1
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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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2
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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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3
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Fold-change of chromatin condensation in yeast is a conserved property. Sci Rep 2022; 12:17393. [PMID: 36253460 PMCID: PMC9576780 DOI: 10.1038/s41598-022-22340-8] [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: 05/04/2022] [Accepted: 10/13/2022] [Indexed: 01/10/2023] Open
Abstract
During mitosis, chromatin is condensed and organized into mitotic chromosomes. Condensation is critical for genome stability and dynamics, yet the degree of condensation is significantly different between multicellular and single-cell eukaryotes. What is less clear is whether there is a minimum degree of chromosome condensation in unicellular eukaryotes. Here, we exploited two-photon microscopy to analyze chromatin condensation in live and fixed cells, enabling studies of some organisms that are not readily amenable to genetic modification. This includes the yeasts Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, and Candida albicans, as well as a protist Trypanosoma brucei. We found that mitotic chromosomes in this range of species are condensed about 1.5-fold relative to interphase chromatin. In addition, we used two-photon microscopy to reveal that chromatin reorganization in interphase human hepatoma cells infected by the hepatitis C virus is decondensed compared to uninfected cells, which correlates with the previously reported viral-induced changes in chromatin dynamics. This work demonstrates the power of two-photon microscopy to analyze chromatin in a broad range of cell types and conditions, including non-model single-cell eukaryotes. We suggest that similar condensation levels are an evolutionarily conserved property in unicellular eukaryotes and important for proper chromosome segregation. Furthermore, this provides new insights into the process of chromatin condensation during mitosis in unicellular organisms as well as the response of human cells to viral infection.
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4
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The Roles of Histone Post-Translational Modifications in the Formation and Function of a Mitotic Chromosome. Int J Mol Sci 2022; 23:ijms23158704. [PMID: 35955838 PMCID: PMC9368973 DOI: 10.3390/ijms23158704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/25/2022] Open
Abstract
During mitosis, many cellular structures are organized to segregate the replicated genome to the daughter cells. Chromatin is condensed to shape a mitotic chromosome. A multiprotein complex known as kinetochore is organized on a specific region of each chromosome, the centromere, which is defined by the presence of a histone H3 variant called CENP-A. The cytoskeleton is re-arranged to give rise to the mitotic spindle that binds to kinetochores and leads to the movement of chromosomes. How chromatin regulates different activities during mitosis is not well known. The role of histone post-translational modifications (HPTMs) in mitosis has been recently revealed. Specific HPTMs participate in local compaction during chromosome condensation. On the other hand, HPTMs are involved in CENP-A incorporation in the centromere region, an essential activity to maintain centromere identity. HPTMs also participate in the formation of regulatory protein complexes, such as the chromosomal passenger complex (CPC) and the spindle assembly checkpoint (SAC). Finally, we discuss how HPTMs can be modified by environmental factors and the possible consequences on chromosome segregation and genome stability.
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5
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Chica N, Portantier M, Nyquist-Andersen M, Espada-Burriel S, Lopez-Aviles S. Uncoupling of Mitosis and Cytokinesis Upon a Prolonged Arrest in Metaphase Is Influenced by Protein Phosphatases and Mitotic Transcription in Fission Yeast. Front Cell Dev Biol 2022; 10:876810. [PMID: 35923846 PMCID: PMC9340479 DOI: 10.3389/fcell.2022.876810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022] Open
Abstract
Depletion of the Anaphase-Promoting Complex/Cyclosome (APC/C) activator Cdc20 arrests cells in metaphase with high levels of the mitotic cyclin (Cyclin B) and the Separase inhibitor Securin. In mammalian cells this arrest has been exploited for the treatment of cancer with drugs that engage the spindle assembly checkpoint and, recently, with chemical inhibitors of the APC/C. While most cells arrested in mitosis for prolonged periods undergo apoptosis, others skip cytokinesis and enter G1 with unsegregated chromosomes. This process, known as mitotic slippage, generates aneuploidy and increases genomic instability in the cancer cell. Here, we analyze the behavior of fission yeast cells arrested in mitosis through the transcriptional silencing of the Cdc20 homolog slp1. While depletion of slp1 readily halts cells in metaphase, this arrest is only transient and a majority of cells eventually undergo cytokinesis and show steady mitotic dephosphorylation. Notably, this occurs in the absence of Cyclin B (Cdc13) degradation. We investigate the involvement of phosphatase activity in these events and demonstrate that PP2A-B55Pab1 is required to prevent septation and, during the arrest, its CDK-mediated inhibition facilitates the induction of cytokinesis. In contrast, deletion of PP2A-B56Par1 completely abrogates septation. We show that this effect is partly due to this mutant entering mitosis with reduced CDK activity. Interestingly, both PP2A-B55Pab1 and PP2A-B56Par1, as well as Clp1 (the homolog of the budding yeast mitotic phosphatase Cdc14) are required for the dephosphorylation of mitotic substrates during the escape. Finally, we show that the mitotic transcriptional wave controlled by the RFX transcription factor Sak1 facilitates the induction of cytokinesis and also requires the activity of PP2A-B56Par1 in a mechanism independent of CDK.
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Affiliation(s)
- Nathalia Chica
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- *Correspondence: Sandra Lopez-Aviles, ; Nathalia Chica,
| | - Marina Portantier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mari Nyquist-Andersen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Silvia Espada-Burriel
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sandra Lopez-Aviles
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- Institute of Biosciences (IBV), Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- *Correspondence: Sandra Lopez-Aviles, ; Nathalia Chica,
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6
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Basu S, Patterson JO, Zeisner TU, Nurse P. A CDK activity buffer ensures mitotic completion. J Cell Sci 2022; 135:275762. [PMID: 35726599 PMCID: PMC9270952 DOI: 10.1242/jcs.259626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
The eukaryotic cell cycle is driven by the activity of cyclin-dependent kinases (CDKs). CDK activity rises over 50-fold during the cell cycle, from a low level in G1 to a high level in mitosis. However, it is not known whether the entire range of CDK activity is necessary for cell cycle progression, or whether cells can tolerate a reduction in CDK activity level. Here, in fission yeast, we show that sublethal CDK inhibition lengthens the time cells spend in mitosis but does not cause misordering of mitotic events. Maximum attainable CDK activity exceeds the amount necessary for mitosis, and thus forms a CDK activity buffer between sufficient and maximal possible CDK activities. This CDK activity buffer is needed for mitotic completion when CDK activity is compromised, and CDK inhibition only becomes lethal to cells when this buffer is exhausted. Finally, we explore what factors influence this CDK activity buffer, and find that it is influenced by CDK-counteracting phosphatases. Therefore, maximum attainable CDK activity is not necessary for mitosis but provides robustness to CDK activity reduction to ensure mitotic completion.
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Affiliation(s)
- Souradeep Basu
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James O Patterson
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Theresa U Zeisner
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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7
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El Dika M, Fritz AJ, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Fidelity of Mechanisms Governing the Cell Cycle. Results Probl Cell Differ 2022; 70:375-396. [PMID: 36348115 PMCID: PMC9703624 DOI: 10.1007/978-3-031-06573-6_13] [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: 11/09/2022]
Abstract
The cell cycle is governed by stringent epigenetic mechanisms that, in response to intrinsic and extrinsic regulatory cues, support fidelity of DNA replication and cell division. We will focus on (1) the complex and interdependent processes that are obligatory for control of proliferation and compromised in cancer, (2) epigenetic and topological domains that are associated with distinct phases of the cell cycle that may be altered in cancer initiation and progression, and (3) the requirement for mitotic bookmarking to maintain intranuclear localization of transcriptional regulatory machinery to reinforce cell identity throughout the cell cycle to prevent malignant transformation.
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Affiliation(s)
- Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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8
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Decombe S, Loll F, Caccianini L, Affannoukoué K, Izeddin I, Mozziconacci J, Escudé C, Lopes J. Epigenetic rewriting at centromeric DNA repeats leads to increased chromatin accessibility and chromosomal instability. Epigenetics Chromatin 2021; 14:35. [PMID: 34321103 PMCID: PMC8317386 DOI: 10.1186/s13072-021-00410-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/18/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Centromeric regions of human chromosomes contain large numbers of tandemly repeated α-satellite sequences. These sequences are covered with constitutive heterochromatin which is enriched in trimethylation of histone H3 on lysine 9 (H3K9me3). Although well studied using artificial chromosomes and global perturbations, the contribution of this epigenetic mark to chromatin structure and genome stability remains poorly known in a more natural context. RESULTS Using transcriptional activator-like effectors (TALEs) fused to a histone lysine demethylase (KDM4B), we were able to reduce the level of H3K9me3 on the α-satellites repeats of human chromosome 7. We show that the removal of H3K9me3 affects chromatin structure by increasing the accessibility of DNA repeats to the TALE protein. Tethering TALE-demethylase to centromeric repeats impairs the recruitment of HP1α and proteins of Chromosomal Passenger Complex (CPC) on this specific centromere without affecting CENP-A loading. Finally, the epigenetic re-writing by the TALE-KDM4B affects specifically the stability of chromosome 7 upon mitosis, highlighting the importance of H3K9me3 in centromere integrity and chromosome stability, mediated by the recruitment of HP1α and the CPC. CONCLUSION Our cellular model allows to demonstrate the direct role of pericentromeric H3K9me3 epigenetic mark on centromere integrity and function in a natural context and opens interesting possibilities for further studies regarding the role of the H3K9me3 mark.
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Affiliation(s)
- Sheldon Decombe
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France.,DCCBR, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - François Loll
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France.,INSERM, UMR 1229, Regenerative Medicine and Skeleton, Université de Nantes, ONIRIS, 44042, Nantes, France
| | - Laura Caccianini
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Sorbonne Université, 75005, Paris, France
| | - Kévin Affannoukoué
- Institut Langevin, ESPCI Paris, PSL Université, CNRS, 75005, Paris, France.,Institut Fresnel, Aix Marseille Université CNRS Centrale Marseille, Marseille, France
| | - Ignacio Izeddin
- Institut Langevin, ESPCI Paris, PSL Université, CNRS, 75005, Paris, France
| | - Julien Mozziconacci
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Christophe Escudé
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Judith Lopes
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France.
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9
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Todd S, Todd P, McGowan SJ, Hughes JR, Kakui Y, Leymarie FF, Latham W, Taylor S. CSynth: an interactive modelling and visualization tool for 3D chromatin structure. Bioinformatics 2021; 37:951-955. [PMID: 32866221 PMCID: PMC8128456 DOI: 10.1093/bioinformatics/btaa757] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools. RESULTS We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualize models of any chromosome conformation capture (3C) data. Unlike other modelling systems, CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues/cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and a public engagement tool. AVAILABILITYAND IMPLEMENTATION CSynth is web based and available to use at csynth.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stephen Todd
- Department of Computing, Goldsmiths, University of London, London, UK
- London Geometry, Ltd., London, UK
| | | | - Simon J McGowan
- Analysis, Visualization and Informatics, MRC Weatherall Institute of Molecular Medicine, Oxford, UK
| | - James R Hughes
- Genome Biology Group, MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Yasutaka Kakui
- The Francis Crick Institute, Chromosome Segregation Laboratory, London, UK
| | - Frederic Fol Leymarie
- Department of Computing, Goldsmiths, University of London, London, UK
- London Geometry, Ltd., London, UK
| | - William Latham
- Department of Computing, Goldsmiths, University of London, London, UK
- London Geometry, Ltd., London, UK
| | - Stephen Taylor
- Analysis, Visualization and Informatics, MRC Weatherall Institute of Molecular Medicine, Oxford, UK
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10
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Rivosecchi J, Jost D, Vachez L, Gautier FD, Bernard P, Vanoosthuyse V. RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes. Life Sci Alliance 2021; 4:4/6/e202101046. [PMID: 33771877 PMCID: PMC8046420 DOI: 10.26508/lsa.202101046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 12/23/2022] Open
Abstract
Using both experiments and mathematical modelling, the authors show that RNA polymerase backtracking contributes to the accumulation of condensin in the termination zone of active genes. The mechanisms leading to the accumulation of the SMC complexes condensins around specific transcription units remain unclear. Observations made in bacteria suggested that RNA polymerases (RNAPs) constitute an obstacle to SMC translocation, particularly when RNAP and SMC travel in opposite directions. Here we show in fission yeast that gene termini harbour intrinsic condensin-accumulating features whatever the orientation of transcription, which we attribute to the frequent backtracking of RNAP at gene ends. Consistent with this, to relocate backtracked RNAP2 from gene termini to gene bodies was sufficient to cancel the accumulation of condensin at gene ends and to redistribute it evenly within transcription units, indicating that RNAP backtracking may play a key role in positioning condensin. Formalization of this hypothesis in a mathematical model suggests that the inclusion of a sub-population of RNAP with longer dwell-times is essential to fully recapitulate the distribution profiles of condensin around active genes. Taken together, our data strengthen the idea that dense arrays of proteins tightly bound to DNA alter the distribution of condensin on chromosomes.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Laetitia Vachez
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - François Dr Gautier
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Pascal Bernard
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
| | - Vincent Vanoosthuyse
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 5239, Lyon, France
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11
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Gerguri T, Fu X, Kakui Y, Khatri BS, Barrington C, Bates PA, Uhlmann F. Comparison of loop extrusion and diffusion capture as mitotic chromosome formation pathways in fission yeast. Nucleic Acids Res 2021; 49:1294-1312. [PMID: 33434270 PMCID: PMC7897502 DOI: 10.1093/nar/gkaa1270] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 01/17/2023] Open
Abstract
Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (loop extrusion), or that they sequentially entrap two DNAs that come into proximity by Brownian motion (diffusion capture). To explore the implications of these two mechanisms, we perform biophysical simulations of a 3.76 Mb-long chromatin chain, the size of the long Schizosaccharomyces pombe chromosome I left arm. On it, the SMC complex condensin is modeled to perform loop extrusion or diffusion capture. We then compare computational to experimental observations of mitotic chromosome formation. Both loop extrusion and diffusion capture can result in native-like contact probability distributions. In addition, the diffusion capture model more readily recapitulates mitotic chromosome axis shortening and chromatin compaction. Diffusion capture can also explain why mitotic chromatin shows reduced, as well as more anisotropic, movements, features that lack support from loop extrusion. The condensin distribution within mitotic chromosomes, visualized by stochastic optical reconstruction microscopy (STORM), shows clustering predicted from diffusion capture. Our results inform the evaluation of current models of mitotic chromosome formation.
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Affiliation(s)
- Tereza Gerguri
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Waseda Institute for Advanced Study, Waseda University, 1-21-1 Nishiwaseda, Shinjuku-ku, Tokyo 169-0051, Japan
| | - Bhavin S Khatri
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Christopher Barrington
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
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12
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Rapsomaniki MA, Maxouri S, Nathanailidou P, Garrastacho MR, Giakoumakis NN, Taraviras S, Lygeros J, Lygerou Z. In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity. NAR Genom Bioinform 2021; 3:lqaa112. [PMID: 33554116 PMCID: PMC7846089 DOI: 10.1093/nargab/lqaa112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/15/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023] Open
Abstract
DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. Here, we present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit a good correlation along the genome, robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to genome plasticity and a plethora of genotypic variations.
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Affiliation(s)
- Maria Anna Rapsomaniki
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Stella Maxouri
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Patroula Nathanailidou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | | | | | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - John Lygeros
- Automatic Control Laboratory, ETH Zurich, 8092 Zurich, Switzerland
| | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
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13
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Sutormin DA, Galivondzhyan AK, Polkhovskiy AV, Kamalyan SO, Severinov KV, Dubiley SA. Diversity and Functions of Type II Topoisomerases. Acta Naturae 2021; 13:59-75. [PMID: 33959387 PMCID: PMC8084294 DOI: 10.32607/actanaturae.11058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022] Open
Abstract
The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect - supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Affiliation(s)
- D. A. Sutormin
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - A. K. Galivondzhyan
- Lomonosov Moscow State University, Moscow, 119991 Russia
- Institute of Molecular Genetics RAS, Moscow, 123182 Russia
| | - A. V. Polkhovskiy
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - S. O. Kamalyan
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - K. V. Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
- Waksman Institute for Microbiology, Piscataway, New Jersey, 08854 USA
| | - S. A. Dubiley
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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14
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Abstract
During the capturing of the time-lapse sequence of fluorescently labeled samples, fluorescence intensity exhibits decays. This phenomenon is known as 'photobleaching' and is a widely known problem in imaging in life sciences. The photobleaching can be attenuated by tuning the imaging set-up, but when such adjustments only partially work, the image sequence can be corrected for the loss of intensity in order to precisely segment the target structure or to quantify true intensity dynamics. We implemented an ImageJ plugin that allows the user to compensate for the photobleaching to estimate the non-bleaching condition with choice of three different algorithms: simple ratio, exponential fitting, and histogram matching methods. The histogram matching method is a novel algorithm for photobleaching correction. This article presents details and characteristics of each algorithm based on application to actual image sequences.
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Affiliation(s)
- Kota Miura
- Nikon Imaging Center, University of Heidelberg, Heidelberg, 69120, Germany.,Centre for Molecular and Cellular Imaging, EMBL, Heidelberg, 69117, Germany
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15
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Kakui Y, Barrington C, Barry DJ, Gerguri T, Fu X, Bates PA, Khatri BS, Uhlmann F. Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage. Genome Biol 2020; 21:272. [PMID: 33153481 PMCID: PMC7643427 DOI: 10.1186/s13059-020-02183-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/19/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood. RESULTS Here, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2-arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite their low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response. CONCLUSIONS In addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.
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Affiliation(s)
- Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Waseda Institute for Advanced Study, Waseda University, 1-21-1, Nishiwaseda, Shinjuku-ku, Tokyo, 169-0051, Japan.
| | - Christopher Barrington
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David J Barry
- Advanced Light Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Tereza Gerguri
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Bhavin S Khatri
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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16
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Muñoz S, Passarelli F, Uhlmann F. Conserved roles of chromatin remodellers in cohesin loading onto chromatin. Curr Genet 2020; 66:951-956. [PMID: 32277274 PMCID: PMC7497338 DOI: 10.1007/s00294-020-01075-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/23/2022]
Abstract
Cohesin is a conserved, ring-shaped protein complex that topologically entraps DNA. This ability makes this member of the structural maintenance of chromosomes (SMC) complex family a central hub of chromosome dynamics regulation. Besides its essential role in sister chromatid cohesion, cohesin shapes the interphase chromatin domain architecture and plays important roles in transcriptional regulation and DNA repair. Cohesin is loaded onto chromosomes at centromeres, at the promoters of highly expressed genes, as well as at DNA replication forks and sites of DNA damage. However, the features that determine these binding sites are still incompletely understood. We recently described a role of the budding yeast RSC chromatin remodeler in cohesin loading onto chromosomes. RSC has a dual function, both as a physical chromatin receptor of the Scc2/Scc4 cohesin loader complex, as well as by providing a nucleosome-free template for cohesin loading. Here, we show that the role of RSC in sister chromatid cohesion is conserved in fission yeast. We discuss what is known about the broader conservation of the contribution of chromatin remodelers to cohesin loading onto chromatin.
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Affiliation(s)
- Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
| | | | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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17
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Abstract
Structural maintenance of chromosomes (SMC) complexes play pivotal roles in controlling chromatin organization. Condensin is an essential SMC complex that compacts chromatin to form condensed chromosomes in mitosis. Complete condensin inactivation is necessary to reveal how condensin converts interphase chromatin into mitotic chromosomes. Here, we have developed a condensin depletion system in fission yeast that combines transcriptional repression with auxin-inducible protein degradation. This achieves efficient condensin depletion without need for a temperature shift. Our system is useful when studying how condensin contributes to chromosome architecture and is applicable to the study of other SMC complexes.
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18
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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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19
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Yamin K, Assa M, Matityahu A, Onn I. Analyzing chromosome condensation in yeast by second-harmonic generation microscopy. Curr Genet 2019; 66:437-443. [PMID: 31535185 DOI: 10.1007/s00294-019-01034-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 08/25/2019] [Accepted: 09/04/2019] [Indexed: 01/02/2023]
Abstract
Condensation is a fundamental property of mitotic chromosomes in eukaryotic cells. However, analyzing chromosome condensation in yeast is a challenging task while existing methods have notable weaknesses. Second-harmonic generation (SHG) microscopy is a label-free, advanced imaging technique for measuring the surface curve of isotropic molecules such as chromatin in live cells. We applied this method to detect changes in chromatin organization throughout the cell cycle in live yeast cells. We showed that SHG microscopy can be used to identify changes in chromatin organization throughout the cell cycle and in response to inactivation of the SMC complexes, cohesin and condensin. Implementation of this method will improve our ability to analyze chromatin structure in protozoa and will enhance our understanding of chromatin organization in eukaryotic cells.
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Affiliation(s)
- Katreena Yamin
- Chromosome Instability and Dynamics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Assa
- Imaging Unit, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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20
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Isolation of Fission Yeast Condensin Temperature-Sensitive Mutants with Single Amino Acid Substitutions Targeted to Hinge Domain. G3-GENES GENOMES GENETICS 2019; 9:1777-1783. [PMID: 30914423 PMCID: PMC6505169 DOI: 10.1534/g3.119.400156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Essential genes cannot be deleted from the genome; therefore, temperature-sensitive (ts) mutants and cold-sensitive (cs) mutants are very useful to discover functions of essential genes in model organisms such as Schizosaccharomyces pombe and Saccharomyces cerevisiae. To isolate ts/cs mutants for essential genes of interest, error-prone mutagenesis (or random mutagenesis) coupled with in vitro selection has been widely used. However, this method often introduces multiple silent mutations, in addition to the mutation responsible for ts/cs, with the result that one cannot discern which mutation is responsible for the ts/cs phenotype. In addition, the location of the responsible mutation introduced is random, whereas it is preferable to isolate ts/cs mutants with single amino acid substitutions, located in a targeted motif or domain of the protein of interest. To solve these problems, we have developed a method to isolate ts/cs mutants with single amino acid substitutions in targeted regions using site-directed mutagenesis. This method takes advantage of the empirical fact that single amino acid substitutions (L/S -> P or G/A -> E/D) often cause ts or cs. Application of the method to condensin and cohesin hinge domains was successful: ∼20% of the selected single amino acid substitutions turned out to be ts or cs. This method is versatile in fission yeast and is expected to be broadly applicable to isolate ts/cs mutants with single amino acid substitutions in targeted regions of essential genes. 11 condensin hinge ts mutants were isolated using the method and their responsible mutations are broadly distributed in hinge domain. Characterization of these mutants will be very helpful to understand the function of hinge domain.
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21
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Hocquet C, Robellet X, Modolo L, Sun XM, Burny C, Cuylen-Haering S, Toselli E, Clauder-Münster S, Steinmetz L, Haering CH, Marguerat S, Bernard P. Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription. eLife 2018; 7:38517. [PMID: 30230473 PMCID: PMC6173581 DOI: 10.7554/elife.38517] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022] Open
Abstract
Condensins are genome organisers that shape chromosomes and promote their accurate transmission. Several studies have also implicated condensins in gene expression, although any mechanisms have remained enigmatic. Here, we report on the role of condensin in gene expression in fission and budding yeasts. In contrast to previous studies, we provide compelling evidence that condensin plays no direct role in the maintenance of the transcriptome, neither during interphase nor during mitosis. We further show that the changes in gene expression in post-mitotic fission yeast cells that result from condensin inactivation are largely a consequence of chromosome missegregation during anaphase, which notably depletes the RNA-exosome from daughter cells. Crucially, preventing karyotype abnormalities in daughter cells restores a normal transcriptome despite condensin inactivation. Thus, chromosome instability, rather than a direct role of condensin in the transcription process, changes gene expression. This knowledge challenges the concept of gene regulation by canonical condensin complexes.
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Affiliation(s)
- Clémence Hocquet
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Xavier Robellet
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Laurent Modolo
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Claire Burny
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Esther Toselli
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
| | | | - Lars Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Samuel Marguerat
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pascal Bernard
- CNRS Laboratory of Biology and Modelling of the Cell, Lyon, France.,Université de Lyon, ENSL, UCBL, Lyon, France
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22
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Schiklenk C, Petrova B, Kschonsak M, Hassler M, Klein C, Gibson TJ, Haering CH. Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1. J Cell Biol 2018; 217:2383-2401. [PMID: 29735745 PMCID: PMC6028546 DOI: 10.1083/jcb.201711097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/28/2018] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
How chromosomes compact into rod-shaped structures is a longstanding unresolved question of cell biology. Schiklenk et al. identify the transcription factor Zas1 as a central regulator of mitotic chromosome condensation in fission yeast and show that it uses a conserved transactivation domain–based mechanism to control gene expression. Although the formation of rod-shaped chromosomes is vital for the correct segregation of eukaryotic genomes during cell divisions, the molecular mechanisms that control the chromosome condensation process have remained largely unknown. Here, we identify the C2H2 zinc-finger transcription factor Zas1 as a key regulator of mitotic condensation dynamics in a quantitative live-cell microscopy screen of the fission yeast Schizosaccharomyces pombe. By binding to specific DNA target sequences in their promoter regions, Zas1 controls expression of the Cnd1 subunit of the condensin protein complex and several other target genes, whose combined misregulation in zas1 mutants results in defects in chromosome condensation and segregation. Genetic and biochemical analysis reveals an evolutionarily conserved transactivation domain motif in Zas1 that is pivotal to its function in gene regulation. Our results suggest that this motif, together with the Zas1 C-terminal helical domain to which it binds, creates a cis/trans switch module for transcriptional regulation of genes that control chromosome condensation.
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Affiliation(s)
- Christoph Schiklenk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Boryana Petrova
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Kschonsak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Markus Hassler
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carlo Klein
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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23
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Hayles J, Nurse P. Introduction to Fission Yeast as a Model System. Cold Spring Harb Protoc 2018; 2018:pdb.top079749. [PMID: 28733415 DOI: 10.1101/pdb.top079749] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here, we briefly outline the history of fission yeast, its life cycle, and aspects of its biology that make it a useful model organism for studying problems of eukaryotic molecular and cell biology.
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Affiliation(s)
- Jacqueline Hayles
- Cell Cycle Laboratory, The Francis Crick Research Institute, London WC2A 3LY, United Kingdom
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Research Institute, London WC2A 3LY, United Kingdom
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24
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Ramos F, Leonard J, Clemente-Blanco A, Aragón L. Cdc14 and Chromosome Condensation: Evaluation of the Recruitment of Condensin to Genomic Regions. Methods Mol Biol 2018; 1505:229-243. [PMID: 27826868 DOI: 10.1007/978-1-4939-6502-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Chromosome condensation is an essential morphological event required for successful DNA segregation during mitosis. The high level of genome compaction achieved during this process is attained by the evolutionary conserved condensin complex. Recently, several lines of evidences have demonstrated that the mitotic phosphatase Cdc14 is required to ensure condensin loading onto chromosomes. To date several approaches have been used in order to characterize condensin activity and regulation, however these techniques are time-consuming and require complex equipment. In this chapter we described an easy and reliable protocol to analyze Cdc14-dependent condensin loading onto specific genomic DNA regions by using a chromatin immunoprecipitation (ChIP) technique.
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Affiliation(s)
- Facundo Ramos
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González 2, Salamanca, 37007, Spain
| | - Joanne Leonard
- Cell Cycle Group, Medical Research Council, Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Andrés Clemente-Blanco
- Cell Cycle and Genome Stability Group, Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca (USAL), C/ Zacarías González 2, Salamanca, 37007, Spain
| | - Luis Aragón
- Cell Cycle Group, Medical Research Council, Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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25
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Piskadlo E, Oliveira RA. A Topology-Centric View on Mitotic Chromosome Architecture. Int J Mol Sci 2017; 18:E2751. [PMID: 29258269 PMCID: PMC5751350 DOI: 10.3390/ijms18122751] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 02/04/2023] Open
Abstract
Mitotic chromosomes are long-known structures, but their internal organization and the exact process by which they are assembled are still a great mystery in biology. Topoisomerase II is crucial for various aspects of mitotic chromosome organization. The unique ability of this enzyme to untangle topologically intertwined DNA molecules (catenations) is of utmost importance for the resolution of sister chromatid intertwines. Although still controversial, topoisomerase II has also been proposed to directly contribute to chromosome compaction, possibly by promoting chromosome self-entanglements. These two functions raise a strong directionality issue towards topoisomerase II reactions that are able to disentangle sister DNA molecules (in trans) while compacting the same DNA molecule (in cis). Here, we review the current knowledge on topoisomerase II role specifically during mitosis, and the mechanisms that directly or indirectly regulate its activity to ensure faithful chromosome segregation. In particular, we discuss how the activity or directionality of this enzyme could be regulated by the SMC (structural maintenance of chromosomes) complexes, predominantly cohesin and condensin, throughout mitosis.
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Affiliation(s)
- Ewa Piskadlo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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26
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Shen D, Skibbens RV. Chl1 DNA helicase and Scc2 function in chromosome condensation through cohesin deposition. PLoS One 2017; 12:e0188739. [PMID: 29186203 PMCID: PMC5706694 DOI: 10.1371/journal.pone.0188739] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/13/2017] [Indexed: 02/02/2023] Open
Abstract
Chl1 DNA helicase promotes sister chromatid cohesion and associates with both the cohesion establishment acetyltransferase Eco1/Ctf7 and the DNA polymerase processivity factor PCNA that supports Eco1/Ctf7 function. Mutation in CHL1 results in precocious sister chromatid separation and cell aneuploidy, defects that arise through reduced levels of chromatin-bound cohesins which normally tether together sister chromatids (trans tethering). Mutation of Chl1 family members (BACH1/BRIP/FANCJ and DDX11/ChlR1) also exhibit genotoxic sensitivities, consistent with a role for Chl1 in trans tethering which is required for efficient DNA repair. Chl1 promotes the recruitment of Scc2 to DNA which is required for cohesin deposition onto DNA. There is limited evidence, however, that Scc2 also directs the deposition onto DNA of condensins which promote tethering in cis (intramolecular DNA links). Here, we test the ability of Chl1 to promote cis tethering and the role of both Chl1 and Scc2 to promote condensin recruitment to DNA. The results reveal that chl1 mutant cells exhibit significant condensation defects both within the rDNA locus and genome-wide. Importantly, chl1 mutant cell condensation defects do not result from reduced chromatin binding of condensin, but instead through reduced chromatin binding of cohesin. We tested scc2-4 mutant cells and similarly found no evidence of reduced condensin recruitment to chromatin. Consistent with a role for Scc2 specifically in cohesin deposition, scc2-4 mutant cell condensation defects are irreversible. We thus term Chl1 a novel regulator of both chromatin condensation and sister chromatid cohesion through cohesin-based mechanisms. These results reveal an exciting interface between DNA structure and the highly conserved cohesin complex.
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Affiliation(s)
- Donglai Shen
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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27
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Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V, Hassler M, Haering CH. Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes. Cell 2017; 171:588-600.e24. [PMID: 28988770 PMCID: PMC5651216 DOI: 10.1016/j.cell.2017.09.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/07/2017] [Accepted: 09/05/2017] [Indexed: 12/13/2022]
Abstract
Condensin protein complexes coordinate the formation of mitotic chromosomes and thereby ensure the successful segregation of replicated genomes. Insights into how condensin complexes bind to chromosomes and alter their topology are essential for understanding the molecular principles behind the large-scale chromatin rearrangements that take place during cell divisions. Here, we identify a direct DNA-binding site in the eukaryotic condensin complex, which is formed by its Ycg1Cnd3 HEAT-repeat and Brn1Cnd2 kleisin subunits. DNA co-crystal structures reveal a conserved, positively charged groove that accommodates the DNA double helix. A peptide loop of the kleisin subunit encircles the bound DNA and, like a safety belt, prevents its dissociation. Firm closure of the kleisin loop around DNA is essential for the association of condensin complexes with chromosomes and their DNA-stimulated ATPase activity. Our data suggest a sophisticated molecular basis for anchoring condensin complexes to chromosomes that enables the formation of large-sized chromatin loops.
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Affiliation(s)
- Marc Kschonsak
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fabian Merkel
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Shveta Bisht
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jutta Metz
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Rybin
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Markus Hassler
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Christian H Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
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28
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Kakui Y, Rabinowitz A, Barry DJ, Uhlmann F. Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast. Nat Genet 2017; 49:1553-1557. [PMID: 28825727 PMCID: PMC5621628 DOI: 10.1038/ng.3938] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/27/2017] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome consists of DNA molecules far longer than the cells that contain them. They reach their greatest compaction during chromosome condensation in mitosis. This process is aided by condensin, a structural maintenance of chromosomes (SMC) family member. The spatial organization of mitotic chromosomes and how condensin shapes chromatin architecture are not yet fully understood. Here we use chromosome conformation capture (Hi-C) to study mitotic chromosome condensation in the fission yeast Schizosaccharomyces pombe. This showed that the interphase landscape characterized by small chromatin domains is replaced by fewer but larger domains in mitosis. Condensin achieves this by setting up longer-range, intrachromosomal DNA interactions, which compact and individualize chromosomes. At the same time, local chromatin contacts are constrained by condensin, with profound implications for local chromatin function during mitosis. Our results highlight condensin as a major determinant that changes the chromatin landscape as cells prepare their genomes for cell division.
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Affiliation(s)
- Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Adam Rabinowitz
- Bioinformatics Core, The Francis Crick Institute, London, UK
| | - David J Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
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29
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Booth DG, Earnshaw WC. Ki-67 and the Chromosome Periphery Compartment in Mitosis. Trends Cell Biol 2017; 27:906-916. [PMID: 28838621 DOI: 10.1016/j.tcb.2017.08.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022]
Abstract
The chromosome periphery is a complex network of proteins and RNA molecules (many derived from nucleoli) that covers the outer surface of chromosomes and whose function remains mysterious. Although it was first described over 130 years ago, technological advances and the recent discovery that Ki-67 acts as an organiser of this region have allowed the chromosome periphery to be dissected in previously unattainable detail, leading to a revival of interest in this obscure chromosomal compartment. Here, we review the most recent advances into the composition, structure and function of the chromosome periphery, discuss possible roles of Ki-67 during mitosis and consider why this structure is likely to remain the focus of ongoing attention in the future.
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Affiliation(s)
- Daniel G Booth
- Centre For Neuroregeneration, Chancellor's Building, University of Edinburgh, Edinburgh, EH16 4SB, UK.
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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30
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On V, Zahedi A, Ethell IM, Bhanu B. Automated spatio-temporal analysis of dendritic spines and related protein dynamics. PLoS One 2017; 12:e0182958. [PMID: 28827828 PMCID: PMC5565271 DOI: 10.1371/journal.pone.0182958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/27/2017] [Indexed: 12/25/2022] Open
Abstract
Cofilin and other Actin-regulating proteins are essential in regulating the shape of dendritic spines, which are sites of neuronal communications in the brain, and their malfunctions are implicated in neurodegeneration related to aging. The analysis of cofilin motility in dendritic spines using fluorescence video-microscopy may allow for the discovery of its effects on synaptic functions. To date, the flow of cofilin has not been analyzed by automatic means. This paper presents Dendrite Protein Analysis (DendritePA), a novel automated pattern recognition software to analyze protein trafficking in neurons. Using spatiotemporal information present in multichannel fluorescence videos, the DendritePA generates a temporal maximum intensity projection that enhances the signal-to-noise ratio of important biological structures, segments and tracks dendritic spines, estimates the density of proteins in spines, and analyzes the flux of proteins through the dendrite/spine boundary. The motion of a dendritic spine is used to generate spine energy images, which are used to automatically classify the shape of common dendritic spines such as stubby, mushroom, or thin. By tracking dendritic spines over time and using their intensity profiles, the system can analyze the flux patterns of cofilin and other fluorescently stained proteins. The cofilin flux patterns are found to correlate with the dynamic changes in dendritic spine shapes. Our results also have shown that the activation of cofilin using genetic manipulations leads to immature spines while its inhibition results in an increase in mature spines.
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Affiliation(s)
- Vincent On
- Department of Electrical and Computer Engineering, University of California Riverside, Riverside, CA, United States of America
- * E-mail:
| | - Atena Zahedi
- Department of Bioengineering, University of California Riverside, Riverside, CA, United States of America
| | - Iryna M. Ethell
- Department of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, United States of America
| | - Bir Bhanu
- Department of Electrical and Computer Engineering, University of California Riverside, Riverside, CA, United States of America
- Department of Bioengineering, University of California Riverside, Riverside, CA, United States of America
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31
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Different Functionality of Cdc20 Binding Sites within the Mitotic Checkpoint Complex. Curr Biol 2017; 27:1213-1220. [PMID: 28366743 DOI: 10.1016/j.cub.2017.03.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 11/21/2022]
Abstract
The mitotic checkpoint is a cellular safeguard that prevents chromosome missegregation in eukaryotic cells [1, 2]. Suboptimal functioning may foster chromosome missegregation in cancer cells [3]. Checkpoint signaling produces the "mitotic checkpoint complex" (MCC), which prevents anaphase by targeting Cdc20, the activator of the anaphase-promoting complex/cyclosome (APC/C). Recent biochemical and structural studies revealed that the human MCC binds two Cdc20 molecules, one (Cdc20M) through well-characterized, cooperative binding to Mad2 and Mad3/BubR1 (forming the "core MCC") and the other one (Cdc20A) through additional binding sequences in Mad3/BubR1 [4-6]. Here, we dissect the different functionality of these sites in vivo. We show in fission yeast that, at low Cdc20 concentrations, Cdc20M binding is sufficient for checkpoint activity and Cdc20A binding becomes dispensable. Cdc20A binding is mediated by the conserved Mad3 ABBA-KEN2-ABBA motif [7, 8], which we find additionally required for binding of the MCC to the APC/C and for MCC disassembly. Strikingly, deletion of the APC/C subunit Apc15 mimics mutations in this motif, revealing a shared function. This function of Apc15 may be masked in human cells by independent mediators of MCC-APC/C binding. Our data provide important in vivo support for the recent structure-based models and functionally dissect three elements of Cdc20 inhibition: (1) sequestration of Cdc20 in the core MCC, sufficient at low Cdc20 concentrations; (2) inhibition of a second Cdc20 through the Mad3 C terminus, independent of Mad2 binding to this Cdc20 molecule; and (3) occupancy of the APC/C with full MCC, where Mad3 and Apc15 are involved.
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32
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Spivey EC, Jones SK, Rybarski JR, Saifuddin FA, Finkelstein IJ. An aging-independent replicative lifespan in a symmetrically dividing eukaryote. eLife 2017; 6:e20340. [PMID: 28139976 PMCID: PMC5332158 DOI: 10.7554/elife.20340] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/27/2017] [Indexed: 12/28/2022] Open
Abstract
The replicative lifespan (RLS) of a cell-defined as the number of cell divisions before death-has informed our understanding of the mechanisms of cellular aging. However, little is known about aging and longevity in symmetrically dividing eukaryotic cells because most prior studies have used budding yeast for RLS studies. Here, we describe a multiplexed fission yeast lifespan micro-dissector (multFYLM) and an associated image processing pipeline for performing high-throughput and automated single-cell micro-dissection. Using the multFYLM, we observe continuous replication of hundreds of individual fission yeast cells for over seventy-five generations. Surprisingly, cells die without the classic hallmarks of cellular aging, such as progressive changes in size, doubling time, or sibling health. Genetic perturbations and drugs can extend the RLS via an aging-independent mechanism. Using a quantitative model to analyze these results, we conclude that fission yeast does not age and that cellular aging and replicative lifespan can be uncoupled in a eukaryotic cell.
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Affiliation(s)
- Eric C Spivey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, United States
| | - Stephen K Jones
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, United States
| | - James R Rybarski
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Fatema A Saifuddin
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, United States
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33
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Schiklenk C, Petrova B, Haering CH. A Protocol for Measuring Mitotic Chromosome Condensation Quantitatively in Fission Yeast Cells. Methods Mol Biol 2017; 1515:245-255. [PMID: 27797084 DOI: 10.1007/978-1-4939-6545-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Even though the formation of compact cylindrical chromosomes early during mitosis or meiosis is a prerequisite for the successful segregation of eukaryotic genomes, little is known about the molecular basis of this chromosome condensation process. Here, we describe in detail the protocol for a quantitative chromosome condensation assay in fission yeast cells, which is based on precise time-resolved measurements of the distances between two fluorescently labeled positions on the same chromosome. In combination with an automated computational analysis pipeline, this assay enables the study of various candidate proteins for their roles in regulating genome topology during cell divisions.
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Affiliation(s)
- Christoph Schiklenk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Boryana Petrova
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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34
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Lampo TJ, Kennard AS, Spakowitz AJ. Physical Modeling of Dynamic Coupling between Chromosomal Loci. Biophys J 2016; 110:338-347. [PMID: 26789757 DOI: 10.1016/j.bpj.2015.11.3520] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/05/2015] [Accepted: 11/23/2015] [Indexed: 11/15/2022] Open
Abstract
The motion of chromosomal DNA is essential to many biological processes, including segregation, transcriptional regulation, recombination, and packaging. Physical understanding of these processes would be dramatically enhanced through predictive, quantitative modeling of chromosome dynamics of multiple loci. Using a polymer dynamics framework, we develop a prediction for the correlation in the velocities of two loci on a single chromosome or otherwise connected by chromatin. These predictions reveal that the signature of correlated motion between two loci can be identified by varying the lag time between locus position measurements. In general, this theory predicts that as the lag time interval increases, the dual-loci dynamic behavior transitions from being completely uncorrelated to behaving as an effective single locus. This transition corresponds to the timescale of the stress communication between loci through the intervening segment. This relatively simple framework makes quantitative predictions based on a single timescale fit parameter that can be directly compared to the in vivo motion of fluorescently labeled chromosome loci. Furthermore, this theoretical framework enables the detection of dynamically coupled chromosome regions from the signature of their correlated motion.
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Affiliation(s)
- Thomas J Lampo
- Chemical Engineering, Stanford University, Stanford, California
| | | | - Andrew J Spakowitz
- Chemical Engineering, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California.
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35
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Takagi M, Natsume T, Kanemaki MT, Imamoto N. Perichromosomal protein Ki67 supports mitotic chromosome architecture. Genes Cells 2016; 21:1113-1124. [DOI: 10.1111/gtc.12420] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/12/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Masatoshi Takagi
- Cellular Dynamics Laboratory; RIKEN; 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Toyoaki Natsume
- Division of Molecular Cell Engineering; National Institute of Genetics, ROIS; and Department of Genetics, SOKENDAI; Yata 1111 Mishima Shizuoka 411-8540 Japan
| | - Masato T. Kanemaki
- Division of Molecular Cell Engineering; National Institute of Genetics, ROIS; and Department of Genetics, SOKENDAI; Yata 1111 Mishima Shizuoka 411-8540 Japan
- PRESTO; Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory; RIKEN; 2-1 Hirosawa Wako Saitama 351-0198 Japan
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36
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Hagan IM, Grallert A, Simanis V. Analysis of the Schizosaccharomyces pombe Cell Cycle. Cold Spring Harb Protoc 2016; 2016:2016/9/pdb.top082800. [PMID: 27587785 DOI: 10.1101/pdb.top082800] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Schizosaccharomyces pombe cells are rod shaped, and they grow by tip elongation. Growth ceases during mitosis and cell division; therefore, the length of a septated cell is a direct measure of the timing of mitotic commitment, and the length of a wild-type cell is an indicator of its position in the cell cycle. A large number of documented stage-specific changes can be used as landmarks to characterize cell cycle progression under specific experimental conditions. Conditional mutations can permanently or transiently block the cell cycle at almost any stage. Large, synchronously dividing cell populations, essential for the biochemical analysis of cell cycle events, can be generated by induction synchrony (arrest-release of a cell cycle mutant) or selection synchrony (centrifugal elutriation or lactose-gradient centrifugation). Schizosaccharomyces pombe cell cycle studies routinely combine particular markers, mutants, and synchronization procedures to manipulate the cycle. We describe these techniques and list key landmarks in the fission yeast mitotic cell division cycle.
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Affiliation(s)
- Iain M Hagan
- CRUK Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester M20 4BX, United Kingdom
| | - Agnes Grallert
- CRUK Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester M20 4BX, United Kingdom
| | - Viesturs Simanis
- EPFL SV ISREC UPSIM, SV2.1830, Station 19, CH-1015 Lausanne, Switzerland
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37
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Abstract
The fidelity of mitosis is essential for life, and successful completion of this process relies on drastic changes in chromosome organization at the onset of nuclear division. The mechanisms that govern chromosome compaction at every cell division cycle are still far from full comprehension, yet recent studies provide novel insights into this problem, challenging classical views on mitotic chromosome assembly. Here, we briefly introduce various models for chromosome assembly and known factors involved in the condensation process (e.g. condensin complexes and topoisomerase II). We will then focus on a few selected studies that have recently brought novel insights into the mysterious way chromosomes are condensed during nuclear division.
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Affiliation(s)
- Ewa Piskadlo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156 , Portugal
| | - Raquel A Oliveira
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156 , Portugal
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38
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Toselli-Mollereau E, Robellet X, Fauque L, Lemaire S, Schiklenk C, Klein C, Hocquet C, Legros P, N'Guyen L, Mouillard L, Chautard E, Auboeuf D, Haering CH, Bernard P. Nucleosome eviction in mitosis assists condensin loading and chromosome condensation. EMBO J 2016; 35:1565-81. [PMID: 27266525 DOI: 10.15252/embj.201592849] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 05/05/2016] [Indexed: 12/15/2022] Open
Abstract
Condensins associate with DNA and shape mitotic chromosomes. Condensins are enriched nearby highly expressed genes during mitosis, but how this binding is achieved and what features associated with transcription attract condensins remain unclear. Here, we report that condensin accumulates at or in the immediate vicinity of nucleosome-depleted regions during fission yeast mitosis. Two transcriptional coactivators, the Gcn5 histone acetyltransferase and the RSC chromatin-remodelling complex, bind to promoters adjoining condensin-binding sites and locally evict nucleosomes to facilitate condensin binding and allow efficient mitotic chromosome condensation. The function of Gcn5 is closely linked to condensin positioning, since neither the localization of topoisomerase II nor that of the cohesin loader Mis4 is altered in gcn5 mutant cells. We propose that nucleosomes act as a barrier for the initial binding of condensin and that nucleosome-depleted regions formed at highly expressed genes by transcriptional coactivators constitute access points into chromosomes where condensin binds free genomic DNA.
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Affiliation(s)
- Esther Toselli-Mollereau
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Xavier Robellet
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Lydia Fauque
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Sébastien Lemaire
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | | | - Carlo Klein
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Clémence Hocquet
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Pénélope Legros
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Lia N'Guyen
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Léo Mouillard
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Emilie Chautard
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Didier Auboeuf
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | | | - Pascal Bernard
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
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39
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Antonin W, Neumann H. Chromosome condensation and decondensation during mitosis. Curr Opin Cell Biol 2016; 40:15-22. [PMID: 26895139 DOI: 10.1016/j.ceb.2016.01.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/08/2016] [Accepted: 01/29/2016] [Indexed: 11/24/2022]
Abstract
During eukaryotic cell division, nuclear chromatin undergoes marked changes with respect to shape and degree of compaction. Although already significantly compacted during interphase, upon entry into mitosis chromatin further condenses and individualizes to discrete chromosomes that are captured and moved independently by the mitotic spindle apparatus. Once segregated by the spindle, chromatin decondenses to re-establish its interphase structure competent for DNA replication and transcription. Although cytologically described a long time ago, the underlying molecular mechanisms of mitotic chromatin condensation and decondensation are still ill-defined. Here we summarize our current knowledge of mitotic chromatin restructuring and recent progress in the field.
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Affiliation(s)
- Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany.
| | - Heinz Neumann
- Georg August University Göttingen, GZMB, Applied Synthetic Biology Group, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany.
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40
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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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41
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Akai Y, Kanai R, Nakazawa N, Ebe M, Toyoshima C, Yanagida M. ATPase-dependent auto-phosphorylation of the open condensin hinge diminishes DNA binding. Open Biol 2015; 4:rsob.140193. [PMID: 25520186 PMCID: PMC4281712 DOI: 10.1098/rsob.140193] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Condensin, which contains two structural maintenance of chromosome (SMC) subunits and three regulatory non-SMC subunits, is essential for many chromosomal functions, including mitotic chromosome condensation and segregation. The ATPase domain of the SMC subunit comprises two termini connected by a long helical domain that is interrupted by a central hinge. The role of the ATPase domain has remained elusive. Here we report that the condensin SMC subunit of the fission yeast Schizosaccharomyces pombe is phosphorylated in a manner that requires the presence of the intact SMC ATPase Walker motif. Principal phosphorylation sites reside in the conserved, glycine-rich stretch at the hinge interface surrounded by the highly basic DNA-binding patch. Phosphorylation reduces affinity for DNA. Consistently, phosphomimetic mutants produce severe mitotic phenotypes. Structural evidence suggests that prior opening (though slight) of the hinge is necessary for phosphorylation, which is implicated in condensin's dissociation from and its progression along DNA.
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Affiliation(s)
- Yuko Akai
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Ryuta Kanai
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Norihiko Nakazawa
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Masahiro Ebe
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Chikashi Toyoshima
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Mitsuhiro Yanagida
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
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42
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Abstract
How eukaryotic genomes are packaged into compact cylindrical chromosomes in preparation for cell divisions has remained one of the major unsolved questions of cell biology. Novel approaches to study the topology of DNA helices inside the nuclei of intact cells, paired with computational modeling and precise biomechanical measurements of isolated chromosomes, have advanced our understanding of mitotic chromosome architecture. In this Review Essay, we discuss - in light of these recent insights - the role of chromatin architecture and the functions and possible mechanisms of SMC protein complexes and other molecular machines in the formation of mitotic chromosomes. Based on the information available, we propose a stepwise model of mitotic chromosome condensation that envisions the sequential generation of intra-chromosomal linkages by condensin complexes in the context of cohesin-mediated inter-chromosomal linkages, assisted by topoisomerase II. The described scenario results in rod-shaped metaphase chromosomes ready for their segregation to the cell poles.
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Affiliation(s)
- Marc Kschonsak
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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43
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Xu X, Nakazawa N, Yanagida M. Condensin HEAT subunits required for DNA repair, kinetochore/centromere function and ploidy maintenance in fission yeast. PLoS One 2015; 10:e0119347. [PMID: 25764183 PMCID: PMC4357468 DOI: 10.1371/journal.pone.0119347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/23/2015] [Indexed: 11/18/2022] Open
Abstract
Condensin, a central player in eukaryotic chromosomal dynamics, contains five evolutionarily-conserved subunits. Two SMC (structural maintenance of chromosomes) subunits contain ATPase, hinge, and coiled-coil domains. One non-SMC subunit is similar to bacterial kleisin, and two other non-SMC subunits contain HEAT (similar to armadillo) repeats. Here we report isolation and characterization of 21 fission yeast (Schizosaccharomyces pombe) mutants for three non-SMC subunits, created using error-prone mutagenesis that resulted in single-amino acid substitutions. Beside condensation, segregation, and DNA repair defects, similar to those observed in previously isolated SMC and cnd2 mutants, novel phenotypes were observed for mutants of HEAT-repeats containing Cnd1 and Cnd3 subunits. cnd3-L269P is hypersensitive to the microtubule poison, thiabendazole, revealing defects in kinetochore/centromere and spindle assembly checkpoints. Three cnd1 and three cnd3 mutants increased cell size and doubled DNA content, thereby eliminating the haploid state. Five of these mutations reside in helix B of HEAT repeats. Two non-SMC condensin subunits, Cnd1 and Cnd3, are thus implicated in ploidy maintenance.
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Affiliation(s)
- Xingya Xu
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Norihiko Nakazawa
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Mitsuhiro Yanagida
- Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- * E-mail:
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44
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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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45
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Nikalayevich E, Ohkura H. The NuRD nucleosome remodelling complex and NHK-1 kinase are required for chromosome condensation in oocytes. J Cell Sci 2015; 128:566-75. [PMID: 25501812 PMCID: PMC4311133 DOI: 10.1242/jcs.158477] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 12/05/2014] [Indexed: 12/31/2022] Open
Abstract
Chromosome condensation during cell division is one of the most dramatic events in the cell cycle. Condensin and topoisomerase II are the most studied factors in chromosome condensation. However, their inactivation leads to only mild defects and little is known about the roles of other factors. Here, we took advantage of Drosophilaoocytes to elucidate the roles of potential condensation factors by performing RNA interference (RNAi). Consistent with previous studies, depletion of condensin I subunits or topoisomerase II in oocytes only mildly affected chromosome condensation. In contrast, we found severe undercondensation of chromosomes after depletion of the Mi-2-containing NuRD nucleosome remodelling complex or the protein kinase NHK-1 (also known as Ballchen in Drosophila). The further phenotypic analysis suggests that Mi-2 and NHK-1 are involved in different pathways of chromosome condensation. We show that the main role of NHK-1 in chromosome condensation is to phosphorylate Barrier-to-autointegration factor (BAF) and suppress its activity in linking chromosomes to nuclear envelope proteins. We further show that NHK-1 is important for chromosome condensation during mitosis as well as in oocytes.
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Affiliation(s)
| | - Hiroyuki Ohkura
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
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46
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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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47
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Wachowicz P, Chasapi A, Krapp A, Cano Del Rosario E, Schmitter D, Sage D, Unser M, Xenarios I, Rougemont J, Simanis V. Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN. J Cell Sci 2014; 128:741-54. [PMID: 25501816 DOI: 10.1242/jcs.160150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Schizosaccharomyces pombe septation initiation network (SIN) regulates cytokinesis, and asymmetric association of SIN proteins with the mitotic spindle pole bodies (SPBs) is important for its regulation. Here, we have used semi-automated image analysis to study SIN proteins in large numbers of wild-type and mutant cells. Our principal conclusions are: first, that the association of Cdc7p with the SPBs in early mitosis is frequently asymmetric, with a bias in favour of the new SPB; second, that the early association of Cdc7p-GFP to the SPB depends on Plo1p but not Spg1p, and is unaffected by mutations that influence its asymmetry in anaphase; third, that Cdc7p asymmetry in anaphase B is delayed by Pom1p and by activation of the spindle assembly checkpoint, and is promoted by Rad24p; and fourth, that the length of the spindle, expressed as a fraction of the length of the cell, at which Cdc7p becomes asymmetric is similar in cells dividing at different sizes. These data reveal that multiple regulatory mechanisms control the SIN in mitosis and lead us to propose a two-state model to describe the SIN.
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Affiliation(s)
- Paulina Wachowicz
- Cell cycle control laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), SV-ISREC, 1015 Lausanne, Switzerland
| | - Anastasia Chasapi
- Swiss-Prot. Group and Vital-IT Group, Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Andrea Krapp
- Cell cycle control laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), SV-ISREC, 1015 Lausanne, Switzerland
| | - Elena Cano Del Rosario
- Cell cycle control laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), SV-ISREC, 1015 Lausanne, Switzerland
| | - Daniel Schmitter
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Daniel Sage
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Michael Unser
- Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ioannis Xenarios
- Swiss-Prot. Group and Vital-IT Group, Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Jacques Rougemont
- Bioinformatics and Biostatistics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Viesturs Simanis
- Cell cycle control laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), SV-ISREC, 1015 Lausanne, Switzerland
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48
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Vanoosthuyse V, Legros P, van der Sar SJA, Yvert G, Toda K, Le Bihan T, Watanabe Y, Hardwick K, Bernard P. CPF-associated phosphatase activity opposes condensin-mediated chromosome condensation. PLoS Genet 2014; 10:e1004415. [PMID: 24945319 PMCID: PMC4063703 DOI: 10.1371/journal.pgen.1004415] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/16/2014] [Indexed: 12/03/2022] Open
Abstract
Functional links connecting gene transcription and condensin-mediated chromosome condensation have been established in species ranging from prokaryotes to vertebrates. However, the exact nature of these links remains misunderstood. Here we show in fission yeast that the 3′ end RNA processing factor Swd2.2, a component of the Cleavage and Polyadenylation Factor (CPF), is a negative regulator of condensin-mediated chromosome condensation. Lack of Swd2.2 does not affect the assembly of the CPF but reduces its association with chromatin. This causes only limited, context-dependent effects on gene expression and transcription termination. However, CPF-associated Swd2.2 is required for the association of Protein Phosphatase 1 PP1Dis2 with chromatin, through an interaction with Ppn1, a protein that we identify as the fission yeast homologue of vertebrate PNUTS. We demonstrate that Swd2.2, Ppn1 and PP1Dis2 form an independent module within the CPF, which provides an essential function in the absence of the CPF-associated Ssu72 phosphatase. We show that Ppn1 and Ssu72, like Swd2.2, are also negative regulators of condensin-mediated chromosome condensation. We conclude that Swd2.2 opposes condensin-mediated chromosome condensation by facilitating the function of the two CPF-associated phosphatases PP1 and Ssu72. Failure to properly condense chromosomes prior to their segregation in mitosis can lead to genome instability. The evolutionary-conserved condensin complex is key to the condensation process but the molecular mechanisms underlying its localization pattern on chromosomes remain unclear. Previous observations showed that the localization of condensin is intimately linked to regions of high transcription, although, somewhat paradoxically, its association with chromatin is disrupted by a processive polymerase activity. Here we identify several RNA processing factors as negative regulators of condensin in fission yeast. Two of these factors associate with PP1 phosphatase as an independent entity within the Cleavage and Polyadenylation Factor (CPF), a complex key for 3′ end RNA processing. Lack of this module induces only minor and context-dependent effects on gene expression. Our data suggest that this module helps maintaining the proper level of phosphatase activity within the CPF and thereby opposes the function of condensin in mitotic chromosome condensation.
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Affiliation(s)
- Vincent Vanoosthuyse
- CNRS, UMR5239, LBMC; Ecole Normale Supérieure de Lyon; Université Lyon 01, Lyon, France
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Pénélope Legros
- CNRS, UMR5239, LBMC; Ecole Normale Supérieure de Lyon; Université Lyon 01, Lyon, France
| | | | - Gaël Yvert
- CNRS, UMR5239, LBMC; Ecole Normale Supérieure de Lyon; Université Lyon 01, Lyon, France
| | - Kenji Toda
- Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Thierry Le Bihan
- SynthSys Edinburgh, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yoshinori Watanabe
- Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Kevin Hardwick
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Pascal Bernard
- CNRS, UMR5239, LBMC; Ecole Normale Supérieure de Lyon; Université Lyon 01, Lyon, France
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49
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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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