1
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Guérin TM, Barrington C, Pobegalov G, Molodtsov MI, Uhlmann F. An extrinsic motor directs chromatin loop formation by cohesin. EMBO J 2024:10.1038/s44318-024-00202-5. [PMID: 39160275 DOI: 10.1038/s44318-024-00202-5] [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: 03/05/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/21/2024] Open
Abstract
The ring-shaped cohesin complex topologically entraps two DNA molecules to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation, and cohesin is thought to achieve this by actively extruding DNA loops without topologically entrapping DNA. The 'loop extrusion' hypothesis finds motivation from in vitro observations-whether this process underlies in vivo chromatin loop formation remains untested. Here, using the budding yeast S. cerevisiae, we generate cohesin variants that have lost their ability to extrude DNA loops but retain their ability to topologically entrap DNA. Analysis of these variants suggests that in vivo chromatin loops form independently of loop extrusion. Instead, we find that transcription promotes loop formation, and acts as an extrinsic motor that expands these loops and defines their ultimate positions. Our results necessitate a re-evaluation of the loop extrusion hypothesis. We propose that cohesin, akin to sister chromatid cohesion establishment at replication forks, forms chromatin loops by DNA-DNA capture at places of transcription, thus unifying cohesin's two roles in chromosome segregation and interphase genome organisation.
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Affiliation(s)
- Thomas M Guérin
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Université Paris Cité and Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Christopher Barrington
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Georgii Pobegalov
- Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Maxim I Molodtsov
- Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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2
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Yan L, Yuan X, Liu M, Chen Q, Zhang M, Xu J, Zeng LH, Zhang L, Huang J, Lu W, He X, Yan H, Wang F. A non-canonical role of the inner kinetochore in regulating sister-chromatid cohesion at centromeres. EMBO J 2024; 43:2424-2452. [PMID: 38714893 PMCID: PMC11182772 DOI: 10.1038/s44318-024-00104-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/27/2024] [Accepted: 04/12/2024] [Indexed: 06/19/2024] Open
Abstract
The 16-subunit Constitutive Centromere-associated Network (CCAN)-based inner kinetochore is well-known for connecting centromeric chromatin to the spindle-binding outer kinetochore. Here, we report a non-canonical role for the inner kinetochore in directly regulating sister-chromatid cohesion at centromeres. We provide biochemical, X-ray crystal structure, and intracellular ectopic localization evidence that the inner kinetochore directly binds cohesin, a ring-shaped multi-subunit complex that holds sister chromatids together from S-phase until anaphase onset. This interaction is mediated by binding of the 5-subunit CENP-OPQUR sub-complex of CCAN to the Scc1-SA2 sub-complex of cohesin. Mutation in the CENP-U subunit of the CENP-OPQUR complex that abolishes its binding to the composite interface between Scc1 and SA2 weakens centromeric cohesion, leading to premature separation of sister chromatids during delayed metaphase. We further show that CENP-U competes with the cohesin release factor Wapl for binding the interface of Scc1-SA2, and that the cohesion-protecting role for CENP-U can be bypassed by depleting Wapl. Taken together, this study reveals an inner kinetochore-bound pool of cohesin, which strengthens centromeric sister-chromatid cohesion to resist metaphase spindle pulling forces.
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Affiliation(s)
- Lu Yan
- Life Sciences Institute, State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of Zhejiang University School of Medicine, MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, 310058, China
| | - Xueying Yuan
- Life Sciences Institute, State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of Zhejiang University School of Medicine, MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, 310058, China
| | - Mingjie Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qinfu Chen
- Department of Gynecological Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Miao Zhang
- Life Sciences Institute, State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of Zhejiang University School of Medicine, MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, 310058, China
| | - Junfen Xu
- Department of Gynecological Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Ling-Hui Zeng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, China
| | - Long Zhang
- Life Sciences Institute, State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of Zhejiang University School of Medicine, MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Jun Huang
- Life Sciences Institute, State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of Zhejiang University School of Medicine, MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Weiguo Lu
- Department of Gynecological Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiaojing He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Haiyan Yan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, China.
| | - Fangwei Wang
- Life Sciences Institute, State Key Laboratory of Transvascular Implantation Devices of the Second Affiliated Hospital of Zhejiang University School of Medicine, MOE Laboratory of Biosystems Homeostasis and Protection, Zhejiang University, Hangzhou, 310058, China.
- Department of Gynecological Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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3
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Cameron G, Gruszka D, Xie S, Kaya Ç, Nasmyth KA, Srinivasan M, Yardimci H. Sister chromatid cohesion establishment during DNA replication termination. Science 2024; 384:119-124. [PMID: 38484038 PMCID: PMC7615807 DOI: 10.1126/science.adf0224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/27/2024] [Indexed: 04/06/2024]
Abstract
Newly copied sister chromatids are tethered together by the cohesin complex, but how sister chromatid cohesion coordinates with DNA replication is poorly understood. Prevailing models suggest that cohesin complexes, bound to DNA before replication, remain behind the advancing replication fork to keep sister chromatids together. By visualizing single replication forks colliding with preloaded cohesin complexes, we find that the replisome instead pushes cohesin to where a converging replisome is met. Whereas the converging replisomes are removed during DNA replication termination, cohesin remains on nascent DNA and provides cohesion. Additionally, we show that CMG (CDC45-MCM2-7-GINS) helicase disassembly during replication termination is vital for proper cohesion in budding yeast. Together, our results support a model wherein sister chromatid cohesion is established during DNA replication termination.
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Affiliation(s)
| | | | - Sherry Xie
- The Francis Crick Institute; London, United Kingdom
| | - Çağla Kaya
- The Francis Crick Institute; London, United Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford; Oxford, United Kingdom
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4
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Golov AK, Gavrilov AA. Cohesin Complex: Structure and Principles of Interaction with DNA. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:585-600. [PMID: 38831498 DOI: 10.1134/s0006297924040011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 06/05/2024]
Abstract
Accurate duplication and separation of long linear genomic DNA molecules is associated with a number of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decatenation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eukaryotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be threaded. Capacity of cohesin for such topological entrapment of DNA is crucial for the phenomenon of post-replicative association of sister chromatids better known as cohesion. Recently, it became apparent that cohesin and other SMC complexes are, in fact, motor proteins with a very peculiar movement pattern leading to formation of DNA loops. This specific process has been called loop extrusion. Extrusion underlies multiple functions of cohesin beyond cohesion, but molecular mechanism of the process remains a mystery. In this review, we summarized the data on molecular architecture of cohesin, effect of ATP hydrolysis cycle on this architecture, and known modes of cohesin-DNA interactions. Many of the seemingly disparate facts presented here will probably be incorporated in a unified mechanistic model of loop extrusion in the not-so-distant future.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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5
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Qin CM, Wei XW, Wu JY, Liu XQ, Lin Y. Decreased NSD2 impairs stromal cell proliferation in human endometrium via reprogramming H3K36me2. Reproduction 2024; 167:e230254. [PMID: 38236723 PMCID: PMC10895284 DOI: 10.1530/rep-23-0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024]
Abstract
In brief The proliferation of the endometrium is regulated by histone methylation. This study shows that decreased NSD2 impairs proliferative-phase endometrial stromal cell proliferation in patients with recurrent implantation failure via epigenetic reprogramming of H3K36me2 methylation on the promoter region of MCM7. Abstract Recurrent implantation failure (RIF) is a formidable challenge in assisted reproductive technology because of its unclear molecular mechanism. Impaired human endometrial stromal cell (HESC) proliferation disrupts the rhythm of the menstrual cycle, resulting in devastating disorders between the embryo and the endometrium. The molecular function of histone methylation enzymes in modulating HESC proliferation remains largely uncharacterized. Herein, we found that the levels of histone methyltransferase nuclear receptor binding SET domain protein 2 (NSD2) and the dimethylation of lysine 36 on histone H3 are decreased significantly in the proliferative-phase endometrium of patients with RIF. Knockdown of NSD2 in an HESC cell line markedly impaired cell proliferation and globally reduced H3K36me2 binding to chromatin, leading to altered expression of many genes. Transcriptomic analyses revealed that cell cycle-related gene sets were downregulated in the endometrium of patients with RIF and in NSD2‑knockdown HESCs. Furthermore, RNA-sequencing and CUT&Tag sequencing analysis suggested that NSD2 knockdown reduced the binding of H3K36me2 to the promoter region of cell cycle marker gene MCM7 (encoding minichromosome maintenance complex component 7) and downregulated its expression. The interaction of H3K36me2 with the MCM7 promoter was verified using chromatin immunoprecipitation-quantitative real-time PCR. Our results demonstrated a unifying epigenome-scale mechanism by which decreased NSD2 impairs endometrial stromal cell proliferation in the proliferative-phase endometrium of patients with RIF.
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Affiliation(s)
- Chuan-Mei Qin
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Wei Wei
- Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Yi Wu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Qing Liu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Lin
- Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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6
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Murayama Y, Endo S, Kurokawa Y, Kurita A, Iwasaki S, Araki H. Coordination of cohesin and DNA replication observed with purified proteins. Nature 2024; 626:653-660. [PMID: 38267580 DOI: 10.1038/s41586-023-07003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/26/2024]
Abstract
Two newly duplicated copies of genomic DNA are held together by the ring-shaped cohesin complex to ensure faithful inheritance of the genome during cell division1-3. Cohesin mediates sister chromatid cohesion by topologically entrapping two sister DNAs during DNA replication4,5, but how cohesion is established at the replication fork is poorly understood. Here, we studied the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins. Once DNA is encircled before replication, the cohesin ring accommodates replication in its entirety, from initiation to termination, leading to topological capture of newly synthesized DNA. This suggests that topological cohesin loading is a critical molecular prerequisite to cope with replication. Paradoxically, topological loading per se is highly rate limiting and hardly occurs under the replication-competent physiological salt concentration. This inconsistency is resolved by the replisome-associated cohesion establishment factors Chl1 helicase and Ctf4 (refs. 6,7), which promote cohesin loading specifically during continuing replication. Accordingly, we found that bubble DNA, which mimics the state of DNA unwinding, induces topological cohesin loading and this is further promoted by Chl1. Thus, we propose that cohesin converts the initial electrostatic DNA-binding mode to a topological embrace when it encounters unwound DNA structures driven by enzymatic activities including replication. Together, our results show how cohesin initially responds to replication, and provide a molecular model for the establishment of sister chromatid cohesion.
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Affiliation(s)
- Yasuto Murayama
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan.
- Department of Genetics, Graduate University for Advanced Studies (SOUKENDAI), Mishima, Japan.
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Japan.
| | - Shizuko Endo
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Yumiko Kurokawa
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOUKENDAI), Mishima, Japan
| | - Ayako Kurita
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Sanae Iwasaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Hiroyuki Araki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
- Joint Support-Centre for Data Science Research, Research Organisation of Information and Systems, Tachikawa, Japan
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7
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Richeldi M, Pobegalov G, Higashi TL, Gmurczyk K, Uhlmann F, Molodtsov MI. Mechanical disengagement of the cohesin ring. Nat Struct Mol Biol 2024; 31:23-31. [PMID: 37872232 DOI: 10.1038/s41594-023-01122-4] [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: 11/11/2022] [Accepted: 09/11/2023] [Indexed: 10/25/2023]
Abstract
Cohesin forms a proteinaceous ring that is thought to link sister chromatids by entrapping DNA and counteracting the forces generated by the mitotic spindle. Whether individual cohesins encircle both sister DNAs and how cohesin opposes spindle-generated forces remains unknown. Here we perform force measurements on individual yeast cohesin complexes either bound to DNA or holding together two DNAs. By covalently closing the hinge and Smc3Psm3-kleisin interfaces we find that the mechanical stability of the cohesin ring entrapping DNA is determined by the hinge domain. Forces of ~20 pN disengage cohesin at the hinge and release DNA, indicating that ~40 cohesin molecules are sufficient to counteract known spindle forces. Our findings provide a mechanical framework for understanding how cohesin interacts with sister chromatids and opposes the spindle-generated tension during mitosis, with implications for other force-generating chromosomal processes including transcription and DNA replication.
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Affiliation(s)
- Martina Richeldi
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Georgii Pobegalov
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
- Kamakura Research Laboratories, Chugai Pharmaceutical Co., Kamakura City, Japan
| | - Karolina Gmurczyk
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
| | - Maxim I Molodtsov
- Biophysics and Mechanobiology Laboratory, The Francis Crick Institute, London, UK.
- Department of Physics and Astronomy, University College London, London, UK.
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8
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Tang M, Pobegalov G, Tanizawa H, Chen ZA, Rappsilber J, Molodtsov M, Noma KI, Uhlmann F. Establishment of dsDNA-dsDNA interactions by the condensin complex. Mol Cell 2023; 83:3787-3800.e9. [PMID: 37820734 PMCID: PMC10842940 DOI: 10.1016/j.molcel.2023.09.019] [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: 05/08/2023] [Revised: 08/13/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Condensin is a structural maintenance of chromosomes (SMC) complex family member thought to build mitotic chromosomes by DNA loop extrusion. However, condensin variants unable to extrude loops, yet proficient in chromosome formation, were recently described. Here, we explore how condensin might alternatively build chromosomes. Using bulk biochemical and single-molecule experiments with purified fission yeast condensin, we observe that individual condensins sequentially and topologically entrap two double-stranded DNAs (dsDNAs). Condensin loading transitions through a state requiring DNA bending, as proposed for the related cohesin complex. While cohesin then favors the capture of a second single-stranded DNA (ssDNA), second dsDNA capture emerges as a defining feature of condensin. We provide complementary in vivo evidence for DNA-DNA capture in the form of condensin-dependent chromatin contacts within, as well as between, chromosomes. Our results support a "diffusion capture" model in which condensin acts in mitotic chromosome formation by sequential dsDNA-dsDNA capture.
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Affiliation(s)
- Minzhe Tang
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Georgii Pobegalov
- Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Hideki Tanizawa
- Division of Genome Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan
| | - Zhuo A Chen
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Maxim Molodtsov
- Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Ken-Ichi Noma
- Division of Genome Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan; Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-0026, Japan.
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9
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Kaushik A, Than T, Petela NJ, Voulgaris M, Percival C, Daniels P, Rafferty JB, Nasmyth KA, Hu B. Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding. Nat Commun 2023; 14:5929. [PMID: 37739959 PMCID: PMC10516938 DOI: 10.1038/s41467-023-41596-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
The ring-shaped cohesin complex is a key player in sister chromatid cohesion, DNA repair, and gene transcription. The loading of cohesin to chromosomes requires the loader Scc2 and is regulated by ATP. This process is hindered by Smc3 acetylation. However, the molecular mechanism underlying this inhibition remains mysterious. Here, using Saccharomyces cerevisiae as a model system, we identify a novel configuration of Scc2 with pre-engaged cohesin and reveal dynamic conformations of the cohesin/Scc2 complex in the loading reaction. We demonstrate that Smc3 acetylation blocks the association of Scc2 with pre-engaged cohesin by impairing the interaction of Scc2 with Smc3's head. Lastly, we show that ATP binding induces the cohesin/Scc2 complex to clamp DNA by promoting the interaction between Scc2 and Smc3 coiled coil. Our results illuminate a dynamic reconfiguration of the cohesin/Scc2 complex during loading and indicate how Smc3 acetylation and ATP regulate this process.
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Affiliation(s)
- Aditi Kaushik
- The Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Thane Than
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Naomi J Petela
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Charlotte Percival
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Peter Daniels
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - John B Rafferty
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bin Hu
- The Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
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10
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Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
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Affiliation(s)
- Claire Hoencamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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11
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Pobegalov G, Chu LY, Peters JM, Molodtsov MI. Single cohesin molecules generate force by two distinct mechanisms. Nat Commun 2023; 14:3946. [PMID: 37402740 DOI: 10.1038/s41467-023-39696-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Spatial organization of DNA is facilitated by cohesin protein complexes that move on DNA and extrude DNA loops. How cohesin works mechanistically as a molecular machine is poorly understood. Here, we measure mechanical forces generated by conformational changes in single cohesin molecules. We show that bending of SMC coiled coils is driven by random thermal fluctuations leading to a ~32 nm head-hinge displacement that resists forces up to 1 pN; ATPase head engagement occurs in a single step of ~10 nm and is driven by an ATP dependent head-head movement, resisting forces up to 15 pN. Our molecular dynamic simulations show that the energy of head engagement can be stored in a mechanically strained conformation of NIPBL and released during disengagement. These findings reveal how single cohesin molecules generate force by two distinct mechanisms. We present a model, which proposes how this ability may power different aspects of cohesin-DNA interaction.
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Affiliation(s)
- Georgii Pobegalov
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Lee-Ya Chu
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria
| | - Maxim I Molodtsov
- The Francis Crick Institute, London, NW1 1AT, UK.
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, 1030, Austria.
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12
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Bürmann F, Löwe J. Structural biology of SMC complexes across the tree of life. Curr Opin Struct Biol 2023; 80:102598. [PMID: 37104976 PMCID: PMC10512200 DOI: 10.1016/j.sbi.2023.102598] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 04/29/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes guard and organize the three-dimensional structure of chromosomal DNA across the tree of life. Many SMC functions can be explained by an inherent motor activity that extrudes large DNA loops while the complexes move along their substrate. Here, we review recent structural insights into the architecture and conservation of these molecular machines, their interaction with DNA, and the conformational changes that are linked to their ATP hydrolysis cycle.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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13
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Shrestha S, Minamino M, Chen ZA, Bouchoux C, Rappsilber J, Uhlmann F. Replisome-cohesin interactions provided by the Tof1-Csm3 and Mrc1 cohesion establishment factors. Chromosoma 2023; 132:117-135. [PMID: 37166686 PMCID: PMC10247859 DOI: 10.1007/s00412-023-00797-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023]
Abstract
The chromosomal cohesin complex establishes sister chromatid cohesion during S phase, which forms the basis for faithful segregation of DNA replication products during cell divisions. Cohesion establishment is defective in the absence of either of three non-essential Saccharomyces cerevisiae replication fork components Tof1-Csm3 and Mrc1. Here, we investigate how these conserved factors contribute to cohesion establishment. Tof1-Csm3 and Mrc1 serve known roles during DNA replication, including replication checkpoint signaling, securing replication fork speed, as well as recruiting topoisomerase I and the histone chaperone FACT. By modulating each of these functions independently, we rule out that one of these known replication roles explains the contribution of Tof1-Csm3 and Mrc1 to cohesion establishment. Instead, using purified components, we reveal direct and multipronged protein interactions of Tof1-Csm3 and Mrc1 with the cohesin complex. Our findings open the possibility that a series of physical interactions between replication fork components and cohesin facilitate successful establishment of sister chromatid cohesion during DNA replication.
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Affiliation(s)
- Sudikchya Shrestha
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Masashi Minamino
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Zhuo A Chen
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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14
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Borrie MS, Kraycer PM, Gartenberg MR. Transcription-Driven Translocation of Cohesive and Non-Cohesive Cohesin In Vivo. Mol Cell Biol 2023; 43:254-268. [PMID: 37178128 PMCID: PMC10251789 DOI: 10.1080/10985549.2023.2199660] [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: 01/03/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 05/15/2023] Open
Abstract
Cohesin is a central architectural element of chromosomes that regulates numerous DNA-based events. The complex holds sister chromatids together until anaphase onset and organizes individual chromosomal DNAs into loops and self-associating domains. Purified cohesin diffuses along DNA in an ATP-independent manner but can be propelled by transcribing RNA polymerase. In conjunction with a cofactor, the complex also extrudes DNA loops in an ATP-dependent manner. In this study we examine transcription-driven translocation of cohesin under various conditions in yeast. To this end, obstacles of increasing size were tethered to DNA to act as roadblocks to complexes mobilized by an inducible gene. The obstacles were built from a GFP-lacI core fused to one or more mCherries. A chimera with four mCherries blocked cohesin passage in late G1. During M phase, the threshold barrier depended on the state of cohesion: non-cohesive complexes were also blocked by four mCherries whereas cohesive complexes were blocked by as few as three mCherries. Furthermore cohesive complexes that were stalled at obstacles, in turn, blocked the passage of non-cohesive complexes. That synthetic barriers capture mobilized cohesin demonstrates that transcription-driven complexes translocate processively in vivo. Together, this study reveals unexplored limitations to cohesin movement on chromosomes.
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Affiliation(s)
- Melinda S. Borrie
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Paul M. Kraycer
- Graduate Program in Cellular and Molecular Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Marc R. Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Member of The Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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15
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Mfarej MG, Hyland CA, Sanchez AC, Falk MM, Iovine MK, Skibbens RV. Cohesin: an emerging master regulator at the heart of cardiac development. Mol Biol Cell 2023; 34:rs2. [PMID: 36947206 PMCID: PMC10162415 DOI: 10.1091/mbc.e22-12-0557] [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: 12/19/2022] [Revised: 03/10/2023] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Cohesins are ATPase complexes that play central roles in cellular processes such as chromosome division, DNA repair, and gene expression. Cohesinopathies arise from mutations in cohesin proteins or cohesin complex regulators and encompass a family of related developmental disorders that present with a range of severe birth defects, affect many different physiological systems, and often lead to embryonic fatality. Treatments for cohesinopathies are limited, in large part due to the lack of understanding of cohesin biology. Thus, characterizing the signaling networks that lie upstream and downstream of cohesin-dependent pathways remains clinically relevant. Here, we highlight alterations in cohesins and cohesin regulators that result in cohesinopathies, with a focus on cardiac defects. In addition, we suggest a novel and more unifying view regarding the mechanisms through which cohesinopathy-based heart defects may arise.
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Affiliation(s)
- Michael G. Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Caitlin A. Hyland
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Annie C. Sanchez
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Matthias M. Falk
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - M. Kathryn Iovine
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
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16
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Porter H, Li Y, Neguembor MV, Beltran M, Varsally W, Martin L, Cornejo MT, Pezić D, Bhamra A, Surinova S, Jenner RG, Cosma MP, Hadjur S. Cohesin-independent STAG proteins interact with RNA and R-loops and promote complex loading. eLife 2023; 12:e79386. [PMID: 37010886 PMCID: PMC10238091 DOI: 10.7554/elife.79386] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Most studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in the localization of cohesin to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin, cluster in 3D and interact with CTCF, as well as with a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA, and R-loops, even in the absence of cohesin. Our results place SA1 on chromatin upstream of the cohesin ring and reveal a role for SA1 in cohesin loading which is independent of NIPBL, the canonical cohesin loader. We propose that SA1 takes advantage of structural R-loop platforms to link cohesin loading and chromatin structure with diverse functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease.
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Affiliation(s)
- Hayley Porter
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Yang Li
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Manuel Beltran
- Regulatory Genomics Group, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Wazeer Varsally
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Laura Martin
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Manuel Tavares Cornejo
- Regulatory Genomics Group, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Dubravka Pezić
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Amandeep Bhamra
- Proteomics Research Translational Technology Platform, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Silvia Surinova
- Proteomics Research Translational Technology Platform, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Richard G Jenner
- Regulatory Genomics Group, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
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17
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [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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18
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Martínez‐García B, Dyson S, Segura J, Ayats A, Cutts EE, Gutierrez‐Escribano P, Aragón L, Roca J. Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage. EMBO J 2023; 42:e111913. [PMID: 36533296 PMCID: PMC9890231 DOI: 10.15252/embj.2022111913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Condensin, an SMC (structural maintenance of chromosomes) protein complex, extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. Here, we show how condensin activity alters the topology of the interacting DNA. High condensin concentrations restrain positive DNA supercoils. However, in experimental conditions of DNA loop extrusion, condensin restrains negative supercoils. Namely, following ATP-mediated loading onto DNA, each condensin complex constrains a DNA linking number difference (∆Lk) of -0.4. This ∆Lk increases to -0.8 during ATP binding and resets to -0.4 upon ATP hydrolysis. These changes in DNA topology do not involve DNA unwinding, do not spread outside the condensin-DNA complex and can occur in the absence of the condensin subunit Ycg1. These findings indicate that during ATP binding, a short DNA domain delimited by condensin is pinched into a negatively supercoiled loop. We propose that this loop is the feeding segment of DNA that is subsequently merged to enlarge an extruding loop. Such a "pinch and merge" mechanism implies that two DNA-binding sites produce the feeding loop, while a third site, plausibly involving Ycg1, might anchor the extruding loop.
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Affiliation(s)
| | - Sílvia Dyson
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Joana Segura
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Alba Ayats
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
| | - Erin E Cutts
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | | | - Luís Aragón
- DNA Motors GroupMRC London Institute of Medical Sciences (LMS)LondonUK
| | - Joaquim Roca
- DNA Topology LabMolecular Biology Institute of Barcelona (IBMB), CSICBarcelonaSpain
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19
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Choudhary K, Kupiec M. The cohesin complex of yeasts: sister chromatid cohesion and beyond. FEMS Microbiol Rev 2023; 47:6825453. [PMID: 36370456 DOI: 10.1093/femsre/fuac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Each time a cell divides, it needs to duplicate the genome and then separate the two copies. In eukaryotes, which usually have more than one linear chromosome, this entails tethering the two newly replicated DNA molecules, a phenomenon known as sister chromatid cohesion (SCC). Cohesion ensures proper chromosome segregation to separate poles during mitosis. SCC is achieved by the presence of the cohesin complex. Besides its canonical function, cohesin is essential for chromosome organization and DNA damage repair. Surprisingly, yeast cohesin is loaded in G1 before DNA replication starts but only acquires its binding activity during DNA replication. Work in microorganisms, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe has greatly contributed to the understanding of cohesin composition and functions. In the last few years, much progress has been made in elucidating the role of cohesin in chromosome organization and compaction. Here, we discuss the different functions of cohesin to ensure faithful chromosome segregation and genome stability during the mitotic cell division in yeast. We describe what is known about its composition and how DNA replication is coupled with SCC establishment. We also discuss current models for the role of cohesin in chromatin loop extrusion and delineate unanswered questions about the activity of this important, conserved complex.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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20
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Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging. Cell Rep 2022; 41:111778. [PMID: 36476856 PMCID: PMC9756111 DOI: 10.1016/j.celrep.2022.111778] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/15/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
SMC complexes play key roles in genome maintenance, where they ensure efficient genome replication and segregation. The SMC complex Smc5/6 is a crucial player in DNA replication and repair, yet many molecular features that determine its roles are unclear. Here, we use single-molecule microscopy to investigate Smc5/6's interaction with DNA. We find that Smc5/6 forms oligomers that dynamically redistribute on dsDNA by 1D diffusion and statically bind to ssDNA. Using combined force manipulation and single-molecule microscopy, we generate ssDNA-dsDNA junctions that mimic structures present in DNA repair intermediates or replication forks. We show that Smc5/6 accumulates at these junction sites, stabilizes the fork, and promotes the retention of RPA. Our observations provide a model for the complex's enrichment at sites of replication stress and DNA lesions from where it coordinates the recruitment and activation of downstream repair proteins.
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21
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Yun Y, Lee S, So C, Manhas R, Kim C, Wibowo T, Hori M, Hunter N. Oocyte Development and Quality in Young and Old Mice following Exposure to Atrazine. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:117007. [PMID: 36367780 PMCID: PMC9651182 DOI: 10.1289/ehp11343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Egg development has unique features that render it vulnerable to environmental perturbation. The herbicide atrazine is an endocrine disruptor shown to have detrimental effects on reproduction across several vertebrate species. OBJECTIVES This study was designed to determine whether exposure to low levels of atrazine impairs meiosis in female mammals, using a mouse model; in particular, the study's researchers sought to determine whether and how the fidelity of oocyte chromosome segregation may be affected and whether aging-related aneuploidy is exacerbated. METHODS Female C57BL/6J mice were exposed to two levels of atrazine in drinking water: The higher level equaled aqueous saturation, and the lower level corresponded to detected environmental contamination. To model developmental exposure, atrazine was ingested by pregnant females at 0.5 d post coitum and continued until pups were weaned at 21 d postpartum. For adult exposure, 2-month-old females ingested atrazine for 3 months. Following exposure, various indicators of oocyte development and quality were determined, including: a) chromosome synapsis and crossing over in fetal oocytes using immunofluorescence staining of prophase-I chromosome preparations; b) sizes of follicle pools in sectioned ovaries; c) efficiencies of in vitro fertilization and early embryogenesis; d) chromosome alignment and segregation in cultured oocytes; e) chromosomal errors in metaphase-I and -II (MI and MII) preparations; and f) sister-chromatid cohesion via immunofluorescence intensity of cohesin subunit REC8 on MI-chromosome preparations, and measurement of interkinetochore distances in MII preparations. RESULTS Mice exposed to atrazine during development showed slightly higher levels of defects in chromosome synapsis, but sizes of initial follicle pools were indistinguishable from controls. However, although more eggs were ovulated, oocyte quality was lower. At the chromosome level, frequencies of spindle misalignment and numerical and structural abnormalities were greater at both meiotic divisions. In vitro fertilization was less efficient, and there were more apoptotic cells in blastocysts derived from eggs of atrazine-exposed females. Similar levels of chromosomal defects were seen in oocytes following both developmental and adult exposure regimens, suggesting quiescent primordial follicles may be a consequential target of atrazine. An important finding was that defects were observed long after exposure was terminated. Moreover, chromosomally abnormal eggs were very frequent in older mice, implying that atrazine exposure during development exacerbates effects of maternal aging on oocyte quality. Indeed, analogous to the effects of maternal age, weaker cohesion between sister chromatids was observed in oocytes from atrazine-exposed animals. CONCLUSION Low-level atrazine exposure caused persistent changes to the female mammalian germline in mice, with potential consequences for reproductive lifespan and congenital disease. https://doi.org/10.1289/EHP11343.
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Affiliation(s)
- Yan Yun
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA
| | - Sunkyung Lee
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Christina So
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Rushali Manhas
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Carol Kim
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Tabitha Wibowo
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Michael Hori
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
| | - Neil Hunter
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
- Howard Hughes Medical Institute, University of California, Davis, Davis, California, USA
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California, USA
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22
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Collier JE, Nasmyth KA. DNA passes through cohesin's hinge as well as its Smc3-kleisin interface. eLife 2022; 11:80310. [PMID: 36094369 PMCID: PMC9467508 DOI: 10.7554/elife.80310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/29/2022] [Indexed: 12/17/2022] Open
Abstract
The ring model proposes that sister chromatid cohesion is mediated by co-entrapment of sister DNAs inside a single tripartite cohesin ring. The model explains how Scc1 cleavage triggers anaphase but has hitherto only been rigorously tested using small circular mini-chromosomes in yeast, where covalently circularizing the ring by crosslinking its three interfaces induces catenation of individual and sister DNAs. If the model applies to real chromatids, then the ring must have a DNA entry gate essential for mitosis. Whether this is situated at the Smc3/Scc1 or Smc1/Smc3 hinge interface is an open question. We have previously demonstrated DNA entrapment by cohesin in vitro (Collier et al., 2020). Here we show that cohesin in fact possesses two DNA gates, one at the Smc3/Scc1 interface and a second at the Smc1/3 hinge. Unlike the Smc3/Scc1 interface, passage of DNAs through SMC hinges depends on both Scc2 and Scc3, a pair of regulatory subunits necessary for entrapment in vivo. This property together with the lethality caused by locking this interface but not that between Smc3 and Scc1 in vivo suggests that passage of DNAs through the hinge is essential for building sister chromatid cohesion. Passage of DNAs through the Smc3/Scc1 interface is necessary for cohesin’s separase-independent release from chromosomes and may therefore largely serve as an exit gate.
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Affiliation(s)
- James E Collier
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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23
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Choudhary K, Itzkovich Z, Alonso-Perez E, Bishara H, Dunn B, Sherlock G, Kupiec M. S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit. mBio 2022; 13:e0142022. [PMID: 35708277 PMCID: PMC9426526 DOI: 10.1128/mbio.01420-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 12/11/2022] Open
Abstract
During DNA replication, the newly created sister chromatids are held together until their separation at anaphase. The cohesin complex is in charge of creating and maintaining sister chromatid cohesion (SCC) in all eukaryotes. In Saccharomyces cerevisiae cells, cohesin is composed of two elongated proteins, Smc1 and Smc3, bridged by the kleisin Mcd1/Scc1. The latter also acts as a scaffold for three additional proteins, Scc3/Irr1, Wpl1/Rad61, and Pds5. Although the HEAT-repeat protein Pds5 is essential for cohesion, its precise function is still debated. Deletion of the ELG1 gene, encoding a PCNA unloader, can partially suppress the temperature-sensitive pds5-1 allele, but not a complete deletion of PDS5. We carried out a genetic screen for high-copy-number suppressors and another for spontaneously arising mutants, allowing the survival of a pds5Δ elg1Δ strain. Our results show that cells remain viable in the absence of Pds5 provided that there is both an elevation in the level of Mcd1 (which can be due to mutations in the CLN2 gene, encoding a G1 cyclin), and an increase in the level of SUMO-modified PCNA on chromatin (caused by lack of PCNA unloading in elg1Δ mutants). The elevated SUMO-PCNA levels increase the recruitment of the Srs2 helicase, which evicts Rad51 molecules from the moving fork, creating single-stranded DNA (ssDNA) regions that serve as sites for increased cohesin loading and SCC establishment. Thus, our results delineate a double role for Pds5 in protecting the cohesin ring and interacting with the DNA replication machinery. IMPORTANCE Sister chromatid cohesion is vital for faithful chromosome segregation, chromosome folding into loops, and gene expression. A multisubunit protein complex known as cohesin holds the sister chromatids from S phase until the anaphase stage. In this study, we explore the function of the essential cohesin subunit Pds5 in the regulation of sister chromatid cohesion. We performed two independent genetic screens to bypass the function of the Pds5 protein. We observe that Pds5 protein is a cohesin stabilizer, and elevating the levels of Mcd1 protein along with SUMO-PCNA accumulation on chromatin can compensate for the loss of the PDS5 gene. In addition, Pds5 plays a role in coordinating the DNA replication and sister chromatid cohesion establishment. This work elucidates the function of cohesin subunit Pds5, the G1 cyclin Cln2, and replication factors PCNA, Elg1, and Srs2 in the proper regulation of sister chromatid cohesion.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Ziv Itzkovich
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Elisa Alonso-Perez
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Hend Bishara
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Barbara Dunn
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Gavin Sherlock
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
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24
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KSHV RTA antagonizes SMC5/6 complex-induced viral chromatin compaction by hijacking the ubiquitin-proteasome system. PLoS Pathog 2022; 18:e1010744. [PMID: 35914008 PMCID: PMC9371351 DOI: 10.1371/journal.ppat.1010744] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 08/11/2022] [Accepted: 07/15/2022] [Indexed: 02/07/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is a double-stranded DNA virus with the capacity to establish life-long latent infection. During latent infection, the viral genome persists as a circular episome that associates with cellular histones and exists as a nonintegrated minichromosome in the nucleus of infected cells. Chromatin structure and epigenetic programming are required for the proper control of viral gene expression and stable maintenance of viral DNA. However, there is still limited knowledge regarding how the host regulates the chromatin structure and maintenance of episomal DNA. Here, we found that the cellular protein structural maintenance of chromosome (SMC) complex SMC5/6 recognizes and associates with the KSHV genome to inhibit its replication. The SMC5/6 complex can bind to the KSHV genome and suppress KSHV gene transcription by condensing the viral chromatin and creating a repressive chromatin structure. Correspondingly, KSHV employs an antagonistic strategy by utilizing the viral protein RTA to degrade the SMC5/6 complex and antagonize the inhibitory effect of this complex on viral gene transcription. Interestingly, this antagonistic mechanism of RTA is evolutionarily conserved among γ-herpesviruses. Our work suggests that the SMC5/6 complex is a new host factor that restricts KSHV replication. KSHV can establish life-long latent infection. During latency, the viral genome is maintained as an extrachromosomal episome in the infected cells. We demonstrated that the host protein SMC5/6 complex associates with the KSHV genome and results in direct transcriptional inhibition by creating a transcriptionally repressive chromatin structure of the viral genome. RTA, the master switch protein of KSHV, can hijack the ubiquitin-proteasome system to degrade the SMC5/6 complex to antagonize its inhibitory effect on viral gene transcription. Interestingly, this function of RTA is evolutionarily conserved among γ-herpesviruses.
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Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ, Alt FW, Jackson SP, Balmus G, Lescale C, Deriano L. SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination. Nat Commun 2022; 13:3707. [PMID: 35764636 PMCID: PMC9240092 DOI: 10.1038/s41467-022-31287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
SHLD1 is part of the Shieldin (SHLD) complex, which acts downstream of 53BP1 to counteract DNA double-strand break (DSB) end resection and promote DNA repair via non-homologous end-joining (NHEJ). While 53BP1 is essential for immunoglobulin heavy chain class switch recombination (CSR), long-range V(D)J recombination and repair of RAG-induced DSBs in XLF-deficient cells, the function of SHLD during these processes remains elusive. Here we report that SHLD1 is dispensable for lymphocyte development and RAG-mediated V(D)J recombination, even in the absence of XLF. By contrast, SHLD1 is essential for restricting resection at AID-induced DSB ends in both NHEJ-proficient and NHEJ-deficient B cells, providing an end-protection mechanism that permits productive CSR by NHEJ and alternative end-joining. Finally, we show that this SHLD1 function is required for orientation-specific joining of AID-initiated DSBs. Our data thus suggest that 53BP1 promotes V(D)J recombination and CSR through two distinct mechanisms: SHLD-independent synapsis of V(D)J segments and switch regions within chromatin, and SHLD-dependent protection of AID-DSB ends against resection.
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Affiliation(s)
- Estelle Vincendeau
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Wenming Wei
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Xuefei Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
| | - Cyril Planchais
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - Wei Yu
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Hélène Lenden-Hasse
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
- Institut Pasteur, Hub de Bioinformatique et Biostatistique, Département de Biologie Computationnelle, 75015, Paris, France
| | - Juliana Pipoli da Fonseca
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Chloé Lescale
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
| | - Ludovic Deriano
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
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Hou W, Li Y, Zhang J, Xia Y, Wang X, Chen H, Lou H. Cohesin in DNA damage response and double-strand break repair. Crit Rev Biochem Mol Biol 2022; 57:333-350. [PMID: 35112600 DOI: 10.1080/10409238.2022.2027336] [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: 08/05/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 11/03/2022]
Abstract
Cohesin, a four-subunit ring comprising SMC1, SMC3, RAD21 and SA1/2, tethers sister chromatids by DNA replication-coupled cohesion (RC-cohesion) to guarantee correct chromosome segregation during cell proliferation. Postreplicative cohesion, also called damage-induced cohesion (DI-cohesion), is an emerging critical player in DNA damage response (DDR). In this review, we sum up recent progress on how cohesin regulates the DNA damage checkpoint activation and repair pathway choice, emphasizing postreplicative cohesin loading and DI-cohesion establishment in yeasts and mammals. DI-cohesion and RC-cohesion show distinct features in many aspects. DI-cohesion near or far from the break sites might undergo different regulations and execute different tasks in DDR and DSB repair. Furthermore, some open questions in this field and the significance of this new scenario to our understanding of genome stability maintenance and cohesinopathies are discussed.
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Affiliation(s)
- Wenya Hou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yan Li
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jiaxin Zhang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yisui Xia
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xueting Wang
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Hongxiang Chen
- Union Shenzhen Hospital, Department of Dermatology, Huazhong University of Science and Technology (Nanshan Hospital), Shenzhen, Guangdong, China
| | - Huiqiang Lou
- Shenzhen University General Hospital, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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Scherzer M, Giordano F, Ferran MS, Ström L. Recruitment of Scc2/4 to double-strand breaks depends on γH2A and DNA end resection. Life Sci Alliance 2022; 5:e202101244. [PMID: 35086935 PMCID: PMC8807874 DOI: 10.26508/lsa.202101244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination enables cells to overcome the threat of DNA double-strand breaks (DSBs), allowing for repair without the loss of genetic information. Central to the homologous recombination repair process is the de novo loading of cohesin around a DSB by its loader complex Scc2/4. Although cohesin's DSB accumulation has been explored in numerous studies, the prerequisites for Scc2/4 recruitment during the repair process are still elusive. To address this question, we combine chromatin immunoprecipitation-qPCR with a site-specific DSB in vivo, in Saccharomyces cerevisiae We find that Scc2 DSB recruitment relies on γH2A and Tel1, but as opposed to cohesin, not on Mec1. We further show that the binding of Scc2, which emanates from the break site, depends on and coincides with DNA end resection. Absence of chromatin remodeling at the DSB affects Scc2 binding and DNA end resection to a comparable degree, further indicating the latter to be a major driver for Scc2 recruitment. Our results shed light on the intricate DSB repair cascade leading to the recruitment of Scc2/4 and subsequent loading of cohesin.
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Affiliation(s)
- Martin Scherzer
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fosco Giordano
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria Solé Ferran
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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28
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A walk through the SMC cycle: From catching DNAs to shaping the genome. Mol Cell 2022; 82:1616-1630. [PMID: 35477004 DOI: 10.1016/j.molcel.2022.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 02/02/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
SMC protein complexes are molecular machines that provide structure to chromosomes. These complexes bridge DNA elements and by doing so build DNA loops in cis and hold together the sister chromatids in trans. We discuss how drastic conformational changes allow SMC complexes to build such intricate DNA structures. The tight regulation of these complexes controls fundamental chromosomal processes such as transcription, recombination, repair, and mitosis.
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29
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Rinaldi L, Fettweis G, Kim S, Garcia DA, Fujiwara S, Johnson TA, Tettey TT, Ozbun L, Pegoraro G, Puglia M, Blagoev B, Upadhyaya A, Stavreva DA, Hager GL. The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation. SCIENCE ADVANCES 2022; 8:eabj8360. [PMID: 35353576 PMCID: PMC8967222 DOI: 10.1126/sciadv.abj8360] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 02/07/2022] [Indexed: 05/13/2023]
Abstract
The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor (TF) and the cohesin loader NIPBL regulate enhancer-dependent gene activity. Using mass spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that the glucocorticoid (GC) receptor (GR) interacts with NIPBL and the cohesin complex at the chromatin level, promoting loop extrusion and long-range gene regulation. Real-time single-molecule experiments show that loss of cohesin markedly diminishes the concentration of TF molecules at specific nuclear confinement sites, increasing TF local concentration and promoting gene regulation. Last, patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to GCs, suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, resulting in poor response to GC treatment.
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Affiliation(s)
- Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A. Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Saori Fujiwara
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas A. Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Theophilus T. Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laurent Ozbun
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD 20892, USA
| | - Michele Puglia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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30
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Osadska M, Selicky T, Kretova M, Jurcik J, Sivakova B, Cipakova I, Cipak L. The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability. Int J Mol Sci 2022; 23:3939. [PMID: 35409298 PMCID: PMC8999970 DOI: 10.3390/ijms23073939] [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: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cohesin, a multi-subunit protein complex, plays important roles in sister chromatid cohesion, DNA replication, chromatin organization, gene expression, transcription regulation, and the recombination or repair of DNA damage. Recently, several studies suggested that the functions of cohesin rely not only on cohesin-related protein-protein interactions, their post-translational modifications or specific DNA modifications, but that some RNA processing factors also play an important role in the regulation of cohesin functions. Therefore, the mutations and changes in the expression of cohesin subunits or alterations in the interactions between cohesin and RNA processing factors have been shown to have an impact on cohesion, the fidelity of chromosome segregation and, ultimately, on genome stability. In this review, we provide an overview of the cohesin complex and its role in chromosome segregation, highlight the causes and consequences of mutations and changes in the expression of cohesin subunits, and discuss the RNA processing factors that participate in the regulation of the processes involved in chromosome segregation. Overall, an understanding of the molecular determinants of the interplay between cohesin and RNA processing factors might help us to better understand the molecular mechanisms ensuring the integrity of the genome.
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Affiliation(s)
- Michaela Osadska
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Miroslava Kretova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia;
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
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31
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Zuilkoski CM, Skibbens RV. Integrating Sister Chromatid Cohesion Establishment to DNA Replication. Genes (Basel) 2022; 13:genes13040625. [PMID: 35456431 PMCID: PMC9032331 DOI: 10.3390/genes13040625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
The intersection through which two fundamental processes meet provides a unique vantage point from which to view cellular regulation. On the one hand, DNA replication is at the heart of cell division, generating duplicate chromosomes that allow each daughter cell to inherit a complete copy of the parental genome. Among other factors, the PCNA (proliferating cell nuclear antigen) sliding clamp ensures processive DNA replication during S phase and is essential for cell viability. On the other hand, the process of chromosome segregation during M phase—an act that occurs long after DNA replication—is equally fundamental to a successful cell division. Eco1/Ctf7 ensures that chromosomes faithfully segregate during mitosis, but functions during DNA replication to activate cohesins and thereby establish cohesion between sister chromatids. To achieve this, Eco1 binds PCNA and numerous other DNA replication fork factors that include MCM helicase, Chl1 helicase, and the Rtt101-Mms1-Mms22 E3 ubiquitin ligase. Here, we review the multi-faceted coordination between cohesion establishment and DNA replication. SUMMARY STATEMENT: New findings provide important insights into the mechanisms through which DNA replication and the establishment of sister chromatid cohesion are coupled.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47401, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, USA;
- Correspondence: ; Tel.: +610-758-6162
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Higashi TL, Uhlmann F. SMC complexes: Lifting the lid on loop extrusion. Curr Opin Cell Biol 2022; 74:13-22. [PMID: 35016058 PMCID: PMC9089308 DOI: 10.1016/j.ceb.2021.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 01/02/2023]
Abstract
Loop extrusion has emerged as a prominent hypothesis for how SMC complexes shape chromosomes - single molecule in vitro observations have yielded fascinating images of this process. When not extruding loops, SMC complexes are known to topologically entrap one or more DNAs. Here, we review how structural insight into the SMC complex cohesin has led to a molecular framework for both activities: a Brownian ratchet motion, associated with topological DNA entry, might repeat itself to elicit loop extrusion. After contrasting alternative loop extrusion models, we explore whether topological loading or loop extrusion is more adept at explaining in vivo SMC complex function. SMC variants that experimentally separate topological loading from loop extrusion will in the future probe their respective contributions to chromosome biology.
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Affiliation(s)
- Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Department of Cellular Biochemistry, Kyushu University, Fukuoka, 812-8582, Japan
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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Bonato A, Michieletto D. Three-dimensional loop extrusion. Biophys J 2021; 120:5544-5552. [PMID: 34793758 PMCID: PMC8715238 DOI: 10.1016/j.bpj.2021.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/30/2022] Open
Abstract
Loop extrusion convincingly describes how certain structural maintenance of chromosome (SMC) proteins mediate the formation of large DNA loops. Yet most of the existing computational models cannot reconcile recent in vitro observations showing that condensins can traverse each other, bypass large roadblocks, and perform steps longer than their own size. To fill this gap, we propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion, which not only reproduces the experimental features of loop extrusion by one SMC complex but also predicts the formation of so-called Z-loops via the interaction of two or more SMCs extruding along the same DNA substrate. By performing molecular dynamics simulations of this model, we discover that the experimentally observed asymmetry in the different types of Z-loops is a natural consequence of the DNA tethering in vitro. Intriguingly, our model predicts this bias to disappear in the absence of tethering and a third type of Z-loop, which has not yet been identified in experiments, to appear. Our model naturally explains roadblock bypassing and the appearance of steps larger than the SMC size as a consequence of non-contiguous DNA grabbing. Finally, this study is the first, to our knowledge, to address how Z-loops and bypassing might occur in a way that is broadly consistent with existing cis-only 1D loop extrusion models.
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Affiliation(s)
- Andrea Bonato
- University of Edinburgh, SUPA, School of Physics and Astronomy, Peter Guthrie Road, Edinburgh, UK
| | - Davide Michieletto
- University of Edinburgh, SUPA, School of Physics and Astronomy, Peter Guthrie Road, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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34
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Yueh WT, Singh VP, Gerton JL. Maternal Smc3 protects the integrity of the zygotic genome through DNA replication and mitosis. Development 2021; 148:dev199800. [PMID: 34935904 PMCID: PMC8722392 DOI: 10.1242/dev.199800] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/22/2021] [Indexed: 01/10/2023]
Abstract
Aneuploidy is frequently observed in oocytes and early embryos, begging the question of how genome integrity is monitored and preserved during this crucial period. SMC3 is a subunit of the cohesin complex that supports genome integrity, but its role in maintaining the genome during this window of mammalian development is unknown. We discovered that, although depletion of Smc3 following meiotic S phase in mouse oocytes allowed accurate meiotic chromosome segregation, adult females were infertile. We provide evidence that DNA lesions accumulated following S phase in SMC3-deficient zygotes, followed by mitosis with lagging chromosomes, elongated spindles, micronuclei, and arrest at the two-cell stage. Remarkably, although centromeric cohesion was defective, the dosage of SMC3 was sufficient to enable embryogenesis in juvenile mutant females. Our findings suggest that, despite previous reports of aneuploidy in early embryos, chromosome missegregation in zygotes halts embryogenesis at the two-cell stage. Smc3 is a maternal gene with essential functions in the repair of spontaneous damage associated with DNA replication and subsequent chromosome segregation in zygotes, making cohesin a key protector of the zygotic genome.
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Affiliation(s)
- Wei-Ting Yueh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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35
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van Schie JJM, de Lange J. The Interplay of Cohesin and the Replisome at Processive and Stressed DNA Replication Forks. Cells 2021; 10:3455. [PMID: 34943967 PMCID: PMC8700348 DOI: 10.3390/cells10123455] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex facilitates faithful chromosome segregation by pairing the sister chromatids after DNA replication until mitosis. In addition, cohesin contributes to proficient and error-free DNA replication. Replisome progression and establishment of sister chromatid cohesion are intimately intertwined processes. Here, we review how the key factors in DNA replication and cohesion establishment cooperate in unperturbed conditions and during DNA replication stress. We discuss the detailed molecular mechanisms of cohesin recruitment and the entrapment of replicated sister chromatids at the replisome, the subsequent stabilization of sister chromatid cohesion via SMC3 acetylation, as well as the role and regulation of cohesin in the response to DNA replication stress.
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Affiliation(s)
- Janne J. M. van Schie
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Job de Lange
- Cancer Center Amsterdam, Department of Human Genetics, Section Oncogenetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
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Kawasumi R, Abe T, Psakhye I, Miyata K, Hirota K, Branzei D. Vertebrate CTF18 and DDX11 essential function in cohesion is bypassed by preventing WAPL-mediated cohesin release. Genes Dev 2021; 35:1368-1382. [PMID: 34503989 PMCID: PMC8494208 DOI: 10.1101/gad.348581.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/16/2021] [Indexed: 01/26/2023]
Abstract
The alternative PCNA loader containing CTF18-DCC1-CTF8 facilitates sister chromatid cohesion (SCC) by poorly defined mechanisms. Here we found that in DT40 cells, CTF18 acts complementarily with the Warsaw breakage syndrome DDX11 helicase in mediating SCC and proliferation. We uncover that the lethality and cohesion defects of ctf18 ddx11 mutants are associated with reduced levels of chromatin-bound cohesin and rescued by depletion of WAPL, a cohesin-removal factor. On the contrary, high levels of ESCO1/2 acetyltransferases that acetylate cohesin to establish SCC do not rescue ctf18 ddx11 phenotypes. Notably, the tight proximity of sister centromeres and increased anaphase bridges characteristic of WAPL-depleted cells are abrogated by loss of both CTF18 and DDX11 The results reveal that vertebrate CTF18 and DDX11 collaborate to provide sufficient amounts of chromatin-loaded cohesin available for SCC generation in the presence of WAPL-mediated cohesin-unloading activity. This process modulates chromosome structure and is essential for cellular proliferation in vertebrates.
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Affiliation(s)
- Ryotaro Kawasumi
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
| | - Takuya Abe
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ivan Psakhye
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
| | - Keiji Miyata
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan
| | - Dana Branzei
- International Foundation of Medicine (IFOM), the Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
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37
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Garcia P, Fernandez-Hernandez R, Cuadrado A, Coca I, Gomez A, Maqueda M, Latorre-Pellicer A, Puisac B, Ramos FJ, Sandoval J, Esteller M, Mosquera JL, Rodriguez J, Pié J, Losada A, Queralt E. Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome. Nat Commun 2021; 12:4551. [PMID: 34315879 PMCID: PMC8316422 DOI: 10.1038/s41467-021-24808-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/05/2021] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, NIPBL/Scc2, were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanisms driving CdLS phenotypes are not understood. In addition to its canonical role in sister chromatid cohesion, cohesin is implicated in the spatial organization of the genome. Here, we investigate the transcriptome of CdLS patient-derived primary fibroblasts and observe the downregulation of genes involved in development and system skeletal organization, providing a link to the developmental alterations and limb abnormalities characteristic of CdLS patients. Genome-wide distribution studies demonstrate a global reduction of NIPBL at the NIPBL-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at NIPBL-occupied sites at CpG islands potentially due to reduced cohesin translocation along chromosomes, and fewer cohesin peaks colocalize with CTCF.
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Affiliation(s)
- Patricia Garcia
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
| | - Rita Fernandez-Hernandez
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ignacio Coca
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Grup de Recerca de Reumatologia, Parc Científic de Barcelona, Barcelona, Spain
| | - Maria Maqueda
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Feliciano J Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit (UByMP) and Epigenomics Core Facility, Health Research Institute La Fe (IISLaFe), Valencia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Jairo Rodriguez
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ethel Queralt
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
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38
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Higashi TL, Pobegalov G, Tang M, Molodtsov MI, Uhlmann F. A Brownian ratchet model for DNA loop extrusion by the cohesin complex. eLife 2021; 10:e67530. [PMID: 34309513 PMCID: PMC8313234 DOI: 10.7554/elife.67530] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin's heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function.
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Affiliation(s)
- Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Georgii Pobegalov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Minzhe Tang
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Maxim I Molodtsov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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39
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Henrikus SS, Costa A. Towards a Structural Mechanism for Sister Chromatid Cohesion Establishment at the Eukaryotic Replication Fork. BIOLOGY 2021; 10:466. [PMID: 34073213 PMCID: PMC8229022 DOI: 10.3390/biology10060466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022]
Abstract
Cohesion between replicated chromosomes is essential for chromatin dynamics and equal segregation of duplicated genetic material. In the G1 phase, the ring-shaped cohesin complex is loaded onto duplex DNA, enriching at replication start sites, or "origins". During the same phase of the cell cycle, and also at the origin sites, two MCM helicases are loaded as symmetric double hexamers around duplex DNA. During the S phase, and through the action of replication factors, cohesin switches from encircling one parental duplex DNA to topologically enclosing the two duplicated DNA filaments, which are known as sister chromatids. Despite its vital importance, the structural mechanism leading to sister chromatid cohesion establishment at the replication fork is mostly elusive. Here we review the current understanding of the molecular interactions between the replication machinery and cohesin, which support sister chromatid cohesion establishment and cohesin function. In particular, we discuss how cryo-EM is shedding light on the mechanisms of DNA replication and cohesin loading processes. We further expound how frontier cryo-EM approaches, combined with biochemistry and single-molecule fluorescence assays, can lead to understanding the molecular basis of sister chromatid cohesion establishment at the replication fork.
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Affiliation(s)
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
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40
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Liang XY, Battini N, Sui YF, Ansari MF, Gan LL, Zhou CH. Aloe-emodin derived azoles as a new structural type of potential antibacterial agents: design, synthesis, and evaluation of the action on membrane, DNA, and MRSA DNA isomerase. RSC Med Chem 2021; 12:602-608. [PMID: 34046631 PMCID: PMC8128066 DOI: 10.1039/d0md00429d] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/30/2022] Open
Abstract
As serious global drug resistance motivated the exploration of new structural drugs, we developed a type of novel structural aloe-emodin azoles as potential antibacterial agents in this work. Some target aloe-emodin azoles displayed effective activity against the tested strains, especially tetrazolyl aloe-emodin 4b showed a low MIC value of 2 μg mL-1 towards MRSA, being more efficient than the reference drug norfloxacin (MIC = 8 μg mL-1). Also, the active molecule 4b exhibited low cytotoxicity against LO2 cells with no distinct tendency to induce the concerned resistance towards MRSA. The tetrazolyl derivative 4b was preliminarily investigated for the possible mechanism; it was revealed that tetrazolyl derivative 4b could both disrupt the integrity of MRSA membrane and form 4b-DNA supramolecular complex by intercalating into DNA. Moreover, tetrazolyl aloe-emodin 4b could bind with MRSA DNA isomerase at multiple sites through hydrogen bonds in molecular simulation.
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Affiliation(s)
- Xin-Yuan Liang
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Narsaiah Battini
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Yan-Fei Sui
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Mohammad Fawad Ansari
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Lin-Ling Gan
- Chongqing Engineering Research Center of Pharmaceutical Sciences, School of Pharmacy, Chongqing Medical and Pharmaceutical College Chongqing 401331 PR China
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
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41
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Sakata R, Niwa K, Ugarte La Torre D, Gu C, Tahara E, Takada S, Nishiyama T. Opening of cohesin's SMC ring is essential for timely DNA replication and DNA loop formation. Cell Rep 2021; 35:108999. [PMID: 33909997 DOI: 10.1016/j.celrep.2021.108999] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/16/2021] [Accepted: 03/24/2021] [Indexed: 11/15/2022] Open
Abstract
The ring-shaped cohesin complex topologically binds to DNA to establish sister chromatid cohesion. This topological binding creates a structural obstacle to genome-wide chromosomal events, such as replication. Here, we examine how conformational changes in cohesin circumvent being an obstacle in human cells. We show that ATP hydrolysis-driven head disengagement, leading to the structural maintenance of chromosome (SMC) ring opening, is essential for the progression of DNA replication. Closure of the SMC ring stalls replication in a checkpoint-independent manner. The SMC ring opening also facilitates sister chromatid resolution and chromosome segregation in mitosis. Single-molecule analyses reveal that forced closure of the SMC ring suppresses the translocation of cohesin on DNA as well as the formation of stable DNA loops. Our results suggest that the ATP hydrolysis-driven SMC ring opening makes topologically bound cohesin dynamic on DNA to achieve replication-dependent cohesion in the S phase and to resolve cohesion in mitosis. Thus, the SMC ring opening could be a fundamental mechanism to modulate both cohesion and higher-order genome structure.
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Affiliation(s)
- Ryota Sakata
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kyoma Niwa
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Diego Ugarte La Torre
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8501, Japan
| | - Chenyang Gu
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8501, Japan
| | - Eri Tahara
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo Kyoto 606-8501, Japan
| | - Tomoko Nishiyama
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
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42
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Studying chromosome biology with single-molecule resolution in Xenopus laevis egg extracts. Essays Biochem 2021; 65:17-26. [PMID: 33438722 PMCID: PMC8056035 DOI: 10.1042/ebc20200026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/16/2020] [Accepted: 11/25/2020] [Indexed: 01/11/2023]
Abstract
Cell-free extracts from Xenopus laevis eggs are a model system for studying chromosome biology. Xenopus egg extracts can be synchronised in different cell cycle stages, making them useful for studying DNA replication, DNA repair and chromosome organisation. Combining single-molecule approaches with egg extracts is an exciting development being used to reveal molecular mechanisms that are difficult to study using conventional approaches. Fluorescence-based single-molecule imaging of surface-tethered DNAs has been used to visualise labelled protein movements on stretched DNA, the dynamics of DNA–protein complexes and extract-dependent structural rearrangement of stained DNA. Force-based single-molecule techniques are an alternative approach to measure mechanics of DNA and proteins. In this essay, the details of these single-molecule techniques, and the insights into chromosome biology they provide, will be discussed.
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43
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Etheridge TJ, Villahermosa D, Campillo-Funollet E, Herbert AD, Irmisch A, Watson AT, Dang HQ, Osborne MA, Oliver AW, Carr AM, Murray JM. Live-cell single-molecule tracking highlights requirements for stable Smc5/6 chromatin association in vivo. eLife 2021; 10:e68579. [PMID: 33860765 PMCID: PMC8075580 DOI: 10.7554/elife.68579] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
The essential Smc5/6 complex is required in response to replication stress and is best known for ensuring the fidelity of homologous recombination. Using single-molecule tracking in live fission yeast to investigate Smc5/6 chromatin association, we show that Smc5/6 is chromatin associated in unchallenged cells and this depends on the non-SMC protein Nse6. We define a minimum of two Nse6-dependent sub-pathways, one of which requires the BRCT-domain protein Brc1. Using defined mutants in genes encoding the core Smc5/6 complex subunits, we show that the Nse3 double-stranded DNA binding activity and the arginine fingers of the two Smc5/6 ATPase binding sites are critical for chromatin association. Interestingly, disrupting the single-stranded DNA (ssDNA) binding activity at the hinge region does not prevent chromatin association but leads to elevated levels of gross chromosomal rearrangements during replication restart. This is consistent with a downstream function for ssDNA binding in regulating homologous recombination.
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Affiliation(s)
- Thomas J Etheridge
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Desiree Villahermosa
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Eduard Campillo-Funollet
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Alex David Herbert
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Anja Irmisch
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Adam T Watson
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Hung Q Dang
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Mark A Osborne
- Chemistry Department, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Johanne M Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
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44
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Boavida A, Santos D, Mahtab M, Pisani FM. Functional Coupling between DNA Replication and Sister Chromatid Cohesion Establishment. Int J Mol Sci 2021; 22:2810. [PMID: 33802105 PMCID: PMC8001024 DOI: 10.3390/ijms22062810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 12/28/2022] Open
Abstract
Several lines of evidence suggest the existence in the eukaryotic cells of a tight, yet largely unexplored, connection between DNA replication and sister chromatid cohesion. Tethering of newly duplicated chromatids is mediated by cohesin, an evolutionarily conserved hetero-tetrameric protein complex that has a ring-like structure and is believed to encircle DNA. Cohesin is loaded onto chromatin in telophase/G1 and converted into a cohesive state during the subsequent S phase, a process known as cohesion establishment. Many studies have revealed that down-regulation of a number of DNA replication factors gives rise to chromosomal cohesion defects, suggesting that they play critical roles in cohesion establishment. Conversely, loss of cohesin subunits (and/or regulators) has been found to alter DNA replication fork dynamics. A critical step of the cohesion establishment process consists in cohesin acetylation, a modification accomplished by dedicated acetyltransferases that operate at the replication forks. Defects in cohesion establishment give rise to chromosome mis-segregation and aneuploidy, phenotypes frequently observed in pre-cancerous and cancerous cells. Herein, we will review our present knowledge of the molecular mechanisms underlying the functional link between DNA replication and cohesion establishment, a phenomenon that is unique to the eukaryotic organisms.
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Affiliation(s)
- Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
| | - Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
| | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Francesca M. Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (A.B.); (D.S.); (M.M.)
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45
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Santos D, Mahtab M, Boavida A, Pisani FM. Role of the DDX11 DNA Helicase in Warsaw Breakage Syndrome Etiology. Int J Mol Sci 2021; 22:2308. [PMID: 33669056 PMCID: PMC7956524 DOI: 10.3390/ijms22052308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/23/2022] Open
Abstract
Warsaw breakage syndrome (WABS) is a genetic disorder characterized by sister chromatid cohesion defects, growth retardation, microcephaly, hearing loss and other variable clinical manifestations. WABS is due to biallelic mutations of the gene coding for the super-family 2 DNA helicase DDX11/ChlR1, orthologous to the yeast chromosome loss protein 1 (Chl1). WABS is classified in the group of "cohesinopathies", rare hereditary diseases that are caused by mutations in genes coding for subunits of the cohesin complex or protein factors having regulatory roles in the sister chromatid cohesion process. In fact, among the cohesion regulators, an important player is DDX11, which is believed to be important for the functional coupling of DNA synthesis and cohesion establishment at the replication forks. Here, we will review what is known about the molecular and cellular functions of human DDX11 and its role in WABS etiopathogenesis, even in light of recent findings on the role of cohesin and its regulator network in promoting chromatin loop formation and regulating chromatin spatial organization.
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Affiliation(s)
- Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| | - Francesca M. Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
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46
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Gerguri T, Fu X, Kakui Y, Khatri BS, Barrington C, Bates PA, Uhlmann F. Comparison of loop extrusion and diffusion capture as mitotic chromosome formation pathways in fission yeast. Nucleic Acids Res 2021; 49:1294-1312. [PMID: 33434270 PMCID: PMC7897502 DOI: 10.1093/nar/gkaa1270] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 01/17/2023] Open
Abstract
Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long Schizosaccharomyces pombe chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin compaction. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.
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Affiliation(s)
- Tereza Gerguri
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Waseda Institute for Advanced Study, Waseda University, 1-21-1 Nishiwaseda, Shinjuku-ku, Tokyo 169-0051, Japan
| | - Bhavin S Khatri
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Christopher Barrington
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Paul A Bates
- Biomolecular Modelling 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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47
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Kurokawa Y, Murayama Y. DNA Binding by the Mis4 Scc2 Loader Promotes Topological DNA Entrapment by the Cohesin Ring. Cell Rep 2020; 33:108357. [PMID: 33176147 DOI: 10.1016/j.celrep.2020.108357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Cohesin, a critical mediator of genome organization including sister chromatid cohesion, is a ring-shaped multi-subunit ATPase that topologically embraces DNA. Its loading and function on chromosomes require the Scc2-Scc4 loader. Using biochemical reconstitution, we show here that the ability of the loader to bind DNA plays a critical role in promoting cohesin loading. Two distinct sites within the Mis4Scc2 subunit are found to cooperatively bind DNA. Mis4Scc2 initially forms a tertiary complex with cohesin on DNA and promotes subsequent topological DNA entrapment by cohesin through its DNA binding activity, a process that requires an additional DNA binding surface provided by Psm3Smc3, the ATPase domain of cohesin. Furthermore, we show that mutations in the two DNA binding sites of Mis4 impair the chromosomal loading of cohesin. These observations demonstrate the physiological importance of DNA binding by the loader and provide mechanistic insights into the process of topological cohesin loading.
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Affiliation(s)
- Yumiko Kurokawa
- Center for Frontier Research, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yasuto Murayama
- Center for Frontier Research, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111, Yata, Mishima, Shizuoka 411-8540, Japan.
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48
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Cutts EE, Vannini A. Condensin complexes: understanding loop extrusion one conformational change at a time. Biochem Soc Trans 2020; 48:2089-2100. [PMID: 33005926 PMCID: PMC7609036 DOI: 10.1042/bst20200241] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Condensin and cohesin, both members of the structural maintenance of chromosome (SMC) family, contribute to the regulation and structure of chromatin. Recent work has shown both condensin and cohesin extrude DNA loops and most likely work via a conserved mechanism. This review focuses on condensin complexes, highlighting recent in vitro work characterising DNA loop formation and protein structure. We discuss similarities between condensin and cohesin complexes to derive a possible mechanistic model, as well as discuss differences that exist between the different condensin isoforms found in higher eukaryotes.
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Affiliation(s)
- Erin E. Cutts
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, U.K
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, U.K
- Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy
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49
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Zuilkoski CM, Skibbens RV. PCNA promotes context-specific sister chromatid cohesion establishment separate from that of chromatin condensation. Cell Cycle 2020; 19:2436-2450. [PMID: 32926661 PMCID: PMC7553509 DOI: 10.1080/15384101.2020.1804221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022] Open
Abstract
Cellular genomes undergo various structural changes that include cis tethering (the tethering together of two loci within a single DNA molecule), which promotes chromosome condensation and transcriptional activation, and trans tethering (the tethering together of two DNA molecules), which promotes sister chromatid cohesion and DNA repair. The protein complex termed cohesin promotes both cis and trans forms of DNA tethering, but the extent to which these cohesin functions occur in temporally or spatially defined contexts remains largely unknown. Prior studies indicate that DNA polymerase sliding clamp PCNA recruits cohesin acetyltransferase Eco1, suggesting that sister chromatid cohesion is established in the context of the DNA replication fork. In support of this model, elevated levels of PCNA rescue the temperature growth and cohesion defects exhibited by eco1 mutant cells. Here, we test whether Eco1-dependent chromatin condensation is also promoted in the context of this DNA replication fork component. Our results reveal that overexpressed PCNA does not promote DNA condensation in eco1 mutant cells, even though Smc3 acetylation levels are increased. We further provide evidence that replication fork-associated E3 ligase impacts on Eco1 are more complex that previously described. In combination, the data suggests that Eco1 acetylates Smc3 and thus promotes sister chromatid cohesion in context of the DNA replication fork, whereas a distinct cohesin population participates in chromatin condensation outside the context of the DNA replication fork.
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Affiliation(s)
- Caitlin M. Zuilkoski
- Department of Biological Sciences, Lehigh University, 18015, Bethlehem, Pennsylvania, USA
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, 18015, Bethlehem, Pennsylvania, USA
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50
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Higashi TL, Eickhoff P, Sousa JS, Locke J, Nans A, Flynn HR, Snijders AP, Papageorgiou G, O'Reilly N, Chen ZA, O'Reilly FJ, Rappsilber J, Costa A, Uhlmann F. A Structure-Based Mechanism for DNA Entry into the Cohesin Ring. Mol Cell 2020; 79:917-933.e9. [PMID: 32755595 PMCID: PMC7507959 DOI: 10.1016/j.molcel.2020.07.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 07/10/2020] [Indexed: 01/26/2023]
Abstract
Despite key roles in sister chromatid cohesion and chromosome organization, the mechanism by which cohesin rings are loaded onto DNA is still unknown. Here we combine biochemical approaches and cryoelectron microscopy (cryo-EM) to visualize a cohesin loading intermediate in which DNA is locked between two gates that lead into the cohesin ring. Building on this structural framework, we design experiments to establish the order of events during cohesin loading. In an initial step, DNA traverses an N-terminal kleisin gate that is first opened upon ATP binding and then closed as the cohesin loader locks the DNA against the ATPase gate. ATP hydrolysis will lead to ATPase gate opening to complete DNA entry. Whether DNA loading is successful or results in loop extrusion might be dictated by a conserved kleisin N-terminal tail that guides the DNA through the kleisin gate. Our results establish the molecular basis for cohesin loading onto DNA.
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Affiliation(s)
- Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Patrik Eickhoff
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Joana S Sousa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Julia Locke
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrea Nans
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Helen R Flynn
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Nicola O'Reilly
- Peptide Chemistry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Zhuo A Chen
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Francis J O'Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alessandro Costa
- Macromolecular Machines 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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