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Arastonejad M, Arab D, Fatemi S, Golshanrad P. Unveiling the Significance of NCAP Family Genes in Adrenocortical Carcinoma and Adenoma Pathogenesis: A Molecular Bioinformatics Exploration. Cancer Inform 2024; 23:11769351241262211. [PMID: 39045040 PMCID: PMC11265250 DOI: 10.1177/11769351241262211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/09/2024] [Indexed: 07/25/2024] Open
Abstract
Objectives Adrenocortical carcinoma (ACC), a rare and aggressive adrenal cortex cancer, poses significant challenges due to high mortality, poor prognosis, and early post-surgery recurrence. Variability in survival across ACC stages emphasizes the need to uncover its molecular underpinnings. Adrenocortical adenoma, a benign tumor, adds to diagnostic challenges, highlighting the necessity for molecular insights. The Non-SMC Associated Condensin Complex (NCAP) gene family, recognized for roles in chromosomal structure and cell cycle control. This study focuses on evaluating NCAP gene functions and importance in ACC through gene expression profiling to identify diagnostic and therapeutic targets. Methods Microarray datasets from ACC patients, obtained from the Gene Expression Omnibus database, were normalized to eliminate batch effects. Differential expression analysis of NCAP family genes, facilitated by the GEPIA2 database, included survival and pathological stage evaluations. A Protein-Protein Interaction network was constructed using GeneMANIA, and additional insights were gained through Gene Ontology enrichment analysis, correlation analysis, and ROC curve analysis. Results ACC samples exhibited elevated levels of NCAPG, NCAPG2, and NCAPH compared to normal and adenoma samples. Increased expression of these genes correlated with poor overall survival, particularly in advanced disease stages. The Protein-Protein Interaction network highlighted interactions with related proteins, and Gene Ontology enrichment analysis demonstrated their involvement in chromosomal structure and control. Differentially expressed NCAP genes showed positive associations, and ROC curve analysis indicated their high discriminatory power in identifying ACC from adenoma and normal samples. Conclusion The study emphasizes the potential importance of NCAPG, NCAPG2, and NCAPH in ACC, suggesting roles in tumor aggressiveness and diagnostic relevance. These genes could serve as therapeutic targets and markers for ACC, but further exploration into their molecular activities and validation studies is imperative to fully harness their diagnostic and therapeutic potential, advancing precision medicine approaches against this rare but lethal malignancy.
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Affiliation(s)
- Mahshid Arastonejad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Daniyal Arab
- Department of Human Genetics, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Somayeh Fatemi
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Pezhman Golshanrad
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
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2
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Golov AK, Gavrilov AA. Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:601-625. [PMID: 38831499 DOI: 10.1134/s0006297924040023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/29/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
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Affiliation(s)
- Arkadiy K Golov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Technion - Israel Institute of Technology, Haifa, 3525433, Israel
| | - Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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3
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Lebreton J, Colin L, Chatre E, Bernard P. RNAP II antagonizes mitotic chromatin folding and chromosome segregation by condensin. Cell Rep 2024; 43:113901. [PMID: 38446663 DOI: 10.1016/j.celrep.2024.113901] [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: 08/27/2023] [Revised: 12/07/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Condensin shapes mitotic chromosomes by folding chromatin into loops, but whether it does so by DNA-loop extrusion remains speculative. Although loop-extruding cohesin is stalled by transcription, the impact of transcription on condensin, which is enriched at highly expressed genes in many species, remains unclear. Using degrons of Rpb1 or the torpedo nuclease Dhp1XRN2 to either deplete or displace RNAPII on chromatin in fission yeast metaphase cells, we show that RNAPII does not load condensin on DNA. Instead, RNAPII retains condensin in cis and hinders its ability to fold mitotic chromatin and to support chromosome segregation, consistent with the stalling of a loop extruder. Transcription termination by Dhp1 limits such a hindrance. Our results shed light on the integrated functioning of condensin, and we argue that a tight control of transcription underlies mitotic chromosome assembly by loop-extruding condensin.
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Affiliation(s)
- Jérémy Lebreton
- ENS de Lyon, University Lyon, 46 allée d'Italie, 69007 Lyon, France
| | - Léonard Colin
- CNRS Laboratory of Biology and Modelling of the Cell, UMR 5239, ENS de Lyon, 46 allée d'Italie, 69007 Lyon, France
| | - Elodie Chatre
- Lymic-Platim, University Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS UAR3444, Inserm US8, SFR Biosciences, 50 Avenue Tony Garnier, 69007 Lyon, France
| | - Pascal Bernard
- ENS de Lyon, University Lyon, 46 allée d'Italie, 69007 Lyon, France; CNRS Laboratory of Biology and Modelling of the Cell, UMR 5239, ENS de Lyon, 46 allée d'Italie, 69007 Lyon, France.
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4
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Colin L, Reyes C, Berthezene J, Maestroni L, Modolo L, Toselli E, Chanard N, Schaak S, Cuvier O, Gachet Y, Coulon S, Bernard P, Tournier S. Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase. eLife 2023; 12:RP89812. [PMID: 37988290 PMCID: PMC10662949 DOI: 10.7554/elife.89812] [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] [Indexed: 11/23/2023] Open
Abstract
The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here, we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.
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Affiliation(s)
- Léonard Colin
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Celine Reyes
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Julien Berthezene
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Laetitia Maestroni
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Laurent Modolo
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Esther Toselli
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Nicolas Chanard
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Stephane Schaak
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Olivier Cuvier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
- CBI, MCD-UMR5077, CNRS, Chromatin Dynamics TeamToulouseFrance
| | - Yannick Gachet
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
| | - Stephane Coulon
- CNRS, INSERM, Aix Marseille Université, Institut Paoli-Calmettes, CRCM, Equipe labellisée par la Ligue Nationale contre le CancerMarseilleFrance
| | - Pascal Bernard
- CNRS - Laboratory of Biology and Modelling of the CellLyonFrance
- ENS de Lyon, Université Lyon, site Jacques MonodLyonFrance
| | - Sylvie Tournier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPSToulouseFrance
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5
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Girke P, Seufert W. Targeting of Hmo1 to subcompartments of the budding yeast nucleolus. Mol Biol Cell 2023; 34:ar22. [PMID: 36696177 PMCID: PMC10011721 DOI: 10.1091/mbc.e22-07-0261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The nucleolus is a multilayered, membraneless organelle made up of liquidlike biogenesis compartments surrounding an array of ribosomal RNA genes (rDNA). Biogenesis factors accumulate in the outer compartments through RNA binding and phase separation promoted by intrinsically disordered protein regions. In contrast, the nucleolar localization of rDNA-binding proteins, which reside in the central chromatin compartment, is less well characterized. To gain mechanistic insight, we analyzed the localization, mitotic segregation, nucleic acid binding, and nuclear dynamics of the budding yeast rDNA-binding protein Hmo1. Deletion of the main DNA-binding domain, the HMG boxB, compromised Hmo1 transfer to daughter cells in mitosis and transcription-independent rDNA association but still allowed nucleolar localization. The C-terminal lysine-rich region turned out to be a combined nuclear and nucleolar localization sequence (NLS-NoLS). Its integrity was required for maximal enrichment and efficient retention of Hmo1 in the nucleolus and nucleolar localization of the ΔboxB construct. Moreover, the NLS-NoLS region was sufficient to promote nucleolar accumulation and bound nucleic acids in vitro with some preference for RNA. Bleaching experiments indicated mobility of Hmo1 inside the nucleolus but little exchange with the nucleoplasm. Thus, a bilayered targeting mechanism secures proper localization of Hmo1 to the nucleolus.
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Affiliation(s)
- Philipp Girke
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Wolfgang Seufert
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
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6
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Dyson S, Segura J, Martínez‐García B, Valdés A, Roca J. Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo. EMBO J 2021; 40:e105393. [PMID: 33155682 PMCID: PMC7780148 DOI: 10.15252/embj.2020105393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 12/24/2022] Open
Abstract
The juxtaposition of intracellular DNA segments, together with the DNA-passage activity of topoisomerase II, leads to the formation of DNA knots and interlinks, which jeopardize chromatin structure and gene expression. Recent studies in budding yeast have shown that some mechanism minimizes the knotting probability of intracellular DNA. Here, we tested whether this is achieved via the intrinsic capacity of topoisomerase II for simplifying the equilibrium topology of DNA; or whether it is mediated by SMC (structural maintenance of chromosomes) protein complexes like condensin or cohesin, whose capacity to extrude DNA loops could enforce dissolution of DNA knots by topoisomerase II. We show that the low knotting probability of DNA does not depend on the simplification capacity of topoisomerase II nor on the activities of cohesin or Smc5/6 complexes. However, inactivation of condensin increases the occurrence of DNA knots throughout the cell cycle. These results suggest an in vivo role for the DNA loop extrusion activity of condensin and may explain why condensin disruption produces a variety of alterations in interphase chromatin, in addition to persistent sister chromatid interlinks in mitotic chromatin.
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Grants
- BFU2015-67007-P Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- PID2019-109482GB-I00 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2016-077806 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2012-061167 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BES-2015-071597 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
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Affiliation(s)
- Sílvia Dyson
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Belén Martínez‐García
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Antonio Valdés
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB)Spanish National Research Council (CSIC)BarcelonaSpain
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7
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Finardi A, Massari LF, Visintin R. Anaphase Bridges: Not All Natural Fibers Are Healthy. Genes (Basel) 2020; 11:genes11080902. [PMID: 32784550 PMCID: PMC7464157 DOI: 10.3390/genes11080902] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
At each round of cell division, the DNA must be correctly duplicated and distributed between the two daughter cells to maintain genome identity. In order to achieve proper chromosome replication and segregation, sister chromatids must be recognized as such and kept together until their separation. This process of cohesion is mainly achieved through proteinaceous linkages of cohesin complexes, which are loaded on the sister chromatids as they are generated during S phase. Cohesion between sister chromatids must be fully removed at anaphase to allow chromosome segregation. Other (non-proteinaceous) sources of cohesion between sister chromatids consist of DNA linkages or sister chromatid intertwines. DNA linkages are a natural consequence of DNA replication, but must be timely resolved before chromosome segregation to avoid the arising of DNA lesions and genome instability, a hallmark of cancer development. As complete resolution of sister chromatid intertwines only occurs during chromosome segregation, it is not clear whether DNA linkages that persist in mitosis are simply an unwanted leftover or whether they have a functional role. In this review, we provide an overview of DNA linkages between sister chromatids, from their origin to their resolution, and we discuss the consequences of a failure in their detection and processing and speculate on their potential role.
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Affiliation(s)
- Alice Finardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Lucia F. Massari
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK;
| | - Rosella Visintin
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Correspondence: ; Tel.: +39-02-5748-9859; Fax: +39-02-9437-5991
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8
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Abstract
Until recently, our understanding of chromosome organization in higher eukaryotic cells has been based on analyses of large-scale, low-resolution changes in chromosomes structure. More recently, CRISPR-Cas9 technologies have allowed us to "zoom in" and visualize specific chromosome regions in live cells so that we can begin to examine in detail the dynamics of chromosome organization in individual cells. In this review, we discuss traditional methods of chromosome locus visualization and look at how CRISPR-Cas9 gene-targeting methodologies have helped improve their application. We also describe recent developments of the CRISPR-Cas9 technology that enable visualization of specific chromosome regions without the requirement for complex genetic manipulation.
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Affiliation(s)
- John K Eykelenboom
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee , Dundee, UK
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9
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Berthezene J, Reyes C, Li T, Coulon S, Bernard P, Gachet Y, Tournier S. Aurora B and condensin are dispensable for chromosome arm and telomere separation during meiosis II. Mol Biol Cell 2020; 31:889-905. [PMID: 32101485 PMCID: PMC7185977 DOI: 10.1091/mbc.e20-01-0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In mitosis, while the importance of kinetochore (KT)-microtubule (MT) attachment has been known for many years, increasing evidence suggests that telomere dysfunctions also perturb chromosome segregation by contributing to the formation of chromatin bridges at anaphase. Recent evidence suggests that Aurora B kinase ensures proper chromosome segregation during mitosis not only by controlling KT-MT attachment but also by regulating telomere and chromosome arm separation. However, whether and how Aurora B governs telomere separation during meiosis has remained unknown. Here, we show that fission yeast Aurora B localizes at telomeres during meiosis I and promotes telomere separation independently of the meiotic cohesin Rec8. In meiosis II, Aurora B controls KT-MT attachment but appears dispensable for telomere and chromosome arm separation. Likewise, condensin activity is nonessential in meiosis II for telomere and chromosome arm separation. Thus, in meiosis, the requirements for Aurora B are distinct at centromeres and telomeres, illustrating the critical differences in the control of chromosome segregation between mitosis and meiosis II.
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Affiliation(s)
- Julien Berthezene
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Céline Reyes
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Tong Li
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, 13273 Marseille, France
| | - Pascal Bernard
- CNRS-Laboratory of Biology and Modelling of the Cell, UMR 5239, 69364 Lyon, France.,ENS de Lyon, Université Lyon, F-69007 Lyon, France
| | - Yannick Gachet
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Sylvie Tournier
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
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10
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Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis. Mol Cell 2019; 75:131-144.e3. [PMID: 31204167 DOI: 10.1016/j.molcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
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Affiliation(s)
- Thomas M Guérin
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Claire Béneut
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Natalja Barinova
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Virginia López
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Alice Deshayes
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Karine Dubrana
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Stéphane Marcand
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France.
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11
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Mirkovic M, Oliveira RA. Centromeric Cohesin: Molecular Glue and Much More. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:485-513. [PMID: 28840250 DOI: 10.1007/978-3-319-58592-5_20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sister chromatid cohesion, mediated by the cohesin complex, is a prerequisite for faithful chromosome segregation during mitosis. Premature release of sister chromatid cohesion leads to random segregation of the genetic material and consequent aneuploidy. Multiple regulatory mechanisms ensure proper timing for cohesion establishment, concomitant with DNA replication, and cohesion release during the subsequent mitosis. Here we summarize the most important phases of the cohesin cycle and the coordination of cohesion release with the progression through mitosis. We further discuss recent evidence that has revealed additional functions for centromeric localization of cohesin in the fidelity of mitosis in metazoans. Beyond its well-established role as "molecular glue", centromeric cohesin complexes are now emerging as a scaffold for multiple fundamental processes during mitosis, including the formation of correct chromosome and kinetochore architecture, force balance with the mitotic spindle, and the association with key molecules that regulate mitotic fidelity, particularly at the chromosomal inner centromere. Centromeric chromatin may be thus seen as a dynamic place where cohesin ensures mitotic fidelity by multiple means.
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Affiliation(s)
- Mihailo Mirkovic
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156, Oeiras, Portugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156, Oeiras, Portugal.
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12
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Eykelenboom JK, Gierliński M, Yue Z, Hegarat N, Pollard H, Fukagawa T, Hochegger H, Tanaka TU. Live imaging of marked chromosome regions reveals their dynamic resolution and compaction in mitosis. J Cell Biol 2019; 218:1531-1552. [PMID: 30858191 PMCID: PMC6504890 DOI: 10.1083/jcb.201807125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/19/2018] [Accepted: 02/05/2019] [Indexed: 01/27/2023] Open
Abstract
When human cells enter mitosis, chromosomes undergo substantial changes in their organization to resolve sister chromatids and compact chromosomes. To comprehend the timing and coordination of these events, we need to evaluate the progression of both sister chromatid resolution and chromosome compaction in one assay. Here we achieved this by analyzing changes in configuration of marked chromosome regions over time, with high spatial and temporal resolution. This assay showed that sister chromatids cycle between nonresolved and partially resolved states with an interval of a few minutes during G2 phase before completing full resolution in prophase. Cohesins and WAPL antagonistically regulate sister chromatid resolution in late G2 and prophase while local enrichment of cohesin on chromosomes prevents precocious sister chromatid resolution. Moreover, our assay allowed quantitative evaluation of condensin II and I activities, which differentially promote sister chromatid resolution and chromosome compaction, respectively. Our assay reveals novel aspects of dynamics in mitotic chromosome resolution and compaction that were previously obscure in global chromosome assays.
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Affiliation(s)
- John K Eykelenboom
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
- Data Analysis Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zuojun Yue
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nadia Hegarat
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Hilary Pollard
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Helfrid Hochegger
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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13
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Girke P, Seufert W. Compositional reorganization of the nucleolus in budding yeast mitosis. Mol Biol Cell 2019; 30:591-606. [PMID: 30625028 PMCID: PMC6589692 DOI: 10.1091/mbc.e18-08-0524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 11/26/2022] Open
Abstract
The nucleolus is a membraneless organelle of the nucleus and the site of rRNA synthesis, maturation, and assembly into preribosomal particles. The nucleolus, organized around arrays of rRNA genes (rDNA), dissolves during prophase of mitosis in metazoans, when rDNA transcription ceases, and reforms in telophase, when rDNA transcription resumes. No such dissolution and reformation cycle exists in budding yeast, and the precise course of nucleolar segregation remains unclear. By quantitative live-cell imaging, we observed that the yeast nucleolus is reorganized in its protein composition during mitosis. Daughter cells received equal shares of preinitiation factors, which bind the RNA polymerase I promoter and the rDNA binding barrier protein Fob1, but only about one-third of RNA polymerase I and the processing factors Nop56 and Nsr1. The distribution bias was diminished in nonpolar chromosome segregation events observable in dyn1 mutants. Unequal distribution, however, was enhanced by defects in RNA polymerase I, suggesting that rDNA transcription supports nucleolar segregation. Indeed, quantification of pre-rRNA levels indicated ongoing rDNA transcription in yeast mitosis. These data, together with photobleaching experiments to measure nucleolar protein dynamics in anaphase, consolidate a model that explains the differential partitioning of nucleolar components in budding yeast mitosis.
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Affiliation(s)
- Philipp Girke
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Wolfgang Seufert
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
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14
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Kruitwagen T, Chymkowitch P, Denoth-Lippuner A, Enserink J, Barral Y. Centromeres License the Mitotic Condensation of Yeast Chromosome Arms. Cell 2018; 175:780-795.e15. [PMID: 30318142 PMCID: PMC6197839 DOI: 10.1016/j.cell.2018.09.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 06/14/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022]
Abstract
During mitosis, chromatin condensation shapes chromosomes as separate, rigid, and compact sister chromatids to facilitate their segregation. Here, we show that, unlike wild-type yeast chromosomes, non-chromosomal DNA circles and chromosomes lacking a centromere fail to condense during mitosis. The centromere promotes chromosome condensation strictly in cis through recruiting the kinases Aurora B and Bub1, which trigger the autonomous condensation of the entire chromosome. Shugoshin and the deacetylase Hst2 facilitated spreading the condensation signal to the chromosome arms. Targeting Aurora B to DNA circles or centromere-ablated chromosomes or releasing Shugoshin from PP2A-dependent inhibition bypassed the centromere requirement for condensation and enhanced the mitotic stability of DNA circles. Our data indicate that yeast cells license the chromosome-autonomous condensation of their chromatin in a centromere-dependent manner, excluding from this process non-centromeric DNA and thereby inhibiting their propagation.
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Affiliation(s)
- Tom Kruitwagen
- Institute of Biochemistry, Biology Department, ETH Zurich, 8093 Zurich, Switzerland
| | - Pierre Chymkowitch
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway
| | | | - Jorrit Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Faculty of Medicine, Center for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Faculty of Mathematics and Natural Sciences, Department of Biosciences, University of Oslo, Norway
| | - Yves Barral
- Institute of Biochemistry, Biology Department, ETH Zurich, 8093 Zurich, Switzerland.
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15
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Paliulis LV, Forer A. A review of "tethers": elastic connections between separating partner chromosomes in anaphase. PROTOPLASMA 2018; 255:733-740. [PMID: 29307016 DOI: 10.1007/s00709-017-1201-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/26/2017] [Indexed: 06/07/2023]
Abstract
Recent work has demonstrated the existence of elastic connections, or tethers, between the telomeres of separating partner chromosomes in anaphase. These tethers oppose the poleward spindle forces in anaphase. Functional evidence for tethers has been found in a wide range of animal taxa, suggesting that they might be present in all dividing cells. An examination of the literature on cell division from the nineteenth century to the present reveals that connections between separating partner chromosomes in anaphase have been described in some of the earliest observations of cell division. Here, we review what is currently known about connections between separating partner chromosomes in anaphase, and we speculate on possible functions of tethers, and on what they are made of and how one might determine their composition.
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Affiliation(s)
| | - Arthur Forer
- Biology Department, York University, North York, Toronto, Ontario, M3J 1P3, Canada
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16
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Wang HZ, Yang SH, Li GY, Cao X. Subunits of human condensins are potential therapeutic targets for cancers. Cell Div 2018; 13:2. [PMID: 29467813 PMCID: PMC5819170 DOI: 10.1186/s13008-018-0035-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/05/2018] [Indexed: 11/16/2022] Open
Abstract
The main role of condensins is to regulate chromosome condensation and segregation during cell cycles. Recently, it has been suggested in the literatures that subunits of condensin I and condensin II are involved in some human cancers. This paper will first briefly discuss discoveries of human condensins, their components and structures, and their multiple cellular functions. This will be followed by reviews of most recent studies on subunits of human condensins and their dysregulations or mutations in human cancers. It can be concluded that many of these subunits have potentials to be novel targets for cancer therapies. However, hCAP-D2, a subunit of human condensin I, has not been directly documented to be associated with any human cancers to date. This review hypothesizes that hCAP-D2 can also be a potential therapeutic target for human cancers, and therefore that all subunits of human condensins are potential therapeutic targets for human cancers.
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Affiliation(s)
- Hong-Zhen Wang
- 1School of Life Sciences, Jilin Normal University, Siping, 136000 P. R. China.,2Key Laboratory for Molecular Enzymology and Engineering of The Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012 P. R. China.,3Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, K1N 6N5 Canada
| | - Si-Han Yang
- 1School of Life Sciences, Jilin Normal University, Siping, 136000 P. R. China
| | - Gui-Ying Li
- 2Key Laboratory for Molecular Enzymology and Engineering of The Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012 P. R. China
| | - Xudong Cao
- 3Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, K1N 6N5 Canada
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17
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Matos-Perdomo E, Machín F. The ribosomal DNA metaphase loop of Saccharomyces cerevisiae gets condensed upon heat stress in a Cdc14-independent TORC1-dependent manner. Cell Cycle 2018; 17:200-215. [PMID: 29166821 PMCID: PMC5884360 DOI: 10.1080/15384101.2017.1407890] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Chromosome morphology in Saccharomyces cerevisiae is only visible at the microscopic level in the ribosomal DNA array (rDNA). The rDNA has been thus used as a model to characterize condensation and segregation of sister chromatids in mitosis. It has been established that the metaphase structure ("loop") depends, among others, on the condensin complex; whereas its segregation also depends on that complex, the Polo-like kinase Cdc5 and the cell cycle master phosphatase Cdc14. In addition, Cdc14 also drives rDNA hypercondensation in telophase. Remarkably, since all these components are essential for cell survival, their role on rDNA condensation and segregation was established by temperature-sensitive (ts) alleles. Here, we show that the heat stress (HS) used to inactivate ts alleles (25 ºC to 37 ºC shift) causes rDNA loop condensation in metaphase-arrested wild type cells, a result that can also be mimicked by other stresses that inhibit the TORC1 pathway. Because this condensation might challenge previous findings with ts alleles, we have repeated classical experiments of rDNA condensation and segregation, yet using instead auxin-driven degradation alleles (aid alleles). We have undertaken the protein degradation at lower temperatures (25 ºC) and concluded that the classical roles for condensin, Cdc5, Cdc14 and Cdc15 still prevailed. Thus, condensin degradation disrupts rDNA higher organization, Cdc14 and Cdc5 degradation precludes rDNA segregation and Cdc15 degradation still allows rDNA hypercompaction in telophase. Finally, we provide direct genetic evidence that this HS-mediated rDNA condensation is dependent on TORC1 but, unlike the one observed in anaphase, is independent of Cdc14.
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Affiliation(s)
- Emiliano Matos-Perdomo
- a Unidad de Investigación , Hospital Universitario Ntra Sra de Candelaria , Ctra del Rosario 145, 38010 , Santa Cruz de Tenerife , Spain.,b Universidad de La Laguna , Tenerife , Spain
| | - Félix Machín
- a Unidad de Investigación , Hospital Universitario Ntra Sra de Candelaria , Ctra del Rosario 145, 38010 , Santa Cruz de Tenerife , Spain
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18
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Abstract
The three-dimensional (3D) genome structure is highly ordered by a hierarchy of organizing events ranging from enhancer-promoter or gene-gene contacts to chromosomal territorial arrangement. It is becoming clear that the cohesin and condensin complexes are key molecular machines that organize the 3D genome structure. These complexes are highly conserved from simple systems, e.g., yeast cells, to the much more complex human system. Therefore, knowledge from the budding and fission yeast systems illuminates highly conserved molecular mechanisms of how cohesin and condensin establish the functional 3D genome structures. Here I discuss how these complexes are recruited across the yeast genomes, mediate distinct genome-organizing events such as gene contacts and topological domain formation, and participate in important nuclear activities including transcriptional regulation and chromosomal dynamics.
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Affiliation(s)
- Ken-Ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA;
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19
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Li S, Yue Z, Tanaka TU. Smc3 Deacetylation by Hos1 Facilitates Efficient Dissolution of Sister Chromatid Cohesion during Early Anaphase. Mol Cell 2017; 68:605-614.e4. [PMID: 29100057 PMCID: PMC5678280 DOI: 10.1016/j.molcel.2017.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/07/2017] [Accepted: 10/06/2017] [Indexed: 12/02/2022]
Abstract
Cohesins establish sister chromatid cohesion during S phase and are removed when cohesin Scc1 is cleaved by separase at anaphase onset. During this process, cohesin Smc3 undergoes a cycle of acetylation: Smc3 acetylation by Eco1 in S phase stabilizes cohesin association with chromosomes, and its deacetylation by Hos1 in anaphase allows re-use of Smc3 in the next cell cycle. Here we find that Smc3 deacetylation by Hos1 has a more immediate effect in the early anaphase of budding yeast. Hos1 depletion significantly delayed sister chromatid separation and segregation. Smc3 deacetylation facilitated removal of cohesins from chromosomes without changing Scc1 cleavage efficiency, promoting dissolution of cohesion. This action is probably due to disengagement of Smc1-Smc3 heads prompted by de-repression of their ATPase activity. We suggest Scc1 cleavage per se is insufficient for efficient dissolution of cohesion in early anaphase; subsequent Smc3 deacetylation, triggered by Scc1 cleavage, is also required.
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Affiliation(s)
- Shuyu Li
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Zuojun Yue
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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20
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Lazar-Stefanita L, Scolari VF, Mercy G, Muller H, Guérin TM, Thierry A, Mozziconacci J, Koszul R. Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle. EMBO J 2017; 36:2684-2697. [PMID: 28729434 PMCID: PMC5599795 DOI: 10.15252/embj.201797342] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions. During replication, cohesion establishment promotes numerous long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. In anaphase, mitotic chromosomes are abruptly reorganized depending on mechanical forces exerted by the mitotic spindle. Formation of a condensin-dependent loop bridging the centromere cluster with the rDNA loci suggests that condensin-mediated forces may also directly facilitate segregation. This work therefore comprehensively recapitulates cell cycle-dependent chromosome dynamics in a unicellular eukaryote, but also unveils new features of chromosome structural reorganization during highly conserved stages of cell division.
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Affiliation(s)
- Luciana Lazar-Stefanita
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, Complexité du Vivant, Paris, France
| | - Vittore F Scolari
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Guillaume Mercy
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, Complexité du Vivant, Paris, France
| | - Héloise Muller
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Thomas M Guérin
- Laboratoire Télomères et Réparation du Chromosome, CEA, INSERM, UMR 967, IRCM, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Agnès Thierry
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Julien Mozziconacci
- Sorbonne Universités, Theoretical Physics for Condensed Matter Lab, UPMC Université Paris 06, Paris, France
- CNRS, UMR 7600, Paris, France
| | - Romain Koszul
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
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21
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Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nat Cell Biol 2017; 19:1071-1080. [PMID: 28825700 PMCID: PMC5640152 DOI: 10.1038/ncb3594] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/19/2017] [Indexed: 12/26/2022]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion. Polymer simulations demonstrate that this role can be fully accounted for through cis-looping of chromatin. Second, condensin is generally dispensable for compaction along chromosome arms. Instead, it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes.
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MESH Headings
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Structures
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Computer Simulation
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Mitosis
- Models, Genetic
- Models, Molecular
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Nucleic Acid Conformation
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Structure-Activity Relationship
- Cohesins
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Affiliation(s)
| | - Anton Goloborodko
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jon-Matthew Belton
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Catrina Miles
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Miao Yu
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jonathan Baxter
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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22
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Papagiannakis A, de Jonge JJ, Zhang Z, Heinemann M. Quantitative characterization of the auxin-inducible degron: a guide for dynamic protein depletion in single yeast cells. Sci Rep 2017; 7:4704. [PMID: 28680098 PMCID: PMC5498663 DOI: 10.1038/s41598-017-04791-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/22/2017] [Indexed: 11/24/2022] Open
Abstract
Perturbations are essential for the interrogation of biological systems. The auxin-inducible degron harbors great potential for dynamic protein depletion in yeast. Here, we thoroughly and quantitatively characterize the auxin-inducible degron in single yeast cells. We show that an auxin concentration of 0.25 mM is necessary for fast and uniform protein depletion between single cells, and that in mother cells proteins are depleted faster than their daughters. Although, protein recovery starts immediately after removal of auxin, it takes multiple generations before equilibrium is reached between protein synthesis and dilution, which is when the original protein levels are restored. Further, we found that blue light, used for GFP excitation, together with auxin results in growth defects, caused by the photo-destruction of auxin to its toxic derivatives, which can be avoided if indole-free auxin substitutes are used. Our work provides guidelines for the successful combination of microscopy, microfluidics and the auxin-inducible degron, offering the yeast community an unprecedented tool for dynamic perturbations on the single cell level.
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Affiliation(s)
- Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janeska J de Jonge
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Zheng Zhang
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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23
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Methods to Study the Atypical Roles of DNA Repair and SMC Proteins in Gene Silencing. Methods Mol Biol 2016. [PMID: 27797079 DOI: 10.1007/978-1-4939-6545-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Silenced heterochromatin influences all nuclear processes including chromosome structure, nuclear organization, transcription, replication, and repair. Proteins that mediate silencing affect all of these nuclear processes. Similarly proteins involved in replication, repair, and chromosome structure play a role in the formation and maintenance of silenced heterochromatin. In this chapter we describe a handful of simple tools and methods that can be used to study the atypical role of proteins in gene silencing.
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24
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Dickerson D, Gierliński M, Singh V, Kitamura E, Ball G, Tanaka TU, Owen-Hughes T. High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division. BMC Cell Biol 2016; 17:33. [PMID: 27609610 PMCID: PMC5016949 DOI: 10.1186/s12860-016-0111-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/25/2016] [Indexed: 01/23/2023] Open
Abstract
Background Genomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy. Results We established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs. Conclusions The directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0111-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Dickerson
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vijender Singh
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Etsushi Kitamura
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Graeme Ball
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. .,Wellcome Trust Building, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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25
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Abstract
SUMMARYAll eukaryotic cells prepare for cell division by forming a "mitotic spindle"-a bipolar machine made from microtubules (MTs) and many associated proteins. This device organizes the already duplicated DNA so one copy of each chromosome attaches to each end of the spindle. Both formation and function of the spindle require controlled MT dynamics, as well as the actions of multiple motor enzymes. Spindle-driven motions separate the duplicated chromosomes into two distinct sets that are then moved toward opposite ends of the cell. The two cells that subsequently form by cytokinesis, therefore, contain all the genes needed to grow and divide again.
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Affiliation(s)
- J Richard McIntosh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
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26
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Leonard J, Sen N, Torres R, Sutani T, Jarmuz A, Shirahige K, Aragón L. Condensin Relocalization from Centromeres to Chromosome Arms Promotes Top2 Recruitment during Anaphase. Cell Rep 2015; 13:2336-2344. [PMID: 26686624 PMCID: PMC4695335 DOI: 10.1016/j.celrep.2015.11.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/08/2015] [Accepted: 11/11/2015] [Indexed: 11/29/2022] Open
Abstract
Condensin is a conserved chromosomal complex necessary to promote mitotic chromosome condensation and sister chromatid resolution during anaphase. Here, we report that yeast condensin binds to replicated centromere regions. We show that centromeric condensin relocalizes to chromosome arms as cells undergo anaphase segregation. We find that condensin relocalization is initiated immediately after the bipolar attachment of sister kinetochores to spindles and requires Polo kinase activity. Moreover, condensin localization during anaphase involves a higher binding rate on DNA and temporally overlaps with condensin’s DNA overwinding activity. Finally, we demonstrate that topoisomerase 2 (Top2) is also recruited to chromosome arms during anaphase in a condensin-dependent manner. Our results uncover a functional relation between condensin and Top2 during anaphase to mediate chromosome segregation. Condensin recruitment to centromeric regions requires DNA replication Centromeric condensin spreads to chromosome arms during anaphase Condensin promotes recruitment of Top2 during anaphase Condensin localization requires Polo kinase and correlates with DNA overwinding
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Affiliation(s)
- Joanne Leonard
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Nicholas Sen
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Raul Torres
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Takashi Sutani
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Adam Jarmuz
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Luis Aragón
- Cell Cycle Group, Medical Research Council (MRC), Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.
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Kruitwagen T, Denoth-Lippuner A, Wilkins BJ, Neumann H, Barral Y. Axial contraction and short-range compaction of chromatin synergistically promote mitotic chromosome condensation. eLife 2015; 4:e1039. [PMID: 26615018 PMCID: PMC4755758 DOI: 10.7554/elife.10396] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/27/2015] [Indexed: 11/16/2022] Open
Abstract
The segregation of eukaryotic chromosomes during mitosis requires their extensive folding into units of manageable size for the mitotic spindle. Here, we report on how phosphorylation at serine 10 of histone H3 (H3 S10) contributes to this process. Using a fluorescence-based assay to study local compaction of the chromatin fiber in living yeast cells, we show that chromosome condensation entails two temporally and mechanistically distinct processes. Initially, nucleosome-nucleosome interaction triggered by H3 S10 phosphorylation and deacetylation of histone H4 promote short-range compaction of chromatin during early anaphase. Independently, condensin mediates the axial contraction of chromosome arms, a process peaking later in anaphase. Whereas defects in chromatin compaction have no observable effect on axial contraction and condensin inactivation does not affect short-range chromatin compaction, inactivation of both pathways causes synergistic defects in chromosome segregation and cell viability. Furthermore, both pathways rely at least partially on the deacetylase Hst2, suggesting that this protein helps coordinating chromatin compaction and axial contraction to properly shape mitotic chromosomes. DOI:http://dx.doi.org/10.7554/eLife.10396.001 DNA in humans, yeast and other eukaryotic organisms is packaged in structures called chromosomes. When a cell divides these chromosomes are copied and then the matching pairs are separated so that each daughter cell has a full set of its genome. To enable these events to take place, the DNA must become more tightly packed so that the chromosomes become rigid units with projections called arms. Any failure in this chromosome “condensation” leads to the loss of chromosomes during cell division. Within a chromosome, sections of DNA are wrapped around groups of proteins to make a series of linked units called nucleosomes, which resemble beads on a string. These units and other scaffold proteins together make a structure called chromatin and establish the overall shape of the chromosome. However, it is not exactly clear how the nucleosomes and scaffold proteins are rearranged during condensation. Kruitwagen et al. used microscopy to study chromosome condensation in budding yeast. The experiments reveal that condensation involves two separate processes. First, modifications to the nucleosomes result in these units becoming more tightly packed in a process called short-range compaction. Second, a group of proteins called condensin is responsible for rearranging the compacted chromatin to enforce higher-order structure on the arms of the condensed chromosome (long-range contraction). Further experiments suggest that an enzyme called Hst2 may help to co-ordinate these processes to ensure that chromosomes adopt the right shape before the cell divides. For example, Hst2 ensures that longer chromosomes condense more than shorter ones. A future challenge will be to find out whether chromosome condensation works in a similar way in humans and other large eukaryotes, which form much larger chromosomes with more complicated structures than yeast. DOI:http://dx.doi.org/10.7554/eLife.10396.002
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Affiliation(s)
- Tom Kruitwagen
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Annina Denoth-Lippuner
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Bryan J Wilkins
- Free Floater (Junior) Research Group "Applied Synthetic Biology," Institute for Microbiology and Genetics, Georg- August University Göttingen, Göttingen, Germany
| | - Heinz Neumann
- Free Floater (Junior) Research Group "Applied Synthetic Biology," Institute for Microbiology and Genetics, Georg- August University Göttingen, Göttingen, Germany
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
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28
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Machín F, Quevedo O, Ramos-Pérez C, García-Luis J. Cdc14 phosphatase: warning, no delay allowed for chromosome segregation! Curr Genet 2015; 62:7-13. [PMID: 26116076 PMCID: PMC4723626 DOI: 10.1007/s00294-015-0502-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023]
Abstract
Cycling events in nature start and end to restart again and again. In the cell cycle, whose purpose is to become two where there was only one, cyclin-dependent kinases (CDKs) are the beginning and, therefore, phosphatases must play a role in the ending. Since CDKs are drivers of the cell cycle and cancer cells uncontrollably divide, much attention has been put into knocking down CDK activity. However, much less is known on the consequences of interfering with the phosphatases that put an end to the cell cycle. We have addressed in recent years the consequences of transiently inactivating the only master cell cycle phosphatase in the model yeast Saccharomyces cerevisiae, Cdc14. Transient inactivation is expected to better mimic the pharmacological action of drugs. Interestingly, we have found that yeast cells tolerate badly a relatively brief inactivation of Cdc14 when cells are already committed into anaphase, the first cell cycle stage where this phosphatase plays important roles. First, we noticed that the segregation of distal regions in the chromosome arm that carries the ribosomal DNA array was irreversibly impaired, leading to an anaphase bridge (AB). Next, we found that this AB could eventually be severed by cytokinesis and led to two different types of genetically compromised daughter cells. All these previous studies were done in haploid cells. We have now recently expanded this analysis to diploid cells and used the advantage of making hybrid diploids to study chromosome rearrangements and changes in the ploidy of the surviving progeny. We have found that the consequences for the genome integrity were far more dramatic than originally envisioned.
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Affiliation(s)
- Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain.
| | - Oliver Quevedo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain.,Center for Chromosome Stability and Department of Biology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Cristina Ramos-Pérez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain
| | - Jonay García-Luis
- Unidad de Investigación, Hospital Universitario Nuestra Señora de la Candelaria, Ctra del Rosario 145, 38010, Santa Cruz de Tenerife, Spain.,Cell Cycle Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN, UK
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29
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Yoshida S, Kaido M, Kitajima TS. Inherent Instability of Correct Kinetochore-Microtubule Attachments during Meiosis I in Oocytes. Dev Cell 2015; 33:589-602. [PMID: 26028219 DOI: 10.1016/j.devcel.2015.04.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/03/2015] [Accepted: 04/24/2015] [Indexed: 01/08/2023]
Abstract
A model for mitosis suggests that correct kinetochore-microtubule (KT-MT) attachments are stabilized by spatial separation of the attachment sites from Aurora B kinase through sister KT stretching. However, the spatiotemporal regulation of attachment stability during meiosis I (MI) in oocytes remains unclear. Here, we found that in mouse oocytes, Aurora B and C (B/C) are located in close proximity to KT-MT attachment sites after bivalent stretching due to an intrinsic property of the MI chromosomes. The Aurora B/C activity destabilizes correct attachments while allowing a considerable amount of incorrect attachments to form. KT-MT attachments are eventually stabilized through KT dephosphorylation by PP2A-B56 phosphatase, which is progressively recruited to KTs depending on the BubR1 phosphorylation resulting from the timer Cdk1 and independent of bivalent stretching. Thus, oocytes lack a mechanism for coordinating bivalent stretching and KT phosphoregulation during MI, which may explain the high frequency of KT-MT attachment errors.
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Affiliation(s)
- Shuhei Yoshida
- Laboratory for Chromosome Segregation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Masako Kaido
- Laboratory for Chromosome Segregation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Tomoya S Kitajima
- Laboratory for Chromosome Segregation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan.
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30
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Condensin confers the longitudinal rigidity of chromosomes. Nat Cell Biol 2015; 17:771-81. [PMID: 25961503 PMCID: PMC5207317 DOI: 10.1038/ncb3167] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/24/2015] [Indexed: 12/14/2022]
Abstract
In addition to inter-chromatid cohesion, mitotic and meiotic chromatids must have three physical properties: compaction into 'threads' roughly co-linear with their DNA sequence, intra-chromatid cohesion determining their rigidity, and a mechanism to promote sister chromatid disentanglement. A fundamental issue in chromosome biology is whether a single molecular process accounts for all three features. There is universal agreement that a pair of Smc-kleisin complexes called condensin I and II facilitate sister chromatid disentanglement, but whether they also confer thread formation or longitudinal rigidity is either controversial or has never been directly addressed respectively. We show here that condensin II (beta-kleisin) has an essential role in all three processes during meiosis I in mouse oocytes and that its function overlaps with that of condensin I (gamma-kleisin), which is otherwise redundant. Pre-assembled meiotic bivalents unravel when condensin is inactivated by TEV cleavage, proving that it actually holds chromatin fibres together.
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31
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Lopez V, Barinova N, Onishi M, Pobiega S, Pringle JR, Dubrana K, Marcand S. Cytokinesis breaks dicentric chromosomes preferentially at pericentromeric regions and telomere fusions. Genes Dev 2015; 29:322-36. [PMID: 25644606 PMCID: PMC4318148 DOI: 10.1101/gad.254664.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. Lopez et al. find that dicentrics without internal telomere sequences preferentially break at pericentromeric regions. In all cases, cleavage does not occur in anaphase but instead requires cytokinesis. Dicentrics cause the spindle pole bodies and centromeres to relocate to the bud neck during cytokinesis, explaining how cytokinesis can sever dicentrics near centromeres. Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. During mitosis, they form anaphase bridges, resulting in chromosome breakage by an unknown mechanism. In budding yeast, dicentrics generated by telomere fusion break at the fusion, a process that restores the parental karyotype and protects cells from rare accidental telomere fusion. Here, we observed that dicentrics lacking telomere fusion preferentially break within a 25- to 30-kb-long region next to the centromeres. In all cases, dicentric breakage requires anaphase exit, ruling out stretching by the elongated mitotic spindle as the cause of breakage. Instead, breakage requires cytokinesis. In the presence of dicentrics, the cytokinetic septa pinch the nucleus, suggesting that dicentrics are severed after actomyosin ring contraction. At this time, centromeres and spindle pole bodies relocate to the bud neck, explaining how cytokinesis can sever dicentrics near centromeres.
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Affiliation(s)
- Virginia Lopez
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Natalja Barinova
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Masayuki Onishi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sabrina Pobiega
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karine Dubrana
- UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France; Laboratoire Instabilité Génétique et Organisation Nucléaire, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France;
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32
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Abstract
The primary goal of mitosis is to partition duplicated chromosomes into daughter cells. Eukaryotic chromosomes are equipped with two distinct classes of intrinsic machineries, cohesin and condensins, that ensure their faithful segregation during mitosis. Cohesin holds sister chromatids together immediately after their synthesis during S phase until the establishment of bipolar attachments to the mitotic spindle in metaphase. Condensins, on the other hand, attempt to "resolve" sister chromatids by counteracting cohesin. The products of the balancing acts of cohesin and condensins are metaphase chromosomes, in which two rod-shaped chromatids are connected primarily at the centromere. In anaphase, this connection is released by the action of separase that proteolytically cleaves the remaining population of cohesin. Recent studies uncover how this series of events might be mechanistically coupled with each other and intricately regulated by a number of regulatory factors.
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Affiliation(s)
- Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama 351-0198, Japan
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33
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Ward JJ, Roque H, Antony C, Nédélec F. Mechanical design principles of a mitotic spindle. eLife 2014; 3:e03398. [PMID: 25521247 PMCID: PMC4290452 DOI: 10.7554/elife.03398] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/17/2014] [Indexed: 12/11/2022] Open
Abstract
An organised spindle is crucial to the fidelity of chromosome segregation, but the relationship between spindle structure and function is not well understood in any cell type. The anaphase B spindle in fission yeast has a slender morphology and must elongate against compressive forces. This 'pushing' mode of chromosome transport renders the spindle susceptible to breakage, as observed in cells with a variety of defects. Here we perform electron tomographic analyses of the spindle, which suggest that it organises a limited supply of structural components to increase its compressive strength. Structural integrity is maintained throughout the spindle's fourfold elongation by organising microtubules into a rigid transverse array, preserving correct microtubule number and dynamically rescaling microtubule length.
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Affiliation(s)
- Jonathan J Ward
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hélio Roque
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claude Antony
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - François Nédélec
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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34
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Snider CE, Stephens AD, Kirkland JG, Hamdani O, Kamakaka RT, Bloom K. Dyskerin, tRNA genes, and condensin tether pericentric chromatin to the spindle axis in mitosis. ACTA ACUST UNITED AC 2014; 207:189-99. [PMID: 25332162 PMCID: PMC4210444 DOI: 10.1083/jcb.201405028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pericentric enrichment of condensin on budding yeast chromosomes, which contributes to chromatin compaction and mitotic spindle structure and integrity, is mediated by condensin interaction with tRNA genes and the tRNA-interacting protein dyskerin. Condensin is enriched in the pericentromere of budding yeast chromosomes where it is constrained to the spindle axis in metaphase. Pericentric condensin contributes to chromatin compaction, resistance to microtubule-based spindle forces, and spindle length and variance regulation. Condensin is clustered along the spindle axis in a heterogeneous fashion. We demonstrate that pericentric enrichment of condensin is mediated by interactions with transfer ribonucleic acid (tRNA) genes and their regulatory factors. This recruitment is important for generating axial tension on the pericentromere and coordinating movement between pericentromeres from different chromosomes. The interaction between condensin and tRNA genes in the pericentromere reveals a feature of yeast centromeres that has profound implications for the function and evolution of mitotic segregation mechanisms.
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Affiliation(s)
- Chloe E Snider
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrew D Stephens
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jacob G Kirkland
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Omar Hamdani
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Rohinton T Kamakaka
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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35
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Oliveira RA, Kotadia S, Tavares A, Mirkovic M, Bowlin K, Eichinger CS, Nasmyth K, Sullivan W. Centromere-independent accumulation of cohesin at ectopic heterochromatin sites induces chromosome stretching during anaphase. PLoS Biol 2014; 12:e1001962. [PMID: 25290697 PMCID: PMC4188515 DOI: 10.1371/journal.pbio.1001962] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/22/2014] [Indexed: 12/25/2022] Open
Abstract
Pericentric heterochromatin, while often considered as "junk" DNA, plays important functions in chromosome biology. It contributes to sister chromatid cohesion, a process mediated by the cohesin complex that ensures proper genome segregation during nuclear division. Long stretches of heterochromatin are almost exclusively placed at centromere-proximal regions but it remains unclear if there is functional (or mechanistic) importance in linking the sites of sister chromatid cohesion to the chromosomal regions that mediate spindle attachment (the centromere). Using engineered chromosomes in Drosophila melanogaster, we demonstrate that cohesin enrichment is dictated by the presence of heterochromatin rather than centromere proximity. This preferential accumulation is caused by an enrichment of the cohesin-loading factor (Nipped-B/NIPBL/Scc2) at dense heterochromatic regions. As a result, chromosome translocations containing ectopic pericentric heterochromatin embedded in euchromatin display additional cohesin-dependent constrictions. These ectopic cohesion sites, placed away from the centromere, disjoin abnormally during anaphase and chromosomes exhibit a significant increase in length during anaphase (termed chromatin stretching). These results provide evidence that long stretches of heterochromatin distant from the centromere, as often found in many cancers, are sufficient to induce abnormal accumulation of cohesin at these sites and thereby compromise the fidelity of chromosome segregation.
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Affiliation(s)
- Raquel A. Oliveira
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Department of Biochemistry, University of Oxford, United Kingdom
| | - Shaila Kotadia
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | | | | | - Katherine Bowlin
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | | | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, United Kingdom
| | - William Sullivan
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
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36
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Abstract
Centromeres are specialized domains of heterochromatin that provide the foundation for the kinetochore. Centromeric heterochromatin is characterized by specific histone modifications, a centromere-specific histone H3 variant (CENP-A), and the enrichment of cohesin, condensin, and topoisomerase II. Centromere DNA varies orders of magnitude in size from 125 bp (budding yeast) to several megabases (human). In metaphase, sister kinetochores on the surface of replicated chromosomes face away from each other, where they establish microtubule attachment and bi-orientation. Despite the disparity in centromere size, the distance between separated sister kinetochores is remarkably conserved (approximately 1 μm) throughout phylogeny. The centromere functions as a molecular spring that resists microtubule-based extensional forces in mitosis. This review explores the physical properties of DNA in order to understand how the molecular spring is built and how it contributes to the fidelity of chromosome segregation.
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Affiliation(s)
- Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280;
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37
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Hériché JK, Lees JG, Morilla I, Walter T, Petrova B, Roberti MJ, Hossain MJ, Adler P, Fernández JM, Krallinger M, Haering CH, Vilo J, Valencia A, Ranea JA, Orengo C, Ellenberg J. Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Mol Biol Cell 2014; 25:2522-36. [PMID: 24943848 PMCID: PMC4142622 DOI: 10.1091/mbc.e13-04-0221] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The advent of genome-wide RNA interference (RNAi)-based screens puts us in the position to identify genes for all functions human cells carry out. However, for many functions, assay complexity and cost make genome-scale knockdown experiments impossible. Methods to predict genes required for cell functions are therefore needed to focus RNAi screens from the whole genome on the most likely candidates. Although different bioinformatics tools for gene function prediction exist, they lack experimental validation and are therefore rarely used by experimentalists. To address this, we developed an effective computational gene selection strategy that represents public data about genes as graphs and then analyzes these graphs using kernels on graph nodes to predict functional relationships. To demonstrate its performance, we predicted human genes required for a poorly understood cellular function-mitotic chromosome condensation-and experimentally validated the top 100 candidates with a focused RNAi screen by automated microscopy. Quantitative analysis of the images demonstrated that the candidates were indeed strongly enriched in condensation genes, including the discovery of several new factors. By combining bioinformatics prediction with experimental validation, our study shows that kernels on graph nodes are powerful tools to integrate public biological data and predict genes involved in cellular functions of interest.
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Affiliation(s)
- Jean-Karim Hériché
- Cell Biology/Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - Jon G Lees
- Research Department of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Ian Morilla
- Department of Molecular Biology and Biochemistry-CIBER de Enfermedades Raras, University of Malaga, Malaga 29071, Spain
| | - Thomas Walter
- Cell Biology/Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - Boryana Petrova
- Cell Biology/Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - M Julia Roberti
- Cell Biology/Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - M Julius Hossain
- Cell Biology/Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - Priit Adler
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - José M Fernández
- Structural Bioinformatics Group, Spanish National Cancer Research Centre and Spanish National Bioinformatics Institute, 28029 Madrid, Spain
| | - Martin Krallinger
- Structural Bioinformatics Group, Spanish National Cancer Research Centre and Spanish National Bioinformatics Institute, 28029 Madrid, Spain
| | - Christian H Haering
- Cell Biology/Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - Jaak Vilo
- Institute of Computer Science, University of Tartu, 50409 Tartu, Estonia
| | - Alfonso Valencia
- Structural Bioinformatics Group, Spanish National Cancer Research Centre and Spanish National Bioinformatics Institute, 28029 Madrid, Spain
| | - Juan A Ranea
- Department of Molecular Biology and Biochemistry-CIBER de Enfermedades Raras, University of Malaga, Malaga 29071, Spain
| | - Christine Orengo
- Research Department of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Jan Ellenberg
- Cell Biology/Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
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38
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Gruber S, Veening JW, Bach J, Blettinger M, Bramkamp M, Errington J. Interlinked sister chromosomes arise in the absence of condensin during fast replication in B. subtilis. Curr Biol 2014; 24:293-8. [PMID: 24440399 PMCID: PMC3919155 DOI: 10.1016/j.cub.2013.12.049] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/28/2013] [Accepted: 12/17/2013] [Indexed: 01/05/2023]
Abstract
Condensin-an SMC-kleisin complex-is essential for efficient segregation of sister chromatids in eukaryotes [1-4]. In Escherichia coli and Bacillus subtilis, deletion of condensin subunits results in severe growth phenotypes and the accumulation of cells lacking nucleoids [5, 6]. In many other bacteria and under slow growth conditions, however, the reported phenotypes are much milder or virtually absent [7-10]. This raises the question of what role prokaryotic condensin might play during chromosome segregation under various growth conditions. In B. subtilis and Streptococcus pneumoniae, condensin complexes are enriched on the circular chromosome near the single origin of replication by ParB proteins bound to parS sequences [11, 12]. Using conditional alleles of condensin in B. subtilis, we demonstrate that depletion of its activity results in an immediate and severe defect in the partitioning of replication origins. Multiple copies of the chromosome remain unsegregated at or near the origin of replication. Surprisingly, the growth and chromosome segregation defects in rich medium are suppressed by a reduction of replication fork velocity but not by partial inhibition of translation or transcription. Prokaryotic condensin likely prevents the formation of sister DNA interconnections at the replication fork or promotes their resolution behind the fork.
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Affiliation(s)
- Stephan Gruber
- Max Planck Institute of Biochemistry, Research Group "Chromosome Organization and Dynamics," Am Klopferspitz 18, 82152 Martinsried, Germany; Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK.
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Juri Bach
- Department of Biology I, Ludwig Maximilians University, Munich, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Martin Blettinger
- Max Planck Institute of Biochemistry, Research Group "Chromosome Organization and Dynamics," Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig Maximilians University, Munich, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK.
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Marston AL. Chromosome segregation in budding yeast: sister chromatid cohesion and related mechanisms. Genetics 2014; 196:31-63. [PMID: 24395824 PMCID: PMC3872193 DOI: 10.1534/genetics.112.145144] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/18/2013] [Indexed: 12/28/2022] Open
Abstract
Studies on budding yeast have exposed the highly conserved mechanisms by which duplicated chromosomes are evenly distributed to daughter cells at the metaphase-anaphase transition. The establishment of proteinaceous bridges between sister chromatids, a function provided by a ring-shaped complex known as cohesin, is central to accurate segregation. It is the destruction of this cohesin that triggers the segregation of chromosomes following their proper attachment to microtubules. Since it is irreversible, this process must be tightly controlled and driven to completion. Furthermore, during meiosis, modifications must be put in place to allow the segregation of maternal and paternal chromosomes in the first division for gamete formation. Here, I review the pioneering work from budding yeast that has led to a molecular understanding of the establishment and destruction of cohesion.
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Affiliation(s)
- Adele L Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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Cuylen S, Metz J, Hruby A, Haering C. Entrapment of Chromosomes by Condensin Rings Prevents Their Breakage during Cytokinesis. Dev Cell 2013; 27:469-78. [DOI: 10.1016/j.devcel.2013.10.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/02/2013] [Accepted: 10/25/2013] [Indexed: 12/27/2022]
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41
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Piazza I, Haering CH, Rutkowska A. Condensin: crafting the chromosome landscape. Chromosoma 2013; 122:175-90. [DOI: 10.1007/s00412-013-0405-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/03/2013] [Accepted: 03/04/2013] [Indexed: 02/06/2023]
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Abstract
Chromosomes undergo extensive conformational rearrangements in preparation for their segregation during cell divisions. Insights into the molecular mechanisms behind this still poorly understood condensation process require the development of new approaches to quantitatively assess chromosome formation in vivo. In this study, we present a live-cell microscopy-based chromosome condensation assay in the fission yeast Schizosaccharomyces pombe. By automatically tracking the three-dimensional distance changes between fluorescently marked chromosome loci at high temporal and spatial resolution, we analyze chromosome condensation during mitosis and meiosis and deduct defined parameters to describe condensation dynamics. We demonstrate that this method can determine the contributions of condensin, topoisomerase II, and Aurora kinase to mitotic chromosome condensation. We furthermore show that the assay can identify proteins required for mitotic chromosome formation de novo by isolating mutants in condensin, DNA polymerase ε, and F-box DNA helicase I that are specifically defective in pro-/metaphase condensation. Thus, the chromosome condensation assay provides a direct and sensitive system for the discovery and characterization of components of the chromosome condensation machinery in a genetically tractable eukaryote.
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Abstract
Condensins are multisubunit protein complexes that play a fundamental role in the structural and functional organization of chromosomes in the three domains of life. Most eukaryotic species have two different types of condensin complexes, known as condensins I and II, that fulfill nonoverlapping functions and are subjected to differential regulation during mitosis and meiosis. Recent studies revealed that the two complexes contribute to a wide variety of interphase chromosome functions, such as gene regulation, recombination, and repair. Also emerging are their cell type- and tissue-specific functions and relevance to human disease. Biochemical and structural analyses of eukaryotic and bacterial condensins steadily uncover the mechanisms of action of this class of highly sophisticated molecular machines. Future studies on condensins will not only enhance our understanding of chromosome architecture and dynamics, but also help address a previously underappreciated yet profound set of questions in chromosome biology.
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Affiliation(s)
- Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan.
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44
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A SUMO-dependent step during establishment of sister chromatid cohesion. Curr Biol 2012; 22:1576-81. [PMID: 22771040 DOI: 10.1016/j.cub.2012.06.046] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 06/15/2012] [Accepted: 06/18/2012] [Indexed: 11/20/2022]
Abstract
Cohesin is a protein complex that ties sister DNA molecules from the time of DNA replication until the metaphase to anaphase transition. Current models propose that the association of the Smc1, Smc3, and Scc1/Mcd1 subunits creates a ring-shaped structure that entraps the two sister DNAs. Cohesin is essential for correct chromosome segregation and recombinational repair. Its activity is therefore controlled by several posttranslational modifications, including acetylation, phosphorylation, sumoylation, and site-specific proteolysis. Here we show that cohesin sumoylation occurs at the time of cohesion establishment, after cohesin loading and ATP binding, and independently from Eco1-mediated cohesin acetylation. In order to test the functional relevance of cohesin sumoylation, we have developed a novel approach in budding yeast to deplete SUMO from all subunits in the cohesin complex, based on fusion of the Scc1 subunit to a SUMO peptidase Ulp domain (UD). Downregulation of cohesin sumoylation is lethal, and the Scc1-UD chimeras have a failure in sister chromatid cohesion. Strikingly, the unsumoylated cohesin rings are acetylated. Our findings indicate that SUMO is a novel molecular determinant for the establishment of sister chromatid cohesion, and we propose that SUMO is required for the entrapment of sister chromatids during the acetylation-mediated closure of the cohesin ring.
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45
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A model for chromosome condensation based on the interplay between condensin and topoisomerase II. Trends Genet 2012; 28:110-7. [DOI: 10.1016/j.tig.2011.11.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 01/15/2023]
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Toda K, Naito K, Mase S, Ueno M, Uritani M, Yamamoto A, Ushimaru T. APC/C-Cdh1-dependent anaphase and telophase progression during mitotic slippage. Cell Div 2012; 7:4. [PMID: 22321970 PMCID: PMC3305350 DOI: 10.1186/1747-1028-7-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 02/09/2012] [Indexed: 11/10/2022] Open
Abstract
Background The spindle assembly checkpoint (SAC) inhibits anaphase progression in the presence of insufficient kinetochore-microtubule attachments, but cells can eventually override mitotic arrest by a process known as mitotic slippage or adaptation. This is a problem for cancer chemotherapy using microtubule poisons. Results Here we describe mitotic slippage in yeast bub2Δ mutant cells that are defective in the repression of precocious telophase onset (mitotic exit). Precocious activation of anaphase promoting complex/cyclosome (APC/C)-Cdh1 caused mitotic slippage in the presence of nocodazole, while the SAC was still active. APC/C-Cdh1, but not APC/C-Cdc20, triggered anaphase progression (securin degradation, separase-mediated cohesin cleavage, sister-chromatid separation and chromosome missegregation), in addition to telophase onset (mitotic exit), during mitotic slippage. This demonstrates that an inhibitory system not only of APC/C-Cdc20 but also of APC/C-Cdh1 is critical for accurate chromosome segregation in the presence of insufficient kinetochore-microtubule attachments. Conclusions The sequential activation of APC/C-Cdc20 to APC/C-Cdh1 during mitosis is central to accurate mitosis. Precocious activation of APC/C-Cdh1 in metaphase (pre-anaphase) causes mitotic slippage in SAC-activated cells. For the prevention of mitotic slippage, concomitant inhibition of APC/C-Cdh1 may be effective for tumor therapy with mitotic spindle poisons in humans.
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Affiliation(s)
- Kazuhiro Toda
- Faculty of Science, Shizuoka University, Shizuoka University, Shizuoka 422-8529, Japan.
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Jin F, Liu H, Li P, Yu HG, Wang Y. Loss of function of the Cik1/Kar3 motor complex results in chromosomes with syntelic attachment that are sensed by the tension checkpoint. PLoS Genet 2012; 8:e1002492. [PMID: 22319456 PMCID: PMC3271067 DOI: 10.1371/journal.pgen.1002492] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 12/06/2011] [Indexed: 11/24/2022] Open
Abstract
The attachment of sister kinetochores by microtubules emanating from opposite spindle poles establishes chromosome bipolar attachment, which generates tension on chromosomes and is essential for sister-chromatid segregation. Syntelic attachment occurs when both sister kinetochores are attached by microtubules from the same spindle pole and this attachment is unable to generate tension on chromosomes, but a reliable method to induce syntelic attachments is not available in budding yeast. The spindle checkpoint can sense the lack of tension on chromosomes as well as detached kinetochores to prevent anaphase onset. In budding yeast Saccharomyces cerevisiae, tension checkpoint proteins Aurora/Ipl1 kinase and centromere-localized Sgo1 are required to sense the absence of tension but are dispensable for the checkpoint response to detached kinetochores. We have found that the loss of function of a motor protein complex Cik1/Kar3 in budding yeast leads to syntelic attachments. Inactivation of either the spindle or tension checkpoint enables premature anaphase entry in cells with dysfunctional Cik1/Kar3, resulting in co-segregation of sister chromatids. Moreover, the abolished Kar3-kinetochore interaction in cik1 mutants suggests that the Cik1/Kar3 complex mediates chromosome movement along microtubules, which could facilitate bipolar attachment. Therefore, we can induce syntelic attachments in budding yeast by inactivating the Cik1/Kar3 complex, and this approach will be very useful to study the checkpoint response to syntelic attachments. Chromosome bipolar attachment occurs when sister chromatids are attached by microtubules emanating from opposite spindle poles and is essential for faithful sister-chromatid segregation. Chromosomes are under tension once bipolar attachment is established. The absence of tension is sensed by the tension checkpoint that prevents chromosome segregation. The attachment of sister chromatids by microtubules from the same spindle pole generates syntelic attachment, which fails to generate tension on chromosomes. However, a reliable method to induce syntelic attachment is not available. Our findings indicate that the inactivation of the motor complex, Cik1/Kar3, results in chromosomes with syntelic attachment in budding yeast. In the absence of the tension checkpoint, yeast cells with dysfunctional Cik1/Kar3 enter anaphase, resulting in co-segregation of sister chromatids. Therefore, with this method we can experimentally induce syntelic attachment in yeast and investigate how cells respond to this incorrect attachment.
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Affiliation(s)
- Fengzhi Jin
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
| | - Hong Liu
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Ping Li
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Hong-Guo Yu
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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48
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Abstract
Cohesin confers both intrachromatid and interchromatid cohesion through formation of a tripartite ring within which DNA is thought to be entrapped. Here, I discuss what is known about the four stages of the cohesin ring cycle using the ring model as an intellectual framework. I postulate that cohesin loading onto chromosomes, catalysed by a separate complex called kollerin, is mediated by the entry of DNA into cohesin rings, whereas dissociation, catalysed by Wapl and several other cohesin subunits (an activity that will be called releasin here), is mediated by the subsequent exit of DNA. I suggest that the ring's entry and exit gates may be separate, with the former and latter taking place at Smc1-Smc3 and Smc3-kleisin interfaces, respectively. Establishment of cohesion during S phase involves neutralization of releasin through acetylation of Smc3 at a site close to the putative exit gate of DNA, which locks rings shut until opened irreversibly by kleisin cleavage through the action of separase, an event that triggers the metaphase to anaphase transition.
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Affiliation(s)
- Kim Nasmyth
- University of Oxford, Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, UK.
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49
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Cuylen S, Haering CH. Deciphering condensin action during chromosome segregation. Trends Cell Biol 2011; 21:552-9. [PMID: 21763138 DOI: 10.1016/j.tcb.2011.06.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 12/24/2022]
Abstract
The correct segregation of eukaryotic genomes requires the resolution of sister DNA molecules and their movement into opposite halves of the cell before cell division. The dynamic changes chromosomes need to undergo during these events depend on the action of a multi-subunit SMC (structural maintenance of chromosomes) protein complex named condensin, but its molecular function in chromosome segregation is still poorly understood. Recent studies suggest that condensin has a role in the removal of sister chromatid cohesin, in sister chromatid decatenation by topoisomerases, and in the structural reconfiguration of mitotic chromosomes. In this review we discuss possible mechanisms that could explain the variety of condensin actions during chromosome segregation.
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Affiliation(s)
- Sara Cuylen
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
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50
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Condensin structures chromosomal DNA through topological links. Nat Struct Mol Biol 2011; 18:894-901. [PMID: 21765419 DOI: 10.1038/nsmb.2087] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 05/10/2011] [Indexed: 12/28/2022]
Abstract
The multisubunit condensin complex is essential for the structural organization of eukaryotic chromosomes during their segregation by the mitotic spindle, but the mechanistic basis for its function is not understood. To address how condensin binds to and structures chromosomes, we have isolated from Saccharomyces cerevisiae cells circular minichromosomes linked to condensin. We find that either linearization of minichromosome DNA or proteolytic opening of the ring-like structure formed through the connection of the two ATPase heads of condensin's structural maintenance of chromosomes (SMC) heterodimer by its kleisin subunit eliminates their association. This suggests that condensin rings encircle chromosomal DNA. We further show that release of condensin from chromosomes by ring opening in dividing cells compromises the partitioning of chromosome regions distal to centromeres. Condensin hence forms topological links within chromatid arms that provide the arms with the structural rigidity necessary for their segregation.
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