstrating causality. In primary human acute myeloid leukemia, mutations in cohesin are highly correlated with distinct patterns of alternative splicing. Cohesin also directly interacts with BRD4, another splicing regulator, to generate a pattern of splicing that is distinct from either factor alone, documenting their functional interaction. These findings identify a role for cohesin in regulating alternative splicing in both normal and leukemic cells and provide insights into the role of cohesin mutations in human disease.
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Affiliation(s)
- Amit K. Singh
- Experimental Immunology Branch, Center for Cancer Research, Bethesda, MD, USA
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Qingrong Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Cu Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
| | - Dinah S. Singer
- Experimental Immunology Branch, Center for Cancer Research, Bethesda, MD, USA
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
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10
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Minamino M, Bouchoux C, Canal B, Diffley JFX, Uhlmann F. A replication fork determinant for the establishment of sister chromatid cohesion. Cell 2023; 186:837-849.e11. [PMID: 36693376 DOI: 10.1016/j.cell.2022.12.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/08/2022] [Accepted: 12/22/2022] [Indexed: 01/24/2023]
Abstract
Concomitant with DNA replication, the chromosomal cohesin complex establishes cohesion between newly replicated sister chromatids. Cohesion establishment requires acetylation of conserved cohesin lysine residues by Eco1 acetyltransferase. Here, we explore how cohesin acetylation is linked to DNA replication. Biochemical reconstitution of replication-coupled cohesin acetylation reveals that transient DNA structures, which form during DNA replication, control the acetylation reaction. As polymerases complete lagging strand replication, strand displacement synthesis produces DNA flaps that are trimmed to result in nicked double-stranded DNA. Both flaps and nicks stimulate cohesin acetylation, while subsequent nick ligation to complete Okazaki fragment maturation terminates the acetylation reaction. A flapped or nicked DNA substrate constitutes a transient molecular clue that directs cohesin acetylation to a window behind the replication fork, next to where cohesin likely entraps both sister chromatids. Our results provide an explanation for how DNA replication is linked to sister chromatid cohesion establishment.
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Affiliation(s)
- Masashi Minamino
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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11
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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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12
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Wu Z, Wang L, Wang X, Sun Y, Li H, Zhang Z, Ren C, Zhang X, Li S, Lu J, Xu L, Yue X, Hong Y, Li Q, Zhu H, Gong Y, Gao C, Hu H, Gao L, Liang X, Ma C. cccDNA Surrogate MC-HBV-Based Screen Identifies Cohesin Complex as a Novel HBV Restriction Factor. Cell Mol Gastroenterol Hepatol 2022; 14:1177-1198. [PMID: 35987451 PMCID: PMC9579331 DOI: 10.1016/j.jcmgh.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV), existing as a stable minichromosome in the hepatocyte, is responsible for persistent HBV infection. Maintenance and sustained replication of cccDNA require its interaction with both viral and host proteins. However, the cccDNA-interacting host factors that limit HBV replication remain elusive. METHODS Minicircle HBV (MC-HBV), a recombinant cccDNA, was constructed based on chimeric intron and minicircle DNA technology. By mass spectrometry based on pull-down with biotinylated MC-HBV, the cccDNA-hepatocyte interaction profile was mapped. HBV replication was assessed in different cell models that support cccDNA formation. RESULTS MC-HBV supports persistent HBV replication and mimics the cccDNA minichromosome. The MC-HBV-based screen identified cohesin complex as a cccDNA binding host factor, leading to reduced HBV replication. Mechanistically, with the help of CCCTC-binding factor (CTCF), which has specific binding sites on cccDNA, cohesin loads on cccDNA and reshapes cccDNA confirmation to prevent RNA polymerase II enrichment. Interestingly, HBV X protein transcriptionally reduces structural maintenance of chromosomes complex expression to partially relieve the inhibitory role of the cohesin complex on HBV replication. CONCLUSIONS Our data not only provide a feasible approach to explore cccDNA-binding factors, but also identify cohesin/CTCF complex as a critical host restriction factor for cccDNA-driven HBV replication. These findings provide a novel insight into cccDNA-host interaction and targeted therapeutic intervention for HBV infection.
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Affiliation(s)
- Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Liyuan Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xin Wang
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Yang Sun
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Haoran Li
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Zhaoying Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Caiyue Ren
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohui Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Shuangjie Li
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Jinghui Lu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Leiqi Xu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Xuetian Yue
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Yue Hong
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Qiang Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yaoqin Gong
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chengjiang Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Huili Hu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China,Correspondence Address correspondence to: Chunhong Ma, PhD, Key Laboratory for Experimental Teratology of Ministry of Education and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012 China.
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13
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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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14
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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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15
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Psakhye I, Branzei D. SMC complexes are guarded by the SUMO protease Ulp2 against SUMO-chain-mediated turnover. Cell Rep 2021; 36:109485. [PMID: 34348159 DOI: 10.1016/j.celrep.2021.109485] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/07/2021] [Accepted: 07/07/2021] [Indexed: 01/01/2023] Open
Abstract
Structural maintenance of chromosomes (SMCs) complexes, cohesin, condensin, and Smc5/6, are essential for viability and participate in multiple processes, including sister chromatid cohesion, chromosome condensation, and DNA repair. Here we show that SUMO chains target all three SMC complexes and are antagonized by the SUMO protease Ulp2 to prevent their turnover. We uncover that the essential role of the cohesin-associated subunit Pds5 is to counteract SUMO chains jointly with Ulp2. Importantly, fusion of Ulp2 to kleisin Scc1 supports viability of PDS5 null cells and protects cohesin from proteasomal degradation mediated by the SUMO-targeted ubiquitin ligase Slx5/Slx8. The lethality of PDS5-deleted cells can also be bypassed by simultaneous loss of the proliferating cell nuclear antigen (PCNA) unloader, Elg1, and the cohesin releaser, Wpl1, but only when Ulp2 is functional. Condensin and Smc5/6 complex are similarly guarded by Ulp2 against unscheduled SUMO chain assembly, which we propose to time the availability of SMC complexes on chromatin.
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Affiliation(s)
- Ivan Psakhye
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy.
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16
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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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17
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Pathania A, Liu W, Matityahu A, Irudayaraj J, Onn I. Chromosome loading of cohesin depends on conserved residues in Scc3. Curr Genet 2021; 67:447-459. [PMID: 33404730 DOI: 10.1007/s00294-020-01150-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
Cohesin is essential for sister chromatid cohesion, which ensures equal segregation of the chromatids to daughter cells. However, the molecular mechanism by which cohesin mediates this function is elusive. Scc3, one of the four core subunits of cohesin, is vital to cohesin activity. However, the mechanism by which Scc3 contributes to the activity and identity of its functional domains is not fully understood. Here, we describe an in-frame five-amino acid insertion mutation after glutamic acid 704 (scc3-E704ins) in yeast Scc3, located in the middle of the second armadillo repeat. Mutated cohesin-scc3-E704ins complexes are unable to establish cohesion. Detailed molecular and genetic analyses revealed that the mutated cohesin has reduced affinity to the Scc2 loader. This inhibits its enrichment at centromeres and chromosomal arms. Mutant complexes show a slow diffusion rate in live cells suggesting that they induce a major conformational change in the complex. The analysis of systematic mutations in the insertion region of Scc3 revealed two conserved aspartic acid residues that are essential for the activity. The study offers a better understanding of the contribution of Scc3 to cohesin activity and the mechanism by which cohesin tethers the sister chromatids during the cell cycle.
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Affiliation(s)
- Anjali Pathania
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, P.O. Box 1589, 1311502, Safed, Israel
| | - Wenjie Liu
- Micro and Nanotechnology Laboratory, Department of Bioengineering, Beckman Institute, Carl Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Foundation Hospital, Mills Breast Cancer Institute, Urbana, IL, USA
| | - Avi Matityahu
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, P.O. Box 1589, 1311502, Safed, Israel
| | - Joseph Irudayaraj
- Micro and Nanotechnology Laboratory, Department of Bioengineering, Beckman Institute, Carl Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Foundation Hospital, Mills Breast Cancer Institute, Urbana, IL, USA
| | - Itay Onn
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, P.O. Box 1589, 1311502, Safed, Israel.
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18
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Rivas MA, Meydan C, Chin CR, Challman MF, Kim D, Bhinder B, Kloetgen A, Viny AD, Teater MR, McNally DR, Doane AS, Béguelin W, Fernández MTC, Shen H, Wang X, Levine RL, Chen Z, Tsirigos A, Elemento O, Mason CE, Melnick AM. Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Nat Immunol 2021; 22:240-253. [PMID: 33432228 PMCID: PMC7855695 DOI: 10.1038/s41590-020-00827-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 10/25/2020] [Indexed: 01/28/2023]
Abstract
During the germinal center (GC) reaction, B cells undergo extensive redistribution of cohesin complex and three-dimensional reorganization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown. Herein we report that homozygous deletion of Smc3, encoding the cohesin ATPase subunit, abrogated GC formation, while, in marked contrast, Smc3 haploinsufficiency resulted in GC hyperplasia, skewing of GC polarity and impaired plasma cell (PC) differentiation. Genome-wide chromosomal conformation and transcriptional profiling revealed defects in GC B cell terminal differentiation programs controlled by the lymphoma epigenetic tumor suppressors Tet2 and Kmt2d and failure of Smc3-haploinsufficient GC B cells to switch from B cell- to PC-defining transcription factors. Smc3 haploinsufficiency preferentially impaired the connectivity of enhancer elements controlling various lymphoma tumor suppressor genes, and, accordingly, Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression. Collectively, our data indicate a dose-dependent function for cohesin in humoral immunity to facilitate the B cell to PC phenotypic switch while restricting malignant transformation.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins/deficiency
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/deficiency
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/deficiency
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Gene Deletion
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Germinal Center/immunology
- Germinal Center/metabolism
- Germinal Center/pathology
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Immunity, Humoral
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice, Inbred C57BL
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Signal Transduction
- Cohesins
- Mice
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Affiliation(s)
- Martín A Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matt F Challman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daleum Kim
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Aaron D Viny
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matt R Teater
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dylan R McNally
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S Doane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Hao Shen
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiang Wang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Institute for Computational Medicine, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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19
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Maksimenko OG, Fursenko DV, Belova EV, Georgiev PG. CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers. Acta Naturae 2021; 13:31-46. [PMID: 33959385 PMCID: PMC8084297 DOI: 10.32607/actanaturae.11206] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.
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Affiliation(s)
- O. G. Maksimenko
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
| | | | - E. V. Belova
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
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20
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Collier JE, Lee BG, Roig MB, Yatskevich S, Petela NJ, Metson J, Voulgaris M, Gonzalez Llamazares A, Löwe J, Nasmyth KA. Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3. eLife 2020; 9:e59560. [PMID: 32930661 PMCID: PMC7492086 DOI: 10.7554/elife.59560] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/30/2020] [Indexed: 12/13/2022] Open
Abstract
In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are 'clamped' in a sub-compartment created by Scc2's association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion.
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Affiliation(s)
- James E Collier
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Byung-Gil Lee
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | - Naomi J Petela
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Jean Metson
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | | | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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21
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Ajam T, De I, Petkau N, Whelan G, Pena V, Eichele G. Alternative catalytic residues in the active site of Esco acetyltransferases. Sci Rep 2020; 10:9828. [PMID: 32555289 PMCID: PMC7300003 DOI: 10.1038/s41598-020-66795-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Cohesin is a protein complex whose core subunits, Smc1, Smc3, Scc1, and SA1/SA2 form a ring-like structure encircling the DNA. Cohesins play a key role in the expression, repair, and segregation of eukaryotic genomes. Following a catalytic mechanism that is insufficiently understood, Esco1 and Esco2 acetyltransferases acetylate the cohesin subunit Smc3, thereby inducing stabilization of cohesin on DNA. As a prerequisite for structure-guided investigation of enzymatic activity, we determine here the crystal structure of the mouse Esco2/CoA complex at 1.8 Å resolution. We reconstitute cohesin as tri- or tetrameric assemblies and use those as physiologically-relevant substrates for enzymatic assays in vitro. Furthermore, we employ cell-based complementation studies in mouse embryonic fibroblast deficient for Esco1 and Esco2, as a means to identify catalytically-important residues in vivo. These analyses demonstrate that D567/S566 and E491/S527, located on opposite sides of the murine Esco2 active site cleft, are critical for catalysis. Our experiments support a catalytic mechanism of acetylation where residues D567 and E491 are general bases that deprotonate the ε-amino group of lysine substrate, also involving two nearby serine residues - S566 and S527- that possess a proton relay function.
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Affiliation(s)
- Tahereh Ajam
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Inessa De
- Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Nikolai Petkau
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Gabriela Whelan
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Vladimir Pena
- Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Structural Biology Division, The Institute of Cancer Research, SW3 6JB, London, United Kingdom.
| | - Gregor Eichele
- Genes and Behavior Department, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
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22
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Muir KW, Li Y, Weis F, Panne D. The structure of the cohesin ATPase elucidates the mechanism of SMC-kleisin ring opening. Nat Struct Mol Biol 2020; 27:233-239. [PMID: 32066964 PMCID: PMC7100847 DOI: 10.1038/s41594-020-0379-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 01/13/2020] [Indexed: 01/26/2023]
Abstract
Genome regulation requires control of chromosome organization by SMC-kleisin complexes. The cohesin complex contains the Smc1 and Smc3 subunits that associate with the kleisin Scc1 to form a ring-shaped complex that can topologically engage chromatin to regulate chromatin structure. Release from chromatin involves opening of the ring at the Smc3-Scc1 interface in a reaction that is controlled by acetylation and engagement of the Smc ATPase head domains. To understand the underlying molecular mechanisms, we have determined the 3.2-Å resolution cryo-electron microscopy structure of the ATPγS-bound, heterotrimeric cohesin ATPase head module and the 2.1-Å resolution crystal structure of a nucleotide-free Smc1-Scc1 subcomplex from Saccharomyces cerevisiae and Chaetomium thermophilium. We found that ATP-binding and Smc1-Smc3 heterodimerization promote conformational changes within the ATPase that are transmitted to the Smc coiled-coil domains. Remodeling of the coiled-coil domain of Smc3 abrogates the binding surface for Scc1, thus leading to ring opening at the Smc3-Scc1 interface.
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Affiliation(s)
- Kyle W Muir
- European Molecular Biology Laboratory, Grenoble, France.
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Yan Li
- European Molecular Biology Laboratory, Grenoble, France
| | - Felix Weis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France.
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK.
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23
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Wutz G, Ladurner R, St Hilaire BG, Stocsits RR, Nagasaka K, Pignard B, Sanborn A, Tang W, Várnai C, Ivanov MP, Schoenfelder S, van der Lelij P, Huang X, Dürnberger G, Roitinger E, Mechtler K, Davidson IF, Fraser P, Lieberman-Aiden E, Peters JM. ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin STAG1 from WAPL. eLife 2020; 9:e52091. [PMID: 32065581 PMCID: PMC7054000 DOI: 10.7554/elife.52091] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/10/2020] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL. Although WAPL limits cohesin's chromatin residence time to minutes, it has been reported that some loops exist for hours. How these loops can persist is unknown. We show that during G1-phase, mammalian cells contain acetylated cohesinSTAG1 which binds chromatin for hours, whereas cohesinSTAG2 binds chromatin for minutes. Our results indicate that CTCF and the acetyltransferase ESCO1 protect a subset of cohesinSTAG1 complexes from WAPL, thereby enable formation of long and presumably long-lived loops, and that ESCO1, like CTCF, contributes to boundary formation in chromatin looping. Our data are consistent with a model of nested loop extrusion, in which acetylated cohesinSTAG1 forms stable loops between CTCF sites, demarcating the boundaries of more transient cohesinSTAG2 extrusion activity.
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Affiliation(s)
- Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Benoit Pignard
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Adrian Sanborn
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Csilla Várnai
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Miroslav P Ivanov
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
| | - Petra van der Lelij
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Xingfan Huang
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Departments of Computer Science and Computational and Applied Mathematics, Rice UniversityHoustonUnited States
- Departments of Computer Science and Genome Sciences, University of WashingtonSeattleUnited States
| | - Gerhard Dürnberger
- Institute of Molecular Biotechnology, Vienna Biocenter (VBC)ViennaAustria
| | | | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology, Vienna Biocenter (VBC)ViennaAustria
| | - Iain Finley Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research CampusCambridgeUnited Kingdom
- Department of Biological Science, Florida State UniversityTallahasseeUnited States
| | - Erez Lieberman-Aiden
- The Center for Genome Architecture, Baylor College of MedicineHoustonUnited States
- Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
- Center for Theoretical Biological Physics, Rice UniversityHoustonUnited States
- Departments of Computer Science and Computational and Applied Mathematics, Rice UniversityHoustonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech UniversityShanghaiChina
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
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24
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Morales C, Ruiz-Torres M, Rodríguez-Acebes S, Lafarga V, Rodríguez-Corsino M, Megías D, Cisneros DA, Peters JM, Méndez J, Losada A. PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection. J Biol Chem 2020; 295:146-157. [PMID: 31757807 PMCID: PMC6952610 DOI: 10.1074/jbc.ra119.011099] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
Cohesin is a chromatin-bound complex that mediates sister chromatid cohesion and facilitates long-range interactions through DNA looping. How the transcription and replication machineries deal with the presence of cohesin on chromatin remains unclear. The dynamic association of cohesin with chromatin depends on WAPL cohesin release factor (WAPL) and on PDS5 cohesin-associated factor (PDS5), which exists in two versions in vertebrate cells, PDS5A and PDS5B. Using genetic deletion in mouse embryo fibroblasts and a combination of CRISPR-mediated gene editing and RNAi-mediated gene silencing in human cells, here we analyzed the consequences of PDS5 depletion for DNA replication. We found that either PDS5A or PDS5B is sufficient for proper cohesin dynamics and that their simultaneous removal increases cohesin's residence time on chromatin and slows down DNA replication. A similar phenotype was observed in WAPL-depleted cells. Cohesin down-regulation restored normal replication fork rates in PDS5-deficient cells, suggesting that chromatin-bound cohesin hinders the advance of the replisome. We further show that PDS5 proteins are required to recruit WRN helicase-interacting protein 1 (WRNIP1), RAD51 recombinase (RAD51), and BRCA2 DNA repair associated (BRCA2) to stalled forks and that in their absence, nascent DNA strands at unprotected forks are degraded by MRE11 homolog double-strand break repair nuclease (MRE11). These findings indicate that PDS5 proteins participate in replication fork protection and also provide insights into how cohesin and its regulators contribute to the response to replication stress, a common feature of cancer cells.
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Affiliation(s)
- Carmen Morales
- Chromosome Dynamics Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Miguel Ruiz-Torres
- Chromosome Dynamics Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Vanesa Lafarga
- Genome Instability Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Miriam Rodríguez-Corsino
- Chromosome Dynamics Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - David A Cisneros
- Research Institute for Molecular Pathology (IMP), Campus Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Jan-Michael Peters
- Research Institute for Molecular Pathology (IMP), Campus Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Juan Méndez
- DNA Replication Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.
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25
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Elbatsh AMO, Kim E, Eeftens JM, Raaijmakers JA, van der Weide RH, García-Nieto A, Bravo S, Ganji M, Uit de Bos J, Teunissen H, Medema RH, de Wit E, Haering CH, Dekker C, Rowland BD. Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation. Mol Cell 2019; 76:724-737.e5. [PMID: 31629658 PMCID: PMC6900782 DOI: 10.1016/j.molcel.2019.09.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/17/2019] [Accepted: 09/13/2019] [Indexed: 01/19/2023]
Abstract
Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin's ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster than wild-type, both in vivo and in vitro. Whereas one site drives loop formation, the second site is involved in the formation of more stable higher-order Z loop structures. Using hyperactive condensin I, we reveal that condensin II is not intrinsically needed for the shortening of mitotic chromosomes. Condensin II rather is required for a straight chromosomal axis and enables faithful chromosome segregation by counteracting the formation of ultrafine DNA bridges. SMC complexes with distinct roles for each ATPase site likely reflect a universal principle that enables these molecular machines to intricately control chromosome architecture.
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Affiliation(s)
- Ahmed M O Elbatsh
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jorine M Eeftens
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jonne A Raaijmakers
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Robin H van der Weide
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alberto García-Nieto
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sol Bravo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jelmi Uit de Bos
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Benjamin D Rowland
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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26
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Lu Y, Chen Y, Cui Z, Xiong B. Distinct roles of cohesin acetyltransferases Esco1 and Esco2 in porcine oocyte meiosis I. Cell Cycle 2019; 18:2481-2494. [PMID: 31387516 PMCID: PMC6739052 DOI: 10.1080/15384101.2019.1651162] [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: 06/23/2019] [Revised: 07/09/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022] Open
Abstract
In mammalian cells, cohesin acetyltransferases Esco1 and Esco2 acetylate cohesin subunit Smc3 to establish chromosome cohesion, ensuring the accurate chromosome segregation. However, we have previously documented that both Esco1 and Esco2 have unique substrates and roles in mouse oocyte meiosis I to orchestrate the meiotic progression, but whether these functions are conserved among species is still not determined. Here, we used porcine oocytes as a model to illustrate that Esco1 and Esco2 exerted conserved functions during oocyte meiosis. We observed that Esco1 and Esco2 exhibited different localization patterns in porcine oocytes. Esco1 was localized to the spindle apparatus while Esco2 was distributed on the chromosomes. Depletion of Esco1 by siRNA microinjection caused the meiotic arrest by showing the reduced frequency of first polar body extrusion and defective spindle/chromosome structure. In addition, Esco1 bound to α-tubulin and was required for its acetylation level to maintain the microtubule dynamics. By contrast, depletion of Esco2 by siRNA microinjection resulted in the accelerated meiotic progression by displaying the precocious polar body extrusion and inactivation of spindle assembly checkpoint. Notably, Esco2 was shown to be associated with histone H4 for the acetylation of H4K16 to modulate the kinetochore function. Collectively, our data reveal that Esco1 and Esco2 perform distinct and conserved functions in oocytes to drive the meiotic progression beyond their canonical roles in the cohesion establishment.
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Affiliation(s)
- Yajuan Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ying Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhaokang Cui
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Bo Xiong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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27
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Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D. Extrusion without a motor: a new take on the loop extrusion model of genome organization. Nucleus 2019; 9:95-103. [PMID: 29300120 PMCID: PMC5973195 DOI: 10.1080/19491034.2017.1421825] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo “Non-equilibrium chromosome looping via molecular slip-links”, Physical Review Letters 119 138101 (2017)
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Affiliation(s)
- C A Brackley
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - J Johnson
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - D Michieletto
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - A N Morozov
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
| | - M Nicodemi
- b Dipartimento di Fisica , Universita' di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo , Naples , Italy
| | - P R Cook
- c Sir William Dunn School of Pathology , University of Oxford , South Parks Road, Oxford , OX1 3RE , UK
| | - D Marenduzzo
- a SUPA, School of Physics and Astronomy , University of Edinburgh , Peter Guthrie Tait Road, Edinburgh , EH9 3FD , UK
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28
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Racko D, Benedetti F, Dorier J, Stasiak A. Are TADs supercoiled? Nucleic Acids Res 2019; 47:521-532. [PMID: 30395328 PMCID: PMC6344874 DOI: 10.1093/nar/gky1091] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/22/2018] [Indexed: 12/13/2022] Open
Abstract
Topologically associating domains (TADs) are megabase-sized building blocks of interphase chromosomes in higher eukaryotes. TADs are chromosomal regions with increased frequency of internal interactions. On average a pair of loci separated by a given genomic distance contact each other 2–3 times more frequently when they are in the same TAD as compared to a pair of loci located in two neighbouring TADs. TADs are also functional blocks of chromosomes as enhancers and their cognate promoters are normally located in the same TAD, even if their genomic distance from each other can be as large as a megabase. The internal structure of TADs, causing their increased frequency of internal interactions, is not established yet. We survey here experimental studies investigating presence of supercoiling in interphase chromosomes. We also review numerical simulation studies testing whether transcription-induced supercoiling of chromatin fibres can explain how TADs are formed and how they can assure very efficient interactions between enhancers and their cognate promoters located in the same TAD.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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29
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Lu Y, Li S, Cui Z, Dai X, Zhang M, Miao Y, Zhou C, Ou X, Xiong B. The cohesion establishment factor Esco1 acetylates α-tubulin to ensure proper spindle assembly in oocyte meiosis. Nucleic Acids Res 2019; 46:2335-2346. [PMID: 29361031 PMCID: PMC5861441 DOI: 10.1093/nar/gky001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/02/2018] [Indexed: 12/18/2022] Open
Abstract
Esco1 has been reported to function as a cohesion establishment factor that mediates chromosome cohesion and segregation in mitotic cells. However, its exact roles in meiosis have not been clearly defined. Here, we document that Esco1 is expressed and localized to both the nucleus and cytoplasm during mouse oocyte meiotic maturation. Depletion of Esco1 by siRNA microinjection causes the meiotic progression arrest with a severe spindle abnormality and chromosome misalignment, which is coupled with a higher incidence of the erroneous kinetochore–microtubule attachments and activation of spindle assembly checkpoint. In addition, depletion of Esco1 leads to the impaired microtubule stability shown by the weakened resistance ability to the microtubule depolymerizing drug nocodazole and the decreased level of acetylated α-tubulin. Conversely, overexpression of Esco1 causes hyperacetylation of α-tubulin and spindle defects. Moreover, we find that Esco1 binds to α-tubulin and is required for its acetylation. The reduced acetylation level of α-tubulin in Esco1-depleted oocytes can be restored by the ectopic expression of exogenous wild-type Esco1 but not enzymatically dead Esco1-G768D. Purified wild-type Esco1 instead of mutant Esco1-G768D acetylates the synthesized peptide of α-tubulin in vitro. Collectively, our data assign a novel function to Esco1 as a microtubule regulator during oocyte meiotic maturation beyond its conventional role in chromosome cohesion.
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Affiliation(s)
- Yajuan Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Sen Li
- Fertility Preservation Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Zhaokang Cui
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoxin Dai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mianqun Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yilong Miao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Changyin Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xianghong Ou
- Fertility Preservation Laboratory, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Bo Xiong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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30
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Holzmann J, Politi AZ, Nagasaka K, Hantsche-Grininger M, Walther N, Koch B, Fuchs J, Dürnberger G, Tang W, Ladurner R, Stocsits RR, Busslinger GA, Novák B, Mechtler K, Davidson IF, Ellenberg J, Peters JM. Absolute quantification of cohesin, CTCF and their regulators in human cells. eLife 2019; 8:e46269. [PMID: 31204999 PMCID: PMC6606026 DOI: 10.7554/elife.46269] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022] Open
Abstract
The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells. In G1-phase, there are ~250,000 nuclear cohesin complexes, of which ~ 160,000 are chromatin-bound. Comparison with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time. We discuss the implications of these findings for how cohesin can contribute to genome organisation and cohesion.
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Affiliation(s)
- Johann Holzmann
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Antonio Z Politi
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | | | - Nike Walther
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Birgit Koch
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Johannes Fuchs
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Rene Ladurner
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Georg A Busslinger
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Béla Novák
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Gregor Mendel Institute, Austrian Academy of SciencesVienna Biocenter (VBC)ViennaAustria
| | - Iain Finley Davidson
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Medical University of ViennaViennaAustria
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31
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Braccioli L, de Wit E. CTCF: a Swiss-army knife for genome organization and transcription regulation. Essays Biochem 2019; 63:157-165. [PMID: 30940740 DOI: 10.1042/ebc20180069] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Orchestrating vertebrate genomes require a complex interplay between the linear composition of the genome and its 3D organization inside the nucleus. This requires the function of specialized proteins, able to tune various aspects of genome organization and gene regulation. The CCCTC-binding factor (CTCF) is a DNA binding factor capable of regulating not only the 3D genome organization, but also key aspects of gene expression, including transcription activation and repression, RNA splicing, and enhancer/promoter insulation. A growing body of evidence proposes that CTCF, together with cohesin contributes to DNA loop formation and 3D genome organization. CTCF binding sites are mutation hotspots in cancer, while mutations in CTCF itself lead to intellectual disabilities, emphasizing its importance in disease etiology. In this review we cover various aspects of CTCF function, revealing the polyvalence of this factor as a highly diversified tool for vertebrate genome organization and transcription regulation.
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Affiliation(s)
- Luca Braccioli
- Oncode Institute and Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Elzo de Wit
- Oncode Institute and Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
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32
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Mondal G, Stevers M, Goode B, Ashworth A, Solomon DA. A requirement for STAG2 in replication fork progression creates a targetable synthetic lethality in cohesin-mutant cancers. Nat Commun 2019; 10:1686. [PMID: 30975996 PMCID: PMC6459917 DOI: 10.1038/s41467-019-09659-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
Cohesin is a multiprotein ring that is responsible for cohesion of sister chromatids and formation of DNA loops to regulate gene expression. Genomic analyses have identified that the cohesin subunit STAG2 is frequently inactivated by mutations in cancer. However, the reason STAG2 mutations are selected during tumorigenesis and strategies for therapeutically targeting mutant cancer cells are largely unknown. Here we show that STAG2 is essential for DNA replication fork progression, whereby STAG2 inactivation in non-transformed cells leads to replication fork stalling and collapse with disruption of interaction between the cohesin ring and the replication machinery as well as failure to establish SMC3 acetylation. As a consequence, STAG2 mutation confers synthetic lethality with DNA double-strand break repair genes and increased sensitivity to select cytotoxic chemotherapeutic agents and PARP or ATR inhibitors. These studies identify a critical role for STAG2 in replication fork procession and elucidate a potential therapeutic strategy for cohesin-mutant cancers.
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Affiliation(s)
- Gourish Mondal
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Meredith Stevers
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Benjamin Goode
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, CA, 94158, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, CA, 94143, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA.
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Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders affecting the gastrointestinal tract. The incidence of IBD is increasing, with more cases occurring in developed countries. Multiple factors such as genetics, environmental changes, gut microbiota, and immune abnormalities have been associated with development of IBD. In recent years, it has become increasingly apparent that epigenetic modifications of chromatin and the manner in which chromatin is organized in the nucleus are additionally important elements that can influence responses induced by the factors described above, and may therefore contribute to the onset and pathogenesis of IBD. Epigenetics and chromatin organization regulate diverse functions that include maintenance of homeostasis in the intestinal epithelium, the development and differentiation of immune cells, and modulation of responses generated by the immune system to defend against potential pathogens. Furthermore, changes in epigenetic chromatin marks and in chromatin organization have now been linked to differential gene expression in IBD patient cells. Although direct evidence for a role of histone modifications in IBD is currently very limited, in this review, we summarize the links between various epigenetic modifications, the proteins that catalyze or recognize these modifications, and the development or progression of IBD in human and experimental IBD. We also discuss how epigenetics influence the organization of DNA contacts to regulate gene expression and the implications this may have for diagnosing and treating IBD.
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Affiliation(s)
- Greeshma Ray
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michelle S Longworth
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA,Address correspondence to: Michelle S. Longworth, 9500 Euclid Ave NC22, Cleveland, OH 44195 ()
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Voulgaris M, Gligoris TG. A Protocol for Assaying the ATPase Activity of Recombinant Cohesin Holocomplexes. Methods Mol Biol 2019; 2004:197-208. [PMID: 31147919 DOI: 10.1007/978-1-4939-9520-2_15] [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] [Indexed: 12/17/2023]
Abstract
Cohesin and other members of the structural maintenance of chromosomes (SMC)-kleisin family such as condensin and Smc5-6, as well as central players in genome function and structure such as topoisomerases, DNA and RNA polymerases, and DNA repair enzymes contain nucleotide binding domains (NBD) which bind and eventually cleave ATP. The released energy is harnessed in various ways by these enzymes in order to fulfill their essential functions. However, unlike other enzymes, Smc-kleisin complexes-well sized, elongated and multisubunit in nature-have only recently been purified as holocomplexes. This progress offers both the opportunity and the challenge to determine in detail the potency of the ATPase activity of these large protein assemblies-typically exceeding 0.5 MDa in molecular weight-and examine its mechanistic features. We describe here in further detail a combined comprehensive protocol which we have successfully employed before for assaying the ATPase activity of recombinant budding yeast cohesin holocomplexes. We believe that with small and appropriate modifications the methods described here should be applicable to other ATPase complexes.
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35
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Ali EI, Loidl J, Howard-Till RA. A streamlined cohesin apparatus is sufficient for mitosis and meiosis in the protist Tetrahymena. Chromosoma 2018; 127:421-435. [PMID: 29948142 PMCID: PMC6208729 DOI: 10.1007/s00412-018-0673-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 02/03/2023]
Abstract
In order to understand its diverse functions, we have studied cohesin in the evolutionarily distant ciliate model organism Tetrahymena thermophila. In this binucleate cell, the heritable germline genome is maintained separately from the transcriptionally active somatic genome. In a previous study, we showed that a minimal cohesin complex in Tetrahymena consisted of homologs of Smc1, Smc3, and Rec8, which are present only in the germline nucleus, where they are needed for normal chromosome segregation as well as meiotic DNA repair. In this study, we confirm that a putative homolog of Scc3 is a member of this complex. In the absence of Scc3, Smc1 and Rec8 fail to localize to germline nuclei, Rec8 is hypo-phosphorylated, and cells show phenotypes similar to depletion of Smc1 and Rec8. We also identify a homolog of Scc2, which in other organisms is part of a heterodimeric complex (Scc2/Scc4) that helps load cohesin onto chromatin. In Tetrahymena, Scc2 interacts with Rec8 and Scc3, and its absence causes defects in mitotic and meiotic divisions. Scc2 is not required for chromosomal association of cohesin, but Rec8 is hypo-phosphorylated in its absence. Moreover, we did not identify a homolog of the cohesin loader Scc4, and no evidence was found of auxiliary factors, such as Eco1, Pds5, or WAPL. We propose that in Tetrahymena, a single, minimal cohesin complex performs all necessary functions for germline mitosis and meiosis, but is dispensable for transcription regulation and chromatin organization of the somatic genome.
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Affiliation(s)
- Emine I Ali
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Josef Loidl
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Rachel A Howard-Till
- Department of Chromosome Biology, Vienna Biocenter, University of Vienna, Vienna, Austria.
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36
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Abstract
Cohesin is a ring-shaped protein complex that organises the genome, enabling its condensation, expression, repair and transmission. Cohesin is best known for its role in chromosome segregation, where it provides the cohesion that is established between the two newly duplicated sister chromatids during S phase. This cohesion enables the proper attachment of sister chromatids to microtubules of the spindle by resisting their opposing pulling forces. Once all chromosomes are correctly attached, cohesin is abruptly destroyed, triggering the equal segregation of sister chromatids to opposite poles in anaphase. Here we summarise the molecular functions and regulation of cohesin that underlie its central role in chromosome segregation during mitosis.
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Affiliation(s)
- Vasso Makrantoni
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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37
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Morales C, Losada A. Establishing and dissolving cohesion during the vertebrate cell cycle. Curr Opin Cell Biol 2018; 52:51-57. [PMID: 29433064 DOI: 10.1016/j.ceb.2018.01.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 01/28/2023]
Abstract
Replicated chromatids are held together from the time they emerge from the replication fork until their separation in anaphase. This process, known as cohesion, promotes faithful DNA repair by homologous recombination in interphase and ensures accurate chromosome segregation in mitosis. Identification of cohesin thirty years ago solved a long-standing question about the nature of the linkage keeping together the sister chromatids. Cohesin is an evolutionarily conserved complex composed of a heterodimer of the Structural Maintenance of Chromosomes (SMC) family of ATPases, Smc1 and Smc3, the kleisin subunit Rad21 and a Huntingtin/EF3/PP2A/Tor1 (HEAT) repeat domain-containing subunit named SA/STAG. In addition to mediating cohesion, cohesin plays a major role in genome organization. Cohesin functions rely on the ability of the complex to entrap DNA topologically and in a dynamic manner. Establishment of cohesion during S phase requires coordination with the DNA replication machinery and restricts the dynamic behaviour of at least a fraction of cohesin. Dissolution of cohesion in subsequent mitosis is regulated by multiple mechanisms that ensure that daughter cells receive the correct number of intact chromosomes. We here review recent progress on our understanding of how these processes are regulated in somatic vertebrate cells.
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Affiliation(s)
- Carmen Morales
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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38
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Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R. The Energetics and Physiological Impact of Cohesin Extrusion. Cell 2018; 173:1165-1178.e20. [PMID: 29706548 PMCID: PMC6065110 DOI: 10.1016/j.cell.2018.03.072] [Citation(s) in RCA: 314] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 12/29/2017] [Accepted: 03/27/2018] [Indexed: 12/25/2022]
Abstract
Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. Strikingly, without ATP, we observe the emergence of hundreds of CTCF-independent loops that link regulatory DNA. We also identify architectural "stripes," where a loop anchor interacts with entire domains at high frequency. Stripes often tether super-enhancers to cognate promoters, and in B cells, they facilitate Igh transcription and recombination. Stripe anchors represent major hotspots for topoisomerase-mediated lesions, which promote chromosomal translocations and cancer. In plasmacytomas, stripes can deregulate Igh-translocated oncogenes. We propose that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.
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Affiliation(s)
- Laura Vian
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Laura Baranello
- Gene Regulation, Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Marei Dose
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Adrian L Sanborn
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Andres Canela
- Laboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA
| | - Yaakov Maman
- Laboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA
| | - Anna Oksanen
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Wolfgang Resch
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Xingwang Li
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | | | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | | | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Ido Machol
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Neva C Durand
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elena K Stamenova
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA
| | | | - David Levens
- Gene Regulation, Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
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Racko D, Benedetti F, Dorier J, Stasiak A. Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes. Nucleic Acids Res 2018; 46:1648-1660. [PMID: 29140466 PMCID: PMC5829651 DOI: 10.1093/nar/gkx1123] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/03/2017] [Accepted: 10/30/2017] [Indexed: 12/16/2022] Open
Abstract
Using molecular dynamics simulations, we show here that growing plectonemes resulting from transcription-induced supercoiling have the ability to actively push cohesin rings along chromatin fibres. The pushing direction is such that within each topologically associating domain (TAD) cohesin rings forming handcuffs move from the source of supercoiling, constituted by RNA polymerase with associated DNA topoisomerase TOP1, towards borders of TADs, where supercoiling is released by topoisomerase TOPIIB. Cohesin handcuffs are pushed by continuous flux of supercoiling that is generated by transcription and is then progressively released by action of TOPIIB located at TADs borders. Our model explains what can be the driving force of chromatin loop extrusion and how it can be ensured that loops grow quickly and in a good direction. In addition, the supercoiling-driven loop extrusion mechanism is consistent with earlier explanations proposing why TADs flanked by convergent CTCF binding sites form more stable chromatin loops than TADs flanked by divergent CTCF binding sites. We discuss the role of supercoiling in stimulating enhancer promoter contacts and propose that transcription of eRNA sends the first wave of supercoiling that can activate mRNA transcription in a given TAD.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
- Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
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40
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Litwin I, Wysocki R. New insights into cohesin loading. Curr Genet 2018; 64:53-61. [PMID: 28631016 DOI: 10.1007/s00294-017-0723-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 01/13/2023]
Abstract
Cohesin is a conserved, ring-shaped protein complex that encircles sister chromatids and ensures correct chromosome segregation during mitosis and meiosis. It also plays a crucial role in the regulation of gene expression, DNA condensation, and DNA repair through both non-homologous end joining and homologous recombination. Cohesins are spatiotemporally regulated by the Scc2-Scc4 complex which facilitates cohesin loading onto chromatin at specific chromosomal sites. Over the last few years, much attention has been paid to cohesin and cohesin loader as it became clear that even minor disruptions of these complexes may lead to developmental disorders and cancers. Here we summarize recent developments in the structure of Scc2-Scc4 complex, cohesin loading process, and mediators that determine the Scc2-Scc4 binding patterns to chromatin.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328, Wroclaw, Poland
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41
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Murayama Y, Samora CP, Kurokawa Y, Iwasaki H, Uhlmann F. Establishment of DNA-DNA Interactions by the Cohesin Ring. Cell 2018; 172:465-477.e15. [PMID: 29358048 PMCID: PMC5786502 DOI: 10.1016/j.cell.2017.12.021] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/12/2017] [Accepted: 12/16/2017] [Indexed: 01/14/2023]
Abstract
The ring-shaped structural maintenance of chromosome (SMC) complexes are multi-subunit ATPases that topologically encircle DNA. SMC rings make vital contributions to numerous chromosomal functions, including mitotic chromosome condensation, sister chromatid cohesion, DNA repair, and transcriptional regulation. They are thought to do so by establishing interactions between more than one DNA. Here, we demonstrate DNA-DNA tethering by the purified fission yeast cohesin complex. DNA-bound cohesin efficiently and topologically captures a second DNA, but only if that is single-stranded DNA (ssDNA). Like initial double-stranded DNA (dsDNA) embrace, second ssDNA capture is ATP-dependent, and it strictly requires the cohesin loader complex. Second-ssDNA capture is relatively labile but is converted into stable dsDNA-dsDNA cohesion through DNA synthesis. Our study illustrates second-DNA capture by an SMC complex and provides a molecular model for the establishment of sister chromatid cohesion.
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Affiliation(s)
- Yasuto Murayama
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Catarina P Samora
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yumiko Kurokawa
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Frank Uhlmann
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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42
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Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, Walther N, Koch B, Kueblbeck M, Ellenberg J, Zuber J, Fraser P, Peters JM. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J 2017; 36:3573-3599. [PMID: 29217591 PMCID: PMC5730888 DOI: 10.15252/embj.201798004] [Citation(s) in RCA: 534] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops. In the absence of WAPL and PDS5 proteins, cohesin forms extended loops, presumably by passing CTCF sites, accumulates in axial chromosomal positions (vermicelli), and condenses chromosomes. Unexpectedly, PDS5 proteins are also required for boundary function. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.
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Affiliation(s)
- Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Csilla Várnai
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - David A Cisneros
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Gregor Jessberger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nike Walther
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Koch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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43
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Eeftens J, Dekker C. Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins. Nat Struct Mol Biol 2017; 24:1012-1020. [DOI: 10.1038/nsmb.3507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022]
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44
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Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D. Nonequilibrium Chromosome Looping via Molecular Slip Links. PHYSICAL REVIEW LETTERS 2017; 119:138101. [PMID: 29341686 DOI: 10.1103/physrevlett.119.138101] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Indexed: 06/07/2023]
Abstract
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J Johnson
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - D Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - A N Morozov
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - M Nicodemi
- Dipartimento di Fisica, Universita' di Napoli Federico II, INFN Napoli, CNR, SPIN, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - P R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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45
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Marcos-Alcalde Í, Mendieta-Moreno JI, Puisac B, Gil-Rodríguez MC, Hernández-Marcos M, Soler-Polo D, Ramos FJ, Ortega J, Pié J, Mendieta J, Gómez-Puertas P. Two-step ATP-driven opening of cohesin head. Sci Rep 2017; 7:3266. [PMID: 28607419 PMCID: PMC5468275 DOI: 10.1038/s41598-017-03118-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023] Open
Abstract
The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the "head" structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.
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Affiliation(s)
| | - Jesús I Mendieta-Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Beatriz Puisac
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Concepción Gil-Rodríguez
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Hernández-Marcos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Diego Soler-Polo
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Feliciano J Ramos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Pié
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Jesús Mendieta
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Departamento de Biotecnología, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223, Madrid, Spain
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46
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Gruber S. Shaping chromosomes by DNA capture and release: gating the SMC rings. Curr Opin Cell Biol 2017; 46:87-93. [PMID: 28460277 DOI: 10.1016/j.ceb.2017.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/22/2022]
Abstract
SMC proteins organize chromosomes to coordinate essential nuclear processes such as gene expression and DNA recombination as well as to segregate chromosomes during cell division. SMC mediated DNA bridging keeps sister chromatids aligned for much of the cell cycle, while the active extrusion of DNA loops by SMC presumably compacts chromosomes. Chromosome superstructure is thus given by the number of DNA linkages and the size of chromosomal DNA loops, which in turn depend on the dynamics of SMC loading and unloading. The latter is regulated by the intrinsic SMC ATPase activity, multiple external factors and post-translational modification. Here, I highlight recent advances in our understanding of DNA capture and release by SMC-with a focus on cohesin.
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Affiliation(s)
- Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland.
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47
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Deshpande RA, Lee JH, Paull TT. Rad50 ATPase activity is regulated by DNA ends and requires coordination of both active sites. Nucleic Acids Res 2017; 45:5255-5268. [PMID: 28369545 PMCID: PMC5435944 DOI: 10.1093/nar/gkx173] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 01/03/2023] Open
Abstract
The Mre11-Rad50-Nbs1(Xrs2) (MRN/X) complex is critical for the repair and signaling of DNA double strand breaks. The catalytic core of MRN/X comprised of the Mre11 nuclease and Rad50 adenosine triphosphatase (ATPase) active sites dimerizes through association between the Rad50 ATPase catalytic domains and undergoes extensive conformational changes upon ATP binding. This ATP-bound 'closed' state promotes binding to DNA, tethering DNA ends and ATM activation, but prevents nucleolytic processing of DNA ends, while ATP hydrolysis is essential for Mre11 endonuclease activity at blocked DNA ends. Here we investigate the regulation of ATP hydrolysis as well as the interdependence of the two functional active sites. We find that double-stranded DNA stimulates ATP hydrolysis by hMRN over ∼20-fold in an end-dependent manner. Using catalytic site mutants to create Rad50 dimers with only one functional ATPase site, we find that both ATPase sites are required for the stimulation by DNA. MRN-mediated endonucleolytic cleavage of DNA at sites of protein adducts requires ATP hydrolysis at both sites, as does the stimulation of ATM kinase activity. These observations suggest that symmetrical engagement of the Rad50 catalytic head domains with ATP bound at both sites is important for MRN functions in eukaryotic cells.
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Affiliation(s)
- Rajashree A. Deshpande
- Howard Hughes Medical Institute, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ji-Hoon Lee
- Howard Hughes Medical Institute, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T. Paull
- Howard Hughes Medical Institute, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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48
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Ouyang Z, Yu H. Releasing the cohesin ring: A rigid scaffold model for opening the DNA exit gate by Pds5 and Wapl. Bioessays 2017; 39. [PMID: 28220956 DOI: 10.1002/bies.201600207] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The ring-shaped ATPase machine, cohesin, regulates sister chromatid cohesion, transcription, and DNA repair by topologically entrapping DNA. Here, we propose a rigid scaffold model to explain how the cohesin regulators Pds5 and Wapl release cohesin from chromosomes. Recent studies have established the Smc3-Scc1 interface as the DNA exit gate of cohesin, revealed a requirement for ATP hydrolysis in ring opening, suggested regulation of the cohesin ATPase activity by DNA and Smc3 acetylation, and provided insights into how Pds5 and Wapl open this exit gate. We hypothesize that Pds5, Wapl, and SA1/2 form a rigid scaffold that docks on Scc1 and anchors the N-terminal domain of Scc1 (Scc1N) to the Smc1 ATPase head. Relative movements between the Smc1-3 ATPase heads driven by ATP and Wapl disrupt the Smc3-Scc1 interface. Pds5 binds the dissociated Scc1N and prolongs this open state of cohesin, releasing DNA. We review the evidence supporting this model and suggest experiments that can further test its key principles.
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Affiliation(s)
- Zhuqing Ouyang
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hongtao Yu
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
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49
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Barrington C, Finn R, Hadjur S. Cohesin biology meets the loop extrusion model. Chromosome Res 2017; 25:51-60. [PMID: 28210885 PMCID: PMC5346154 DOI: 10.1007/s10577-017-9550-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/26/2016] [Accepted: 01/09/2017] [Indexed: 12/05/2022]
Abstract
Extensive research has revealed that cohesin acts as a topological device, trapping chromosomal DNA within a large tripartite ring. In so doing, cohesin contributes to the formation of compact and organized genomes. How exactly the cohesin subunits interact, how it opens, closes, and translocates on chromatin, and how it actually tethers DNA strands together are still being elucidated. A comprehensive understanding of these questions will shed light on how cohesin performs its many functions, including its recently proposed role as a chromatid loop extruder. Here, we discuss this possibility in light of our understanding of the molecular properties of cohesin complexes.
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Affiliation(s)
- Christopher Barrington
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Ronald Finn
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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50
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Huang CJ, Yuan YF, Wu D, Khan FA, Jiao XF, Huo LJ. The cohesion stabilizer sororin favors DNA repair and chromosome segregation during mouse oocyte meiosis. In Vitro Cell Dev Biol Anim 2017; 53:258-264. [PMID: 27826797 DOI: 10.1007/s11626-016-0107-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/11/2016] [Indexed: 12/11/2022]
Abstract
Maintenance and timely termination of cohesion on chromosomes ensures accurate chromosome segregation to guard against aneuploidy in mammalian oocytes and subsequent chromosomally abnormal pregnancies. Sororin, a cohesion stabilizer whose relevance in antagonizing the anti-cohesive property of Wings-apart like protein (Wapl), has been characterized in mitosis; however, the role of Sororin remains unclear during mammalian oocyte meiosis. Here, we show that Sororin is required for DNA damage repair and cohesion maintenance on chromosomes, and consequently, for mouse oocyte meiotic program. Sororin is constantly expressed throughout meiosis and accumulates on chromatins at germinal vesicle (GV) stage/G2 phase. It localizes onto centromeres from germinal vesicle breakdown (GVBD) to metaphase II stage. Inactivation of Sororin compromises the GVBD and first polar body extrusion (PBE). Furthermore, Sororin inactivation induces DNA damage indicated by positive γH2AX foci in GV oocytes and precocious chromatin segregation in MII oocytes. Finally, our data indicate that PlK1 and MPF dissociate Sororin from chromosome arms without affecting its centromeric localization. Our results define Sororin as a determinant during mouse oocyte meiotic maturation by favoring DNA damage repair and chromosome separation, and thereby, maintaining the genome stability and generating haploid gametes.
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Affiliation(s)
- Chun-Jie Huang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Yi-Feng Yuan
- Department of Gynecology and Obstetrics, Peking University Third University, Beijing, China
| | - Di Wu
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Faheem Ahmed Khan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Fei Jiao
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Li-Jun Huo
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China.
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