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Kunchala P, Varberg JM, O'Toole E, Gardner J, Smith SE, McClain M, Jaspersen SL, Hawley RS, Gerton JL. Plasticity of the mitotic spindle in response to karyotype variation. Curr Biol 2024; 34:3416-3428.e4. [PMID: 39043187 DOI: 10.1016/j.cub.2024.06.058] [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: 11/22/2023] [Revised: 04/09/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024]
Abstract
Karyotypes, composed of chromosomes, must be accurately partitioned by the mitotic spindle for optimal cell health. However, it is unknown how underlying characteristics of karyotypes, such as chromosome number and size, govern the scaling of the mitotic spindle to ensure accurate chromosome segregation and cell proliferation. We utilize budding yeast strains engineered with fewer chromosomes, including just two "mega chromosomes," to study how spindle size and function are responsive to, and scaled by, karyotype. We determined that deletion and overexpression of spindle-related genes are detrimental to the growth of strains with two chromosomes, suggesting that mega chromosomes exert altered demands on the spindle. Using confocal microscopy, we demonstrate that cells with fewer but longer chromosomes have smaller spindle pole bodies, fewer microtubules, and longer spindles. Moreover, using electron tomography and confocal imaging, we observe elongated, bent anaphase spindles with fewer core microtubules in strains with mega chromosomes. Cells harboring mega chromosomes grow more slowly, are delayed in mitosis, and a subset struggle to complete chromosome segregation. We propose that the karyotype of the cell dictates the microtubule number, type, spindle pole body size, and spindle length, subsequently influencing the dynamics of mitosis, such as the rate of spindle elongation and the velocity of pole separation. Taken together, our results suggest that mitotic spindles are highly plastic ultrastructures that can accommodate and adjust to a variety of karyotypes, even within a species.
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Affiliation(s)
- Preethi Kunchala
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Joseph M Varberg
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Eileen O'Toole
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80302, USA
| | - Jennifer Gardner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sarah E Smith
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melainia McClain
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - R Scott Hawley
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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2
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Murayama Y, Endo S, Kurokawa Y, Kurita A, Iwasaki S, Araki H. Coordination of cohesin and DNA replication observed with purified proteins. Nature 2024; 626:653-660. [PMID: 38267580 DOI: 10.1038/s41586-023-07003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/26/2024]
Abstract
Two newly duplicated copies of genomic DNA are held together by the ring-shaped cohesin complex to ensure faithful inheritance of the genome during cell division1-3. Cohesin mediates sister chromatid cohesion by topologically entrapping two sister DNAs during DNA replication4,5, but how cohesion is established at the replication fork is poorly understood. Here, we studied the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins. Once DNA is encircled before replication, the cohesin ring accommodates replication in its entirety, from initiation to termination, leading to topological capture of newly synthesized DNA. This suggests that topological cohesin loading is a critical molecular prerequisite to cope with replication. Paradoxically, topological loading per se is highly rate limiting and hardly occurs under the replication-competent physiological salt concentration. This inconsistency is resolved by the replisome-associated cohesion establishment factors Chl1 helicase and Ctf4 (refs. 6,7), which promote cohesin loading specifically during continuing replication. Accordingly, we found that bubble DNA, which mimics the state of DNA unwinding, induces topological cohesin loading and this is further promoted by Chl1. Thus, we propose that cohesin converts the initial electrostatic DNA-binding mode to a topological embrace when it encounters unwound DNA structures driven by enzymatic activities including replication. Together, our results show how cohesin initially responds to replication, and provide a molecular model for the establishment of sister chromatid cohesion.
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Affiliation(s)
- Yasuto Murayama
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan.
- Department of Genetics, Graduate University for Advanced Studies (SOUKENDAI), Mishima, Japan.
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Japan.
| | - Shizuko Endo
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Yumiko Kurokawa
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOUKENDAI), Mishima, Japan
| | - Ayako Kurita
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Sanae Iwasaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
| | - Hiroyuki Araki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Japan
- Joint Support-Centre for Data Science Research, Research Organisation of Information and Systems, Tachikawa, Japan
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3
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Abramczyk D, Del Carmen Sanchez Olmos M, Rojas AAR, Schindler D, Robertson D, McColm S, Marston AL, Barlow PN. A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. Microb Cell Fact 2023; 22:259. [PMID: 38104077 PMCID: PMC10724962 DOI: 10.1186/s12934-023-02262-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Komagataella phaffii (Pichia pastoris) is a methylotrophic commercially important non-conventional species of yeast that grows in a fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored in this organism to facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes in K. phaffii could offer unique advantages by accommodating multiple integrations of extraneous genes and their promoters without accumulating perturbations of native chromosomes or exhausting the availability of selection markers. RESULTS Here, we describe a linear "nano"chromosome (of 15-25 kb) that, according to whole-genome sequencing, persists in K. phaffii over many generations with a copy number per cell of one, provided non-homologous end joining is compromised (by KU70-knockout). The nanochromosome includes a copy of the centromere from K. phaffii chromosome 3, a K. phaffii-derived autonomously replicating sequence on either side of the centromere, and a pair of K. phaffii-like telomeres. It contains, within its q arm, a landing zone in which genes of interest alternate with long (approx. 1-kb) non-coding DNA chosen to facilitate homologous recombination and serve as spacers. The landing zone can be extended along the nanochromosome, in an inch-worming mode of sequential gene integrations, accompanied by recycling of just two antibiotic-resistance markers. The nanochromosome was used to express PDI, a gene encoding protein disulfide isomerase. Co-expression with PDI allowed the production, from a genomically integrated gene, of secreted murine complement factor H, a plasma protein containing 40 disulfide bonds. As further proof-of-principle, we co-expressed, from a nanochromosome, both PDI and a gene for GFP-tagged human complement factor H under the control of PAOX1 and demonstrated that the secreted protein was active as a regulator of the complement system. CONCLUSIONS We have added K. phaffii to the list of organisms that can produce human proteins from genes carried on a stable, linear, artificial chromosome. We envisage using nanochromosomes as repositories for numerous extraneous genes, allowing intensive engineering of K. phaffii without compromising its genome or weakening the resulting strain.
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Affiliation(s)
| | | | | | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Robertson
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Paul N Barlow
- School of Chemistry, University of Edinburgh, Edinburgh, UK.
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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4
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Litwin I, Nowicka M, Markowska K, Maciaszczyk-Dziubińska E, Tomaszewska P, Wysocki R, Kramarz K. ISW1a modulates cohesin distribution in centromeric and pericentromeric regions. Nucleic Acids Res 2023; 51:9101-9121. [PMID: 37486771 PMCID: PMC10516642 DOI: 10.1093/nar/gkad612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Cohesin is a highly conserved, multiprotein complex whose canonical function is to hold sister chromatids together to ensure accurate chromosome segregation. Cohesin association with chromatin relies on the Scc2-Scc4 cohesin loading complex that enables cohesin ring opening and topological entrapment of sister DNAs. To better understand how sister chromatid cohesion is regulated, we performed a proteomic screen in budding yeast that identified the Isw1 chromatin remodeler as a cohesin binding partner. In addition, we found that Isw1 also interacts with Scc2-Scc4. Lack of Isw1 protein, the Ioc3 subunit of ISW1a or Isw1 chromatin remodeling activity resulted in increased accumulation of cohesin at centromeres and pericentromeres, suggesting that ISW1a may promote efficient translocation of cohesin from the centromeric site of loading to neighboring regions. Consistent with the role of ISW1a in the chromatin organization of centromeric regions, Isw1 was found to be recruited to centromeres. In its absence we observed changes in the nucleosomal landscape at centromeres and pericentromeres. Finally, we discovered that upon loss of RSC functionality, ISW1a activity leads to reduced cohesin binding and cohesion defect. Taken together, our results support the notion of a key role of chromatin remodelers in the regulation of cohesin distribution on chromosomes.
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Affiliation(s)
- Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Małgorzata Nowicka
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Katarzyna Markowska
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubińska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Paulina Tomaszewska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Karol Kramarz
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
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5
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Gordon MR, Zhu J, Sun G, Li R. Suppression of chromosome instability by targeting a DNA helicase in budding yeast. Mol Biol Cell 2023; 34:ar3. [PMID: 36350688 PMCID: PMC9816644 DOI: 10.1091/mbc.e22-09-0395] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Chromosome instability (CIN) is an important driver of cancer initiation, progression, drug resistance, and aging. As such, genes whose inhibition suppresses CIN are potential therapeutic targets. We report here that deletion of an accessory DNA helicase, Rrm3, suppresses high CIN caused by a wide range of genetic or pharmacological perturbations in yeast. Although this helicase mutant has altered cell cycle dynamics, suppression of CIN by rrm3∆ is independent of the DNA damage and spindle assembly checkpoints. Instead, the rrm3∆ mutant may have increased kinetochore-microtubule error correction due to an altered localization of Aurora B kinase and associated phosphatase, PP2A-Rts1.
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Affiliation(s)
- Molly R. Gordon
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jin Zhu
- Mechanobiology Institute and
| | - Gordon Sun
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Biomedical Engineering and
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Mechanobiology Institute and
- Department of Biological Sciences, National University of Singapore, 117411
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218
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6
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Cairo G, MacKenzie A, Tsuchiya D, Lacefield S. Use of Time-Lapse Microscopy and Stage-Specific Nuclear Depletion of Proteins to Study Meiosis in S. Cerevisiae. J Vis Exp 2022:10.3791/64580. [PMID: 36314815 PMCID: PMC10114469 DOI: 10.3791/64580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Time-lapse fluorescence microscopy has revolutionized the understanding of meiotic cell-cycle events by providing temporal and spatial data that is often not seen by imaging fixed cells. Budding yeast has proved to be an important model organism to study meiotic chromosome segregation because many meiotic genes are highly conserved. Time-lapse microscopy of meiosis in budding yeast allows the monitoring of different meiotic mutants to show how the mutation disrupts meiotic processes. However, many proteins function at multiple points in meiosis. The use of loss-of-function or meiotic null mutants can therefore disrupt an early process, blocking or disturbing the later process and making it difficult to determine the phenotypes associated with each individual role. To circumvent this challenge, this protocol describes how the proteins can be conditionally depleted from the nucleus at specific stages of meiosis while monitoring meiotic events using time-lapse microscopy. Specifically, this protocol describes how the cells are synchronized in prophase I, how the anchor away technique is used to deplete proteins from the nucleus at specific meiotic stages, and how time-lapse imaging is used to monitor meiotic chromosome segregation. As an example of the usefulness of the technique, the kinetochore protein Ctf19 was depleted from the nucleus at different time points during meiosis, and the number of chromatin masses was analyzed at the end of meiosis II. Overall, this protocol can be adapted to deplete different nuclear proteins from the nucleus while monitoring the meiotic divisions.
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Affiliation(s)
| | | | - Dai Tsuchiya
- Department of Biology, Indiana University; Stowers Institute for Biomedical Research
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7
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Mechanisms of DNA Mobilization and Sequestration. Genes (Basel) 2022; 13:genes13020352. [PMID: 35205396 PMCID: PMC8872102 DOI: 10.3390/genes13020352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 12/04/2022] Open
Abstract
The entire genome becomes mobilized following DNA damage. Understanding the mechanisms that act at the genome level requires that we embrace experimental and computational strategies to capture the behavior of the long-chain DNA polymer, which is the building block for the chromosome. Long-chain polymers exhibit constrained, sub-diffusive motion in the nucleus. Cross-linking proteins, including cohesin and condensin, have a disproportionate effect on genome organization in their ability to stabilize transient interactions. Cross-linking proteins can segregate the genome into sub-domains through polymer–polymer phase separation (PPPS) and can drive the formation of gene clusters through small changes in their binding kinetics. Principles from polymer physics provide a means to unravel the mysteries hidden in the chains of life.
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8
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Mehta G, Sanyal K, Abhishek S, Rajakumara E, Ghosh SK. Minichromosome maintenance proteins in eukaryotic chromosome segregation. Bioessays 2021; 44:e2100218. [PMID: 34841543 DOI: 10.1002/bies.202100218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/02/2023]
Abstract
Minichromosome maintenance (Mcm) proteins are well-known for their functions in DNA replication. However, their roles in chromosome segregation are yet to be reviewed in detail. Following the discovery in 1984, a group of Mcm proteins, known as the ARS-nonspecific group consisting of Mcm13, Mcm16-19, and Mcm21-22, were characterized as bonafide kinetochore proteins and were shown to play significant roles in the kinetochore assembly and high-fidelity chromosome segregation. This review focuses on the structure, function, and evolution of this group of Mcm proteins. Our in silico analysis of the physical interactors of these proteins reveals that they share non-overlapping functions despite being copurified in biochemically stable complexes. We have discussed the contrasting results reported in the literature and experimental strategies to address them. Taken together, this review focuses on the structure-function of the ARS-nonspecific Mcm proteins and their evolutionary flexibility to maintain genome stability in various organisms.
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Affiliation(s)
- Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Kaustuv Sanyal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
| | - Suman Abhishek
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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9
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The Proteomic Landscape of Centromeric Chromatin Reveals an Essential Role for the Ctf19 CCAN Complex in Meiotic Kinetochore Assembly. Curr Biol 2021; 31:283-296.e7. [PMID: 33157029 PMCID: PMC7846277 DOI: 10.1016/j.cub.2020.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/10/2020] [Accepted: 10/08/2020] [Indexed: 11/23/2022]
Abstract
Kinetochores direct chromosome segregation in mitosis and meiosis. Faithful gamete formation through meiosis requires that kinetochores take on new functions that impact homolog pairing, recombination, and the orientation of kinetochore attachment to microtubules in meiosis I. Using an unbiased proteomics pipeline, we determined the composition of centromeric chromatin and kinetochores at distinct cell-cycle stages, revealing extensive reorganization of kinetochores during meiosis. The data uncover a network of meiotic chromosome axis and recombination proteins that bind to centromeres in the absence of the microtubule-binding outer kinetochore sub-complexes during meiotic prophase. We show that the Ctf19cCCAN inner kinetochore complex is essential for kinetochore organization in meiosis. Our functional analyses identify a Ctf19cCCAN-dependent kinetochore assembly pathway that is dispensable for mitotic growth but becomes critical upon meiotic entry. Therefore, changes in kinetochore composition and a distinct assembly pathway specialize meiotic kinetochores for successful gametogenesis. The composition of meiotic centromeres and kinetochores is revealed Kinetochores undergo extensive changes between meiotic prophase I and metaphase I The Ctf19CCAN orchestrates meiotic kinetochore specialization A Ctf19CCAN-directed kinetochore assembly pathway is uniquely critical in meiosis
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10
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Singh P, Pesenti ME, Maffini S, Carmignani S, Hedtfeld M, Petrovic A, Srinivasamani A, Bange T, Musacchio A. BUB1 and CENP-U, Primed by CDK1, Are the Main PLK1 Kinetochore Receptors in Mitosis. Mol Cell 2021; 81:67-87.e9. [PMID: 33248027 PMCID: PMC7837267 DOI: 10.1016/j.molcel.2020.10.040] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/08/2020] [Accepted: 10/28/2020] [Indexed: 02/02/2023]
Abstract
Reflecting its pleiotropic functions, Polo-like kinase 1 (PLK1) localizes to various sub-cellular structures during mitosis. At kinetochores, PLK1 contributes to microtubule attachments and mitotic checkpoint signaling. Previous studies identified a wealth of potential PLK1 receptors at kinetochores, as well as requirements for various mitotic kinases, including BUB1, Aurora B, and PLK1 itself. Here, we combine ectopic localization, in vitro reconstitution, and kinetochore localization studies to demonstrate that most and likely all of the PLK1 is recruited through BUB1 in the outer kinetochore and centromeric protein U (CENP-U) in the inner kinetochore. BUB1 and CENP-U share a constellation of sequence motifs consisting of a putative PP2A-docking motif and two neighboring PLK1-docking sites, which, contingent on priming phosphorylation by cyclin-dependent kinase 1 and PLK1 itself, bind PLK1 and promote its dimerization. Our results rationalize previous observations and describe a unifying mechanism for recruitment of PLK1 to human kinetochores.
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Affiliation(s)
- Priyanka Singh
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Marion E Pesenti
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Sara Carmignani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Marius Hedtfeld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Anupallavi Srinivasamani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitätsstrasse, 45141 Essen, Germany.
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11
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Vijay N. Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast. PeerJ 2020; 8:e10085. [PMID: 33062452 PMCID: PMC7531349 DOI: 10.7717/peerj.10085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/11/2020] [Indexed: 01/28/2023] Open
Abstract
Background The genomic sequences of centromeres, as well as the set of proteins that recognize and interact with centromeres, are known to quickly diverge between lineages potentially contributing to post-zygotic reproductive isolation. However, the actual sequence of events and processes involved in the divergence of the kinetochore machinery is not known. The patterns of gene loss that occur during evolution concomitant with phenotypic changes have been used to understand the timing and order of molecular changes. Methods I screened the high-quality genomes of twenty budding yeast species for the presence of well-studied kinetochore genes. Based on the conserved gene order and complete genome assemblies, I identified gene loss events. Subsequently, I searched the intergenic regions to identify any un-annotated genes or gene remnants to obtain additional evidence of gene loss. Results My analysis identified the loss of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) of the inner kinetochore constitutive centromere-associated network (CCAN/also known as CTF19 complex in yeast) in both the Naumovozyma species for which genome assemblies are available. Surprisingly, this collective loss of four genes of the CCAN/CTF19 complex coincides with the emergence of unconventional centromeres in N. castellii and N. dairenensis. My study suggests a tentative link between the emergence of unconventional point centromeres and the turnover of kinetochore genes in budding yeast.
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Affiliation(s)
- Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
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12
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Kuhl LM, Makrantoni V, Recknagel S, Vaze AN, Marston AL, Vader G. A dCas9-Based System Identifies a Central Role for Ctf19 in Kinetochore-Derived Suppression of Meiotic Recombination. Genetics 2020; 216:395-408. [PMID: 32843356 PMCID: PMC7536843 DOI: 10.1534/genetics.120.303384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/23/2020] [Indexed: 11/18/2022] Open
Abstract
In meiosis, crossover (CO) formation between homologous chromosomes is essential for faithful segregation. However, misplaced meiotic recombination can have catastrophic consequences on genome stability. Within pericentromeres, COs are associated with meiotic chromosome missegregation. In organisms ranging from yeast to humans, pericentromeric COs are repressed. We previously identified a role for the kinetochore-associated Ctf19 complex (Ctf19c) in pericentromeric CO suppression. Here, we develop a dCas9/CRISPR-based system that allows ectopic targeting of Ctf19c-subunits. Using this approach, we query sufficiency in meiotic CO suppression, and identify Ctf19 as a mediator of kinetochore-associated CO control. The effect of Ctf19 is encoded in its NH2-terminal tail, and depends on residues important for the recruitment of the Scc2-Scc4 cohesin regulator. This work provides insight into kinetochore-derived control of meiotic recombination. We establish an experimental platform to investigate and manipulate meiotic CO control. This platform can easily be adapted in order to investigate other aspects of chromosome biology.
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Affiliation(s)
- Lisa-Marie Kuhl
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Vasso Makrantoni
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF, United Kingdom
| | - Sarah Recknagel
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Animish N Vaze
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
| | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF, United Kingdom
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
- International Max Planck Research School (IMPRS) in Chemical and Molecular Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
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13
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Meiotic CENP-C is a shepherd: bridging the space between the centromere and the kinetochore in time and space. Essays Biochem 2020; 64:251-261. [PMID: 32794572 DOI: 10.1042/ebc20190080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023]
Abstract
While many of the proteins involved in the mitotic centromere and kinetochore are conserved in meiosis, they often gain a novel function due to the unique needs of homolog segregation during meiosis I (MI). CENP-C is a critical component of the centromere for kinetochore assembly in mitosis. Recent work, however, has highlighted the unique features of meiotic CENP-C. Centromere establishment and stability require CENP-C loading at the centromere for CENP-A function. Pre-meiotic loading of proteins necessary for homolog recombination as well as cohesion also rely on CENP-C, as do the main scaffolding components of the kinetochore. Much of this work relies on new technologies that enable in vivo analysis of meiosis like never before. Here, we strive to highlight the unique role of this highly conserved centromere protein that loads on to centromeres prior to M-phase onset, but continues to perform critical functions through chromosome segregation. CENP-C is not merely a structural link between the centromere and the kinetochore, but also a functional one joining the processes of early prophase homolog synapsis to late metaphase kinetochore assembly and signaling.
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14
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Paldi F, Alver B, Robertson D, Schalbetter SA, Kerr A, Kelly DA, Baxter J, Neale MJ, Marston AL. Convergent genes shape budding yeast pericentromeres. Nature 2020; 582:119-123. [PMID: 32494069 PMCID: PMC7279958 DOI: 10.1038/s41586-020-2244-6] [Citation(s) in RCA: 33] [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: 03/11/2019] [Accepted: 02/25/2020] [Indexed: 11/08/2022]
Abstract
The three-dimensional architecture of the genome governs its maintenance, expression and transmission. The cohesin protein complex organizes the genome by topologically linking distant loci, and is highly enriched in specialized chromosomal domains surrounding centromeres, called pericentromeres1-6. Here we report the three-dimensional structure of pericentromeres in budding yeast (Saccharomyces cerevisiae) and establish the relationship between genome organization and function. We find that convergent genes mark pericentromere borders and, together with core centromeres, define their structure and function by positioning cohesin. Centromeres load cohesin, and convergent genes at pericentromere borders trap it. Each side of the pericentromere is organized into a looped conformation, with border convergent genes at the base. Microtubule attachment extends a single pericentromere loop, size-limited by convergent genes at its borders. Reorienting genes at borders into a tandem configuration repositions cohesin, enlarges the pericentromere and impairs chromosome biorientation during mitosis. Thus, the linear arrangement of transcriptional units together with targeted cohesin loading shapes pericentromeres into a structure that is competent for chromosome segregation. Our results reveal the architecture of the chromosomal region within which kinetochores are embedded, as well as the restructuring caused by microtubule attachment. Furthermore, we establish a direct, causal relationship between the three-dimensional genome organization of a specific chromosomal domain and cellular function.
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Affiliation(s)
- Flora Paldi
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Bonnie Alver
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Daniel Robertson
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Kerr
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - David A Kelly
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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15
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Ming Sun S, Batté A, Elmer M, van der Horst SC, van Welsem T, Bean G, Ideker T, van Leeuwen F, van Attikum H. A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae. J Cell Sci 2020; 133:jcs237628. [PMID: 32299836 PMCID: PMC7325435 DOI: 10.1242/jcs.237628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/26/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic chromosomes are replicated in interphase and the two newly duplicated sister chromatids are held together by the cohesin complex and several cohesin auxiliary factors. Sister chromatid cohesion is essential for accurate chromosome segregation during mitosis, yet has also been implicated in other processes, including DNA damage repair, transcription and DNA replication. To assess how cohesin and associated factors functionally interconnect and coordinate with other cellular processes, we systematically mapped the genetic interactions of 17 cohesin genes centered on quantitative growth measurements of >52,000 gene pairs in the budding yeast Saccharomyces cerevisiae Integration of synthetic genetic interactions unveiled a cohesin functional map that constitutes 373 genetic interactions, revealing novel functional connections with post-replication repair, microtubule organization and protein folding. Accordingly, we show that the microtubule-associated protein Irc15 and the prefoldin complex members Gim3, Gim4 and Yke2 are new factors involved in sister chromatid cohesion. Our genetic interaction map thus provides a unique resource for further identification and functional interrogation of cohesin proteins. Since mutations in cohesin proteins have been associated with cohesinopathies and cancer, it may also help in identifying cohesin interactions relevant in disease etiology.
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Affiliation(s)
- Su Ming Sun
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
| | - Amandine Batté
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
| | - Mireille Elmer
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
- Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2600 AA, Delft, Netherlands
| | - Sophie C van der Horst
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Gordon Bean
- Bioinformatics and Systems Biology Program, University of California, San Diego; La Jolla, CA, 92093, USA
| | - Trey Ideker
- Bioinformatics and Systems Biology Program, University of California, San Diego; La Jolla, CA, 92093, USA
- Department of Medicine, Division of Genetics, University of California, San Diego; La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego; La Jolla, CA, 92093, USA
- Cancer Cell Map Initiative (CCMI), Moores UCSD Cancer Center, La Jolla, CA, 92093, USA
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
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16
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Hsieh YYP, Makrantoni V, Robertson D, Marston AL, Murray AW. Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis. PLoS Biol 2020; 18:e3000635. [PMID: 32155147 PMCID: PMC7138332 DOI: 10.1371/journal.pbio.3000635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/07/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
The role of proteins often changes during evolution, but we do not know how cells adapt when a protein is asked to participate in a different biological function. We forced the budding yeast, Saccharomyces cerevisiae, to use the meiosis-specific kleisin, recombination 8 (Rec8), during the mitotic cell cycle, instead of its paralog, Scc1. This perturbation impairs sister chromosome linkage, advances the timing of genome replication, and reduces reproductive fitness by 45%. We evolved 15 parallel populations for 1,750 generations, substantially increasing their fitness, and analyzed the genotypes and phenotypes of the evolved cells. Only one population contained a mutation in Rec8, but many populations had mutations in the transcriptional mediator complex, cohesin-related genes, and cell cycle regulators that induce S phase. These mutations improve sister chromosome cohesion and delay genome replication in Rec8-expressing cells. We conclude that changes in known and novel partners allow cells to use an existing protein to participate in new biological functions.
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Affiliation(s)
- Yu-Ying Phoebe Hsieh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Vasso Makrantoni
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel Robertson
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Adèle L. Marston
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew W. Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
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17
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Delamarre A, Barthe A, de la Roche Saint-André C, Luciano P, Forey R, Padioleau I, Skrzypczak M, Ginalski K, Géli V, Pasero P, Lengronne A. MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading. Mol Cell 2020; 77:395-410.e3. [PMID: 31759824 DOI: 10.1016/j.molcel.2019.10.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/09/2019] [Accepted: 10/17/2019] [Indexed: 01/04/2023]
Abstract
The recovery of stalled replication forks depends on the controlled resection of nascent DNA and on the loading of cohesin. These processes operate in the context of nascent chromatin, but the impact of nucleosome structure on a fork restart remains poorly understood. Here, we show that the Mre11-Rad50-Xrs2 (MRX) complex acts together with the chromatin modifiers Gcn5 and Set1 and the histone remodelers RSC, Chd1, and Isw1 to promote chromatin remodeling at stalled forks. Increased chromatin accessibility facilitates the resection of nascent DNA by the Exo1 nuclease and the Sgs1 and Chl1 DNA helicases. Importantly, increased ssDNA promotes the recruitment of cohesin to arrested forks in a Scc2-Scc4-dependent manner. Altogether, these results indicate that MRX cooperates with chromatin modifiers to orchestrate the action of remodelers, nucleases, and DNA helicases, promoting the resection of nascent DNA and the loading of cohesin, two key processes involved in the recovery of arrested forks.
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Affiliation(s)
- Axel Delamarre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Christophe de la Roche Saint-André
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Pierre Luciano
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Ismaël Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
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18
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Lawrimore CJ, Bloom K. Common Features of the Pericentromere and Nucleolus. Genes (Basel) 2019; 10:E1029. [PMID: 31835574 PMCID: PMC6947172 DOI: 10.3390/genes10121029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 12/20/2022] Open
Abstract
Both the pericentromere and the nucleolus have unique characteristics that distinguish them amongst the rest of genome. Looping of pericentromeric DNA, due to structural maintenance of chromosome (SMC) proteins condensin and cohesin, drives its ability to maintain tension during metaphase. Similar loops are formed via condensin and cohesin in nucleolar ribosomal DNA (rDNA). Condensin and cohesin are also concentrated in transfer RNA (tRNA) genes, genes which may be located within the pericentromere as well as tethered to the nucleolus. Replication fork stalling, as well as downstream consequences such as genomic recombination, are characteristic of both the pericentromere and rDNA. Furthermore, emerging evidence suggests that the pericentromere may function as a liquid-liquid phase separated domain, similar to the nucleolus. We therefore propose that the pericentromere and nucleolus, in part due to their enrichment of SMC proteins and others, contain similar domains that drive important cellular activities such as segregation, stability, and repair.
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Affiliation(s)
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA;
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19
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Crane MM, Russell AE, Schafer BJ, Blue BW, Whalen R, Almazan J, Hong MG, Nguyen B, Goings JE, Chen KL, Kelly R, Kaeberlein M. DNA damage checkpoint activation impairs chromatin homeostasis and promotes mitotic catastrophe during aging. eLife 2019; 8:e50778. [PMID: 31714209 PMCID: PMC6850777 DOI: 10.7554/elife.50778] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/30/2019] [Indexed: 02/01/2023] Open
Abstract
Genome instability is a hallmark of aging and contributes to age-related disorders such as cancer and Alzheimer's disease. The accumulation of DNA damage during aging has been linked to altered cell cycle dynamics and the failure of cell cycle checkpoints. Here, we use single cell imaging to study the consequences of increased genomic instability during aging in budding yeast and identify striking age-associated genome missegregation events. This breakdown in mitotic fidelity results from the age-related activation of the DNA damage checkpoint and the resulting degradation of histone proteins. Disrupting the ability of cells to degrade histones in response to DNA damage increases replicative lifespan and reduces genomic missegregations. We present several lines of evidence supporting a model of antagonistic pleiotropy in the DNA damage response where histone degradation, and limited histone transcription are beneficial to respond rapidly to damage but reduce lifespan and genomic stability in the long term.
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Affiliation(s)
- Matthew M Crane
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Adam E Russell
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Brent J Schafer
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Ben W Blue
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Riley Whalen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Jared Almazan
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Mung Gi Hong
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Bao Nguyen
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Joslyn E Goings
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Kenneth L Chen
- Department of PathologyUniversity of WashingtonSeattleUnited States
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Medical Scientist Training ProgramUniversity of WashingtonSeattleUnited States
| | - Ryan Kelly
- Department of PathologyUniversity of WashingtonSeattleUnited States
| | - Matt Kaeberlein
- Department of PathologyUniversity of WashingtonSeattleUnited States
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20
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Garcia-Luis J, Lazar-Stefanita L, Gutierrez-Escribano P, Thierry A, Cournac A, García A, González S, Sánchez M, Jarmuz A, Montoya A, Dore M, Kramer H, Karimi MM, Antequera F, Koszul R, Aragon L. FACT mediates cohesin function on chromatin. Nat Struct Mol Biol 2019; 26:970-979. [PMID: 31582854 PMCID: PMC6779571 DOI: 10.1038/s41594-019-0307-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/21/2019] [Indexed: 11/09/2022]
Abstract
Cohesin is a regulator of genome architecture with roles in sister chromatid cohesion and chromosome compaction. The recruitment and mobility of cohesin complexes on DNA is restricted by nucleosomes. Here, we show that the role of cohesin in chromosome organization requires the histone chaperone FACT ('facilitates chromatin transcription') in Saccharomyces cerevisiae. We find that FACT interacts directly with cohesin, and is dynamically required for its localization on chromatin. Depletion of FACT in metaphase cells prevents cohesin accumulation at pericentric regions and causes reduced binding on chromosome arms. Using the Hi-C technique, we show that cohesin-dependent TAD (topological associated domain)-like structures in G1 and metaphase chromosomes are reduced in the absence of FACT. Sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our data show that FACT contributes to the formation of cohesin-dependent TADs, thus uncovering a new role for this complex in nuclear organization during interphase and mitotic chromosome folding.
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Affiliation(s)
- Jonay Garcia-Luis
- Cell Cycle Group, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Department of Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
| | | | - Agnes Thierry
- Institut Pasteur, Department of Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
| | - Axel Cournac
- Institut Pasteur, Department of Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
| | - Alicia García
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Sara González
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Adam Jarmuz
- Cell Cycle Group, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Marian Dore
- Bioinformatics Facility, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Mohammad M Karimi
- Bioinformatics Facility, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica (IBFG), CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Romain Koszul
- Institut Pasteur, Department of Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France.
| | - Luis Aragon
- Cell Cycle Group, MRC London Institute of Medical Sciences (LMS), London, UK.
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21
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Prasad P, Sanyal K, Ghosh SK. Sth1, the Key Subunit of the RSC Chromatin Remodeling Complex, Is Essential in Maintaining Chromosomal Integrity and Mediating High Fidelity Chromosome Segregation in the Human Fungal Pathogen Candida albicans. Front Microbiol 2019; 10:1303. [PMID: 31249561 PMCID: PMC6582774 DOI: 10.3389/fmicb.2019.01303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022] Open
Abstract
Chromatin architecture influences gene expression and makes specialized chromatin domains. Factors including histone variants, histone modifiers and chromatin remodelers that define chromatin architecture impact chromosome related processes in Candida albicans. In this context, we sought to investigate the roles of the ATP-dependent chromatin remodeler, Remodel the Structure of Chromatin (RSC) in chromosome segregation of C. albicans. Sth1 is the key ATPase component of RSC and has profound roles in different cellular processes in Saccharomyces cerevisiae. We demonstrate that STH1 is an essential gene in C. albicans. The depletion of Sth1 induces pseudohyphal cells, abnormal spindle morphology, sensitivity toward anti-mitotic drugs and global cohesion defect suggesting an important role of Sth1 in kinetochore-microtubule related processes in C. albicans. Strikingly, Sth1 is required to maintain clustered kinetochores revealing the fact that RSC is required in kinetochore integrity. Taken together, we show that RSC plays an important role in various chromatin-templated processes including chromosome segregation in C. albicans.
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Affiliation(s)
- Priya Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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22
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Fischböck-Halwachs J, Singh S, Potocnjak M, Hagemann G, Solis-Mezarino V, Woike S, Ghodgaonkar-Steger M, Weissmann F, Gallego LD, Rojas J, Andreani J, Köhler A, Herzog F. The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore. eLife 2019; 8:42879. [PMID: 31112132 PMCID: PMC6546395 DOI: 10.7554/elife.42879] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/20/2019] [Indexed: 01/14/2023] Open
Abstract
Kinetochores are macromolecular protein complexes at centromeres that ensure accurate chromosome segregation by attaching chromosomes to spindle microtubules and integrating safeguard mechanisms. The inner kinetochore is assembled on CENP-A nucleosomes and has been implicated in establishing a kinetochore-associated pool of Aurora B kinase, a chromosomal passenger complex (CPC) subunit, which is essential for chromosome biorientation. By performing crosslink-guided in vitro reconstitution of budding yeast kinetochore complexes we showed that the Ame1/Okp1CENP-U/Q heterodimer, which forms the COMA complex with Ctf19/Mcm21CENP-P/O, selectively bound Cse4CENP-A nucleosomes through the Cse4 N-terminus. The Sli15/Ipl1INCENP/Aurora-B core-CPC interacted with COMA in vitro through the Ctf19 C-terminus whose deletion affected chromosome segregation fidelity in Sli15 wild-type cells. Tethering Sli15 to Ame1/Okp1 rescued synthetic lethality upon Ctf19 depletion in a Sli15 centromere-targeting deficient mutant. This study shows molecular characteristics of the point-centromere kinetochore architecture and suggests a role for the Ctf19 C-terminus in mediating CPC-binding and accurate chromosome segregation.
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Affiliation(s)
- Josef Fischböck-Halwachs
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sylvia Singh
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mia Potocnjak
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Götz Hagemann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victor Solis-Mezarino
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan Woike
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Medini Ghodgaonkar-Steger
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Laura D Gallego
- Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Julie Rojas
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alwin Köhler
- Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Franz Herzog
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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23
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García-Rodríguez LJ, Kasciukovic T, Denninger V, Tanaka TU. Aurora B-INCENP Localization at Centromeres/Inner Kinetochores Is Required for Chromosome Bi-orientation in Budding Yeast. Curr Biol 2019; 29:1536-1544.e4. [PMID: 31006569 PMCID: PMC6509284 DOI: 10.1016/j.cub.2019.03.051] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/06/2019] [Accepted: 03/22/2019] [Indexed: 12/24/2022]
Abstract
For proper chromosome segregation in mitosis, sister kinetochores must interact with microtubules from opposite spindle poles (chromosome bi-orientation) [1, 2]. To promote bi-orientation, Aurora B kinase disrupts aberrant kinetochore-microtubule interactions [3, 4, 5, 6]. It has long been debated how Aurora B halts this action when bi-orientation is established and tension is applied across sister kinetochores. A popular explanation for it is that, upon bi-orientation, sister kinetochores are pulled in opposite directions, stretching the outer kinetochores [7, 8] and moving Aurora B substrates away from Aurora-B-localizing sites at centromeres (spatial separation model) [3, 5, 9]. This model predicts that Aurora B localization at centromeres is required for bi-orientation. However, this notion was challenged by the observation that Bir1 (yeast survivin), which recruits Ipl1-Sli15 (yeast Aurora B-INCENP) to centromeres, can become dispensable for bi-orientation [10]. This raised the possibility that Aurora B localization at centromeres is dispensable for bi-orientation. Alternatively, there might be a Bir1-independent mechanism for recruiting Ipl1-Sli15 to centromeres or inner kinetochores [5, 9]. Here, we show that the COMA inner kinetochore sub-complex physically interacts with Sli15, recruits Ipl1-Sli15 to the inner kinetochore, and promotes chromosome bi-orientation, independently of Bir1, in budding yeast. Moreover, using an engineered recruitment of Ipl1-Sli15 to the inner kinetochore when both Bir1 and COMA are defective, we show that localization of Ipl1-Sli15 at centromeres or inner kinetochores is required for bi-orientation. Our results give important insight into how Aurora B disrupts kinetochore-microtubule interaction in a tension-dependent manner to promote chromosome bi-orientation. The COMA inner kinetochore sub-complex facilitates chromosome bi-orientation COMA physically interacts with Sli15 and recruits Ipl1-Sli15 to the inner kinetochore This function of COMA is independent of Bir1 and its role supporting robust cohesion Localizing Ipl1-Sli15 at centromeres/inner kinetochores is crucial for bi-orientation
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Affiliation(s)
- Luis J García-Rodríguez
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Taciana Kasciukovic
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Viola Denninger
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Mittal P, Chavan A, Trakroo D, Shah S, Ghosh SK. Outer kinetochore protein Dam1 promotes centromere clustering in parallel with Slk19 in budding yeast. Chromosoma 2019; 128:133-148. [PMID: 30903360 DOI: 10.1007/s00412-019-00694-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 01/14/2019] [Accepted: 02/11/2019] [Indexed: 12/16/2022]
Abstract
A higher order organization of the centromeres in the form of clustering of these DNA loci has been observed in many organisms. While centromere clustering is biologically significant to achieve faithful chromosome segregation, the underlying molecular mechanism is yet to be fully understood. In budding yeast, a kinetochore-associated protein Slk19 is shown to have a role in clustering in association with the microtubules whereas removal of either Slk19 or microtubules alone does not have any effect on the centromere clustering. Furthermore, Slk19 is non-essential for growth and becomes cleaved during anaphase whereas clustering being an essential event occurs throughout the cell cycle. Hence, we searched for an additional factor involved in the clustering and since the integrity of the kinetochore complex is shown to be crucial for centromere clustering, we restricted our search within the complex. We observed that the outermost kinetochore protein Dam1 promotes centromere clustering through stabilization of the kinetochore integrity. While in the absence of Dam1 we failed to detect Slk19 at the centromere, on the other hand, we found almost no Dam1 at the centromere in the absence of Slk19 and microtubules suggesting interdependency between these two pathways. Strikingly, we observed that overexpression of Dam1 or Slk19 could restore the centromere clustering largely in the cells devoid of Slk19 and microtubules or Dam1, respectively. Thus, we propose that in budding yeast, centromere clustering is achieved at least by two parallel pathways, through Dam1 and another via Slk19, in concert with the microtubules suggesting that having a dual mechanism may be crucial for ensuring microtubule capture by the point centromeres where each attaches to only one microtubule.
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Affiliation(s)
- Priyanka Mittal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ankita Chavan
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT, 06269, USA
| | - Deepika Trakroo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sanket Shah
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, 410210, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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25
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Kuhl L, Vader G. Kinetochores, cohesin, and DNA breaks: Controlling meiotic recombination within pericentromeres. Yeast 2019; 36:121-127. [PMID: 30625250 PMCID: PMC6519163 DOI: 10.1002/yea.3366] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 11/26/2022] Open
Abstract
In meiosis, DNA break formation and repair are essential for the formation of crossovers between homologous chromosomes. Without crossover formation, faithful meiotic chromosome segregation and sexual reproduction cannot occur. Crossover formation is initiated by the programmed, meiosis-specific introduction of numerous DNA double-strand breaks, after which specific repair pathways promote recombination between homologous chromosomes. Despite its crucial nature, meiotic recombination is fraud with danger: When positioned or repaired inappropriately, DNA breaks can have catastrophic consequences on genome stability of the resulting gametes. As such, DNA break formation and repair needs to be carefully controlled. Within centromeres and surrounding regions (i.e., pericentromeres), meiotic crossover recombination is repressed in organisms ranging from yeast to humans, and a failure to do so is implicated in chromosome missegregation and developmental aneuploidy. (Peri)centromere sequence identity and organization diverge considerably across eukaryotes, yet suppression of meiotic DNA break formation and repair appear universal. Here, we discuss emerging work that has used budding and fission yeast systems to study the mechanisms underlying pericentromeric suppression of DNA break formation and repair. We particularly highlight a role for the kinetochore, a universally conserved, centromere-associated structure essential for chromosome segregation, in suppressing (peri)centromeric DNA break formation and repair. We discuss the current understanding of kinetochore-associated and chromosomal factors involved in this regulation and suggest future avenues of research.
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Affiliation(s)
- Lisa‐Marie Kuhl
- Department of Mechanistic Cell BiologyMax Planck Institute of Molecular PhysiologyDortmundGermany
| | - Gerben Vader
- Department of Mechanistic Cell BiologyMax Planck Institute of Molecular PhysiologyDortmundGermany
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26
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Makrantoni V, Robertson D, Marston AL. Analysis of the Chromosomal Localization of Yeast SMC Complexes by Chromatin Immunoprecipitation. Methods Mol Biol 2019; 2004:119-138. [PMID: 31147914 PMCID: PMC7115940 DOI: 10.1007/978-1-4939-9520-2_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein-DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells.
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Affiliation(s)
- Vasso Makrantoni
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Daniel Robertson
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Adele L. Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF UK,To whom correspondence should be addressed:
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27
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Cook DM, Bennett M, Friedman B, Lawrimore J, Yeh E, Bloom K. Fork pausing allows centromere DNA loop formation and kinetochore assembly. Proc Natl Acad Sci U S A 2018; 115:11784-11789. [PMID: 30373818 PMCID: PMC6243264 DOI: 10.1073/pnas.1806791115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
De novo kinetochore assembly, but not template-directed assembly, is dependent on COMA, the kinetochore complex engaged in cohesin recruitment. The slowing of replication fork progression by treatment with phleomycin (PHL), hydroxyurea, or deletion of the replication fork protection protein Csm3 can activate de novo kinetochore assembly in COMA mutants. Centromere DNA looping at the site of de novo kinetochore assembly can be detected shortly after exposure to PHL. Using simulations to explore the thermodynamics of DNA loops, we propose that loop formation is disfavored during bidirectional replication fork migration. One function of replication fork stalling upon encounters with DNA damage or other blockades may be to allow time for thermal fluctuations of the DNA chain to explore numerous configurations. Biasing thermodynamics provides a mechanism to facilitate macromolecular assembly, DNA repair, and other nucleic acid transactions at the replication fork. These loop configurations are essential for sister centromere separation and kinetochore assembly in the absence of the COMA complex.
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Affiliation(s)
- Diana M Cook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Maggie Bennett
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Brandon Friedman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Elaine Yeh
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280
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28
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Batrakou DG, Heron ED, Nieduszynski CA. Rapid high-resolution measurement of DNA replication timing by droplet digital PCR. Nucleic Acids Res 2018; 46:e112. [PMID: 29986073 PMCID: PMC6212846 DOI: 10.1093/nar/gky590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/11/2018] [Accepted: 06/18/2018] [Indexed: 02/03/2023] Open
Abstract
Genomes are replicated in a reproducible temporal pattern. Current methods for assaying allele replication timing are time consuming and/or expensive. These include high-throughput sequencing which can be used to measure DNA copy number as a proxy for allele replication timing. Here, we use droplet digital PCR to study DNA replication timing at multiple loci in budding yeast and human cells. We establish that the method has temporal and spatial resolutions comparable to the high-throughput sequencing approaches, while being faster than alternative locus-specific methods. Furthermore, the approach is capable of allele discrimination. We apply this method to determine relative replication timing across timing transition zones in cultured human cells. Finally, multiple samples can be analysed in parallel, allowing us to rapidly screen kinetochore mutants for perturbation to centromere replication timing. Therefore, this approach is well suited to the study of locus-specific replication and the screening of cis- and trans-acting mutants to identify mechanisms that regulate local genome replication timing.
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Affiliation(s)
- Dzmitry G Batrakou
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Emma D Heron
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Conrad A Nieduszynski
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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29
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Kruitwagen T, Chymkowitch P, Denoth-Lippuner A, Enserink J, Barral Y. Centromeres License the Mitotic Condensation of Yeast Chromosome Arms. Cell 2018; 175:780-795.e15. [PMID: 30318142 PMCID: PMC6197839 DOI: 10.1016/j.cell.2018.09.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 06/14/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022]
Abstract
During mitosis, chromatin condensation shapes chromosomes as separate, rigid, and compact sister chromatids to facilitate their segregation. Here, we show that, unlike wild-type yeast chromosomes, non-chromosomal DNA circles and chromosomes lacking a centromere fail to condense during mitosis. The centromere promotes chromosome condensation strictly in cis through recruiting the kinases Aurora B and Bub1, which trigger the autonomous condensation of the entire chromosome. Shugoshin and the deacetylase Hst2 facilitated spreading the condensation signal to the chromosome arms. Targeting Aurora B to DNA circles or centromere-ablated chromosomes or releasing Shugoshin from PP2A-dependent inhibition bypassed the centromere requirement for condensation and enhanced the mitotic stability of DNA circles. Our data indicate that yeast cells license the chromosome-autonomous condensation of their chromatin in a centromere-dependent manner, excluding from this process non-centromeric DNA and thereby inhibiting their propagation.
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Affiliation(s)
- Tom Kruitwagen
- Institute of Biochemistry, Biology Department, ETH Zurich, 8093 Zurich, Switzerland
| | - Pierre Chymkowitch
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway
| | | | - Jorrit Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway; Faculty of Medicine, Center for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Faculty of Mathematics and Natural Sciences, Department of Biosciences, University of Oslo, Norway
| | - Yves Barral
- Institute of Biochemistry, Biology Department, ETH Zurich, 8093 Zurich, Switzerland.
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30
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Petela NJ, Gligoris TG, Metson J, Lee BG, Voulgaris M, Hu B, Kikuchi S, Chapard C, Chen W, Rajendra E, Srinivisan M, Yu H, Löwe J, Nasmyth KA. Scc2 Is a Potent Activator of Cohesin's ATPase that Promotes Loading by Binding Scc1 without Pds5. Mol Cell 2018; 70:1134-1148.e7. [PMID: 29932904 PMCID: PMC6028919 DOI: 10.1016/j.molcel.2018.05.022] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 04/10/2018] [Accepted: 05/18/2018] [Indexed: 01/10/2023]
Abstract
Cohesin organizes DNA into chromatids, regulates enhancer-promoter interactions, and confers sister chromatid cohesion. Its association with chromosomes is regulated by hook-shaped HEAT repeat proteins that bind Scc1, namely Scc3, Pds5, and Scc2. Unlike Pds5, Scc2 is not a stable cohesin constituent but, as shown here, transiently replaces Pds5. Scc1 mutations that compromise its interaction with Scc2 adversely affect cohesin's ATPase activity and loading. Moreover, Scc2 mutations that alter how the ATPase responds to DNA abolish loading despite cohesin's initial association with loading sites. Lastly, Scc2 mutations that permit loading in the absence of Scc4 increase Scc2's association with chromosomal cohesin and reduce that of Pds5. We suggest that cohesin switches between two states: one with Pds5 bound that is unable to hydrolyze ATP efficiently but is capable of release from chromosomes and another in which Scc2 replaces Pds5 and stimulates ATP hydrolysis necessary for loading and translocation from loading sites.
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Affiliation(s)
- Naomi J Petela
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Thomas G Gligoris
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jean Metson
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Byung-Gil Lee
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Bin Hu
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Sotaro Kikuchi
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Wentao Chen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Eeson Rajendra
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Hongtao Yu
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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31
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Murayama Y, Samora CP, Kurokawa Y, Iwasaki H, Uhlmann F. Establishment of DNA-DNA Interactions by the Cohesin Ring. Cell 2018; 172:465-477.e15. [PMID: 29358048 PMCID: PMC5786502 DOI: 10.1016/j.cell.2017.12.021] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/12/2017] [Accepted: 12/16/2017] [Indexed: 01/14/2023]
Abstract
The ring-shaped structural maintenance of chromosome (SMC) complexes are multi-subunit ATPases that topologically encircle DNA. SMC rings make vital contributions to numerous chromosomal functions, including mitotic chromosome condensation, sister chromatid cohesion, DNA repair, and transcriptional regulation. They are thought to do so by establishing interactions between more than one DNA. Here, we demonstrate DNA-DNA tethering by the purified fission yeast cohesin complex. DNA-bound cohesin efficiently and topologically captures a second DNA, but only if that is single-stranded DNA (ssDNA). Like initial double-stranded DNA (dsDNA) embrace, second ssDNA capture is ATP-dependent, and it strictly requires the cohesin loader complex. Second-ssDNA capture is relatively labile but is converted into stable dsDNA-dsDNA cohesion through DNA synthesis. Our study illustrates second-DNA capture by an SMC complex and provides a molecular model for the establishment of sister chromatid cohesion.
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Affiliation(s)
- Yasuto Murayama
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Catarina P Samora
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yumiko Kurokawa
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Frank Uhlmann
- Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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32
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Lacefield S. Chromosome Biology: Specification of the Kinetochore for Cohesin Recruitment. Curr Biol 2017; 27:R1319-R1321. [PMID: 29257967 DOI: 10.1016/j.cub.2017.10.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Additional cohesin loaded at the centromere helps to facilitate proper chromosome segregation. A new study reveals the mechanism by which kinetochores recruit the cohesin loader to establish centromere cohesion.
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Affiliation(s)
- Soni Lacefield
- Department of Biology, Indiana University, Bloomington, IN, USA.
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33
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Schmitzberger F, Richter MM, Gordiyenko Y, Robinson CV, Dadlez M, Westermann S. Molecular basis for inner kinetochore configuration through RWD domain-peptide interactions. EMBO J 2017; 36:3458-3482. [PMID: 29046335 PMCID: PMC5709738 DOI: 10.15252/embj.201796636] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 07/31/2017] [Accepted: 09/08/2017] [Indexed: 01/05/2023] Open
Abstract
Kinetochores are dynamic cellular structures that connect chromosomes to microtubules. They form from multi‐protein assemblies that are evolutionarily conserved between yeasts and humans. One of these assemblies—COMA—consists of subunits Ame1CENP‐U, Ctf19CENP‐P, Mcm21CENP‐O and Okp1CENP‐Q. A description of COMA molecular organization has so far been missing. We defined the subunit topology of COMA, bound with inner kinetochore proteins Nkp1 and Nkp2, from the yeast Kluyveromyces lactis, with nanoflow electrospray ionization mass spectrometry, and mapped intermolecular contacts with hydrogen‐deuterium exchange coupled to mass spectrometry. Our data suggest that the essential Okp1 subunit is a multi‐segmented nexus with distinct binding sites for Ame1, Nkp1‐Nkp2 and Ctf19‐Mcm21. Our crystal structure of the Ctf19‐Mcm21 RWD domains bound with Okp1 shows the molecular contacts of this important inner kinetochore joint. The Ctf19‐Mcm21 binding motif in Okp1 configures a branch of mitotic inner kinetochores, by tethering Ctf19‐Mcm21 and Chl4CENP‐N‐Iml3CENP‐L. Absence of this motif results in dependence on the mitotic checkpoint for viability.
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Affiliation(s)
- Florian Schmitzberger
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA .,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Magdalena M Richter
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Yuliya Gordiyenko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Genetics and Biotechnology, Biology Department, Warsaw University, Warsaw, Poland
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34
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Kinetochore Function from the Bottom Up. Trends Cell Biol 2017; 28:22-33. [PMID: 28985987 DOI: 10.1016/j.tcb.2017.09.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023]
Abstract
During a single human lifetime, nearly one quintillion chromosomes separate from their sisters and transit to their destinations in daughter cells. Unlike DNA replication, chromosome segregation has no template, and, unlike transcription, errors frequently lead to a total loss of cell viability. Rapid progress in recent years has shown how kinetochores enable faithful execution of this process by connecting chromosomal DNA to microtubules. These findings have transformed our idea of kinetochores from cytological features to immense molecular machines and now allow molecular interpretation of many long-appreciated kinetochore functions. In this review we trace kinetochore protein connectivity from chromosomal DNA to microtubules, relating new findings to important points of regulation and function.
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35
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Hinshaw SM, Makrantoni V, Harrison SC, Marston AL. The Kinetochore Receptor for the Cohesin Loading Complex. Cell 2017; 171:72-84.e13. [PMID: 28938124 PMCID: PMC5610175 DOI: 10.1016/j.cell.2017.08.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/03/2017] [Accepted: 08/09/2017] [Indexed: 12/29/2022]
Abstract
The ring-shaped cohesin complex brings together distant DNA domains to maintain, express, and segregate the genome. Establishing specific chromosomal linkages depends on cohesin recruitment to defined loci. One such locus is the budding yeast centromere, which is a paradigm for targeted cohesin loading. The kinetochore, a multiprotein complex that connects centromeres to microtubules, drives the recruitment of high levels of cohesin to link sister chromatids together. We have exploited this system to determine the mechanism of specific cohesin recruitment. We show that phosphorylation of the Ctf19 kinetochore protein by a conserved kinase, DDK, provides a binding site for the Scc2/4 cohesin loading complex, thereby directing cohesin loading to centromeres. A similar mechanism targets cohesin to chromosomes in vertebrates. These findings represent a complete molecular description of targeted cohesin loading, a phenomenon with wide-ranging importance in chromosome segregation and, in multicellular organisms, transcription regulation.
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Affiliation(s)
- Stephen M Hinshaw
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Vasso Makrantoni
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Adèle L Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
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36
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Makrantoni V, Ciesiolka A, Lawless C, Fernius J, Marston A, Lydall D, Stark MJR. A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis. G3 (BETHESDA, MD.) 2017; 7:3203-3215. [PMID: 28754723 PMCID: PMC5592945 DOI: 10.1534/g3.117.300089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/25/2017] [Indexed: 11/18/2022]
Abstract
The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional proteins (Survivin/Bir1 and Borealin/Nbl1). Here, we report a genome-wide genetic interaction screen in Saccharomyces cerevisiae using the bir1-17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers and suppressors. Gene knockouts affecting the Ctf19 kinetochore complex were identified as the strongest enhancers of bir1-17, while mutations affecting the large ribosomal subunit or the mRNA nonsense-mediated decay pathway caused strong phenotypic suppression. Thus, cells lacking a functional Ctf19 complex become highly dependent on Bir1 function and vice versa. The negative genetic interaction profiles of bir1-17 and the cohesin mutant mcd1-1 showed considerable overlap, underlining the strong functional connection between sister chromatid cohesion and chromosome biorientation. Loss of some Ctf19 components, such as Iml3 or Chl4, impacted differentially on bir1-17 compared with mutations affecting other CPC components: despite the synthetic lethality shown by either iml3∆ or chl4∆ in combination with bir1-17, neither gene knockout showed any genetic interaction with either ipl1-321 or sli15-3 Our data therefore imply a specific functional connection between the Ctf19 complex and Bir1 that is not shared with Ipl1.
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Affiliation(s)
- Vasso Makrantoni
- Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3BF, UK
| | - Adam Ciesiolka
- Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4HH, UK
| | - Conor Lawless
- Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4HH, UK
| | - Josefin Fernius
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3BF, UK
| | - Adele Marston
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, EH9 3BF, UK
| | - David Lydall
- Institute for Cell and Molecular Biosciences, Newcastle University, NE2 4HH, UK
| | - Michael J R Stark
- Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
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37
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Schalch T, Steiner FA. Structure of centromere chromatin: from nucleosome to chromosomal architecture. Chromosoma 2017; 126:443-455. [PMID: 27858158 PMCID: PMC5509776 DOI: 10.1007/s00412-016-0620-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 12/14/2022]
Abstract
The centromere is essential for the segregation of chromosomes, as it serves as attachment site for microtubules to mediate chromosome segregation during mitosis and meiosis. In most organisms, the centromere is restricted to one chromosomal region that appears as primary constriction on the condensed chromosome and is partitioned into two chromatin domains: The centromere core is characterized by the centromere-specific histone H3 variant CENP-A (also called cenH3) and is required for specifying the centromere and for building the kinetochore complex during mitosis. This core region is generally flanked by pericentric heterochromatin, characterized by nucleosomes containing H3 methylated on lysine 9 (H3K9me) that are bound by heterochromatin proteins. During mitosis, these two domains together form a three-dimensional structure that exposes CENP-A-containing chromatin to the surface for interaction with the kinetochore and microtubules. At the same time, this structure supports the tension generated during the segregation of sister chromatids to opposite poles. In this review, we discuss recent insight into the characteristics of the centromere, from the specialized chromatin structures at the centromere core and the pericentromere to the three-dimensional organization of these regions that make up the functional centromere.
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Affiliation(s)
- Thomas Schalch
- Department of Molecular Biology, Sciences III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
| | - Florian A Steiner
- Department of Molecular Biology, Sciences III, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science 2017; 355:eaaf4791. [PMID: 28280153 PMCID: PMC5390853 DOI: 10.1126/science.aaf4791] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/01/2017] [Indexed: 12/15/2022]
Abstract
Here, we report the successful design, construction, and characterization of a 770-kilobase synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels-including phenomics, transcriptomics, proteomics, chromosome segregation, and replication analysis-to provide a thorough and comprehensive analysis of a synthetic chromosome. Our Trans-Omics analyses reveal a modest but potentially relevant pervasive up-regulation of translational machinery observed in synII, mainly caused by the deletion of 13 transfer RNAs. By both complementation assays and SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution), we targeted and debugged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the high-osmolarity glycerol response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain.
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Affiliation(s)
- Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
- BGI-Qingdao, Qingdao 266555, China
| | - Yun Wang
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Qingdao, Qingdao 266555, China
| | - Tai Chen
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Qingdao, Qingdao 266555, China
| | - Feng Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Dariusz Abramczyk
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Roy Walker
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | | | - Wei Liu
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Yisha Luo
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Carolin A. Müller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | - Bonnie Alver
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Giovanni Stracquadanio
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 21205 USA
- Department of Biomedical Engineering, School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218 USA
| | - Leslie A. Mitchell
- Institute for Systems Genetics, NYU Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016
| | - Zhouqing Luo
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | | | | | - Bo Wen
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Jin Zi
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zexiong Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Bingzhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Kun Yang
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 21205 USA
| | - Sarah M. Richardson
- High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, 21205 USA
- Department of Biomedical Engineering, School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218 USA
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Romain Koszul
- Department of Genomes and Genetics, Institut Pasteur / CNRS UMR3525, 25-28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Adele L. Marston
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Joel S. Bader
- Department of Biomedical Engineering, School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218 USA
- Institute for Systems Genetics, NYU Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016
| | - Junbiao Dai
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Qingdao, Qingdao 266555, China
| | - Yizhi Cai
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
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Musacchio A, Desai A. A Molecular View of Kinetochore Assembly and Function. BIOLOGY 2017; 6:E5. [PMID: 28125021 PMCID: PMC5371998 DOI: 10.3390/biology6010005] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/15/2022]
Abstract
Kinetochores are large protein assemblies that connect chromosomes to microtubules of the mitotic and meiotic spindles in order to distribute the replicated genome from a mother cell to its daughters. Kinetochores also control feedback mechanisms responsible for the correction of incorrect microtubule attachments, and for the coordination of chromosome attachment with cell cycle progression. Finally, kinetochores contribute to their own preservation, across generations, at the specific chromosomal loci devoted to host them, the centromeres. They achieve this in most species by exploiting an epigenetic, DNA-sequence-independent mechanism; notable exceptions are budding yeasts where a specific sequence is associated with centromere function. In the last 15 years, extensive progress in the elucidation of the composition of the kinetochore and the identification of various physical and functional modules within its substructure has led to a much deeper molecular understanding of kinetochore organization and the origins of its functional output. Here, we provide a broad summary of this progress, focusing primarily on kinetochores of humans and budding yeast, while highlighting work from other models, and present important unresolved questions for future studies.
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Affiliation(s)
- Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Straße 11, Dortmund 44227, Germany.
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen 45117, Germany.
| | - Arshad Desai
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
- Department of Cellular & Molecular Medicine, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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40
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Prajapati HK, Rizvi SMA, Rathore I, Ghosh SK. Microtubule-associated proteins, Bik1 and Bim1, are required for faithful partitioning of the endogenous 2 micron plasmids in budding yeast. Mol Microbiol 2017; 103:1046-1064. [PMID: 28004422 DOI: 10.1111/mmi.13608] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2016] [Indexed: 12/01/2022]
Abstract
The 2 μ plasmid of budding yeast shows high mitotic stability similar to that of chromosomes by using its self-encoded systems, namely partitioning and amplification. The partitioning system consists of the plasmid-borne proteins Rep1, Rep2 and a cis-acting locus STB that, along with several host factors, ensures efficient segregation of the plasmid. The plasmids show high stability as they presumably co-segregate with chromosomes through utilization of various host factors. To acquire these host factors, the plasmids are thought to localize to a certain sub-nuclear locale probably assisted by the motor protein, Kip1 and microtubules. Here, we show that the microtubule-associated proteins Bik1 and Bim1 are also important host factors in this process, perhaps by acting as an adapter between the plasmid and the motor and thus helping to anchor the plasmid to microtubules. Abrogation of Kip1 recruitment at STB in the absence of Bik1 argues for its function at STB upstream of Kip1. Consistent with this, both Bik1 and Bim1 associate with plasmids without any assistance from the Rep proteins. As observed earlier with other host factors, lack of Bik1 or Bim1 also causes a cohesion defect between sister plasmids leading to plasmid missegregation.
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Affiliation(s)
- Hemant Kumar Prajapati
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Syed Meraj Azhar Rizvi
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Ishan Rathore
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076, India
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41
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Abstract
The kollerin complex, consisting of Scc2/Scc4 in yeast and Nipbl/Mau2 in vertebrates, is crucial for the chromatin-association of the cohesin complex and therefore for the critical functions of cohesin in cell division, transcriptional regulation and chromatin organisation. Despite the recent efforts to determine the genomic localization of the kollerin complex in different cell lines, major questions still remain unresolved, for instance where cohesin is actually loaded onto chromatin. Further, Nipbl seems to have also additional roles, for instance as transcription factor.This chapter summarizes our current knowledge on kollerin function and the recent studies on the genomic localization of Scc2, highlighting and critically discussing controversial data.
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Affiliation(s)
- Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Faculty Building, Room Ee1020, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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42
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Bhardwaj S, Schlackow M, Rabajdova M, Gullerova M. Transcription facilitates sister chromatid cohesion on chromosomal arms. Nucleic Acids Res 2016; 44:6676-92. [PMID: 27084937 PMCID: PMC5001582 DOI: 10.1093/nar/gkw252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cohesin is a multi-subunit protein complex essential for sister chromatid cohesion, gene expression and DNA damage repair. Although structurally well studied, the underlying determinant of cohesion establishment on chromosomal arms remains enigmatic. Here, we show two populations of functionally distinct cohesin on chromosomal arms using a combination of genomics and single-locus specific DNA-FISH analysis. Chromatin bound cohesin at the loading sites co-localizes with Pds5 and Eso1 resulting in stable cohesion. In contrast, cohesin independent of its loader is unable to maintain cohesion and associates with chromatin in a dynamic manner. Cohesive sites coincide with highly expressed genes and transcription inhibition leads to destabilization of cohesin on chromatin. Furthermore, induction of transcription results in de novo recruitment of cohesive cohesin. Our data suggest that transcription facilitates cohesin loading onto chromosomal arms and is a key determinant of cohesive sites in fission yeast.
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Affiliation(s)
- Shweta Bhardwaj
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | | | | | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
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43
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A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2016; 6:669-82. [PMID: 26747203 PMCID: PMC4777129 DOI: 10.1534/g3.115.024380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions.
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44
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Vincenten N, Kuhl LM, Lam I, Oke A, Kerr AR, Hochwagen A, Fung J, Keeney S, Vader G, Marston AL. The kinetochore prevents centromere-proximal crossover recombination during meiosis. eLife 2015. [PMID: 26653857 DOI: 10.7554/elife.10850.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
During meiosis, crossover recombination is essential to link homologous chromosomes and drive faithful chromosome segregation. Crossover recombination is non-random across the genome, and centromere-proximal crossovers are associated with an increased risk of aneuploidy, including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub-complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the Ctf19 complex, operating across distinct chromosomal distances. The Ctf19 complex prevents meiotic DNA break formation, the initiating event of recombination, proximal to the centromere. The Ctf19 complex independently drives the enrichment of cohesin throughout the broader pericentromere to suppress crossovers, but not DNA breaks. This non-canonical role of the kinetochore in defining a chromosome domain that is refractory to crossovers adds a new layer of functionality by which the kinetochore prevents the incidence of chromosome segregation errors that generate aneuploid gametes.
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Affiliation(s)
- Nadine Vincenten
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lisa-Marie Kuhl
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Isabel Lam
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, United States
| | - Alastair Rw Kerr
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Jennifer Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, United States
| | - Scott Keeney
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Adèle L Marston
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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Vincenten N, Kuhl LM, Lam I, Oke A, Kerr AR, Hochwagen A, Fung J, Keeney S, Vader G, Marston AL. The kinetochore prevents centromere-proximal crossover recombination during meiosis. eLife 2015; 4. [PMID: 26653857 PMCID: PMC4749563 DOI: 10.7554/elife.10850] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/13/2015] [Indexed: 11/13/2022] Open
Abstract
During meiosis, crossover recombination is essential to link homologous chromosomes and drive faithful chromosome segregation. Crossover recombination is non-random across the genome, and centromere-proximal crossovers are associated with an increased risk of aneuploidy, including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub-complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the Ctf19 complex, operating across distinct chromosomal distances. The Ctf19 complex prevents meiotic DNA break formation, the initiating event of recombination, proximal to the centromere. The Ctf19 complex independently drives the enrichment of cohesin throughout the broader pericentromere to suppress crossovers, but not DNA breaks. This non-canonical role of the kinetochore in defining a chromosome domain that is refractory to crossovers adds a new layer of functionality by which the kinetochore prevents the incidence of chromosome segregation errors that generate aneuploid gametes.
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Affiliation(s)
- Nadine Vincenten
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lisa-Marie Kuhl
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Isabel Lam
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, United States
| | - Alastair Rw Kerr
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Jennifer Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, United States
| | - Scott Keeney
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Adèle L Marston
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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46
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Hu B, Petela N, Kurze A, Chan KL, Chapard C, Nasmyth K. Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq. Nucleic Acids Res 2015; 43:e132. [PMID: 26130708 PMCID: PMC4787748 DOI: 10.1093/nar/gkv670] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 01/26/2023] Open
Abstract
Sequencing DNA fragments associated with proteins following in vivo cross-linking with formaldehyde (known as ChIP-seq) has been used extensively to describe the distribution of proteins across genomes. It is not widely appreciated that this method merely estimates a protein's distribution and cannot reveal changes in occupancy between samples. To do this, we tagged with the same epitope orthologous proteins in Saccharomyces cerevisiae and Candida glabrata, whose sequences have diverged to a degree that most DNA fragments longer than 50 bp are unique to just one species. By mixing defined numbers of C. glabrata cells (the calibration genome) with S. cerevisiae samples (the experimental genomes) prior to chromatin fragmentation and immunoprecipitation, it is possible to derive a quantitative measure of occupancy (the occupancy ratio - OR) that enables a comparison of occupancies not only within but also between genomes. We demonstrate for the first time that this 'internal standard' calibration method satisfies the sine qua non for quantifying ChIP-seq profiles, namely linearity over a wide range. Crucially, by employing functional tagged proteins, our calibration process describes a method that distinguishes genuine association within ChIP-seq profiles from background noise. Our method is applicable to any protein, not merely highly conserved ones, and obviates the need for the time consuming, expensive, and technically demanding quantification of ChIP using qPCR, which can only be performed on individual loci. As we demonstrate for the first time in this paper, calibrated ChIP-seq represents a major step towards documenting the quantitative distributions of proteins along chromosomes in different cell states, which we term biological chromodynamics.
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Affiliation(s)
- Bin Hu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Naomi Petela
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alexander Kurze
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Kok-Lung Chan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Christophe Chapard
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Kim Nasmyth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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47
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Meyer RE, Chuong HH, Hild M, Hansen CL, Kinter M, Dawson DS. Ipl1/Aurora-B is necessary for kinetochore restructuring in meiosis I in Saccharomyces cerevisiae. Mol Biol Cell 2015; 26:2986-3000. [PMID: 26157162 PMCID: PMC4551314 DOI: 10.1091/mbc.e15-01-0032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/30/2015] [Indexed: 11/11/2022] Open
Abstract
In mitosis, the centromeres of sister chromosomes are pulled toward opposite poles of the spindle. In meiosis I, the opposite is true: the sister centromeres move together to the same pole, and the homologous chromosomes are pulled apart. This change in segregation patterns demands that between the final mitosis preceding meiosis and the first meiotic division, the kinetochores must be restructured. In budding yeast, unlike mammals, kinetochores are largely stable throughout the mitotic cycle. In contrast, previous work with budding and fission yeast showed that some outer kinetochore proteins are lost in early meiosis. We use quantitative mass spectrometry methods and imaging approaches to explore the kinetochore restructuring process that occurs in meiosis I in budding yeast. The Ndc80 outer kinetochore complex, but not other subcomplexes, is shed upon meiotic entry. This shedding is regulated by the conserved protein kinase Ipl1/Aurora-B and promotes the subsequent assembly of a kinetochore that will confer meiosis-specific segregation patterns on the chromosome.
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Affiliation(s)
- Régis E Meyer
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Hoa H Chuong
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Marrett Hild
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Christina L Hansen
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Michael Kinter
- Program in Free Radical Biology and Aging, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Dean S Dawson
- Program in Cell Cycle and Cancer Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104 Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
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Hinshaw SM, Makrantoni V, Kerr A, Marston AL, Harrison SC. Structural evidence for Scc4-dependent localization of cohesin loading. eLife 2015; 4:e06057. [PMID: 26038942 PMCID: PMC4471937 DOI: 10.7554/elife.06057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 06/01/2015] [Indexed: 01/21/2023] Open
Abstract
The cohesin ring holds newly replicated sister chromatids together until their separation at anaphase. Initiation of sister chromatid cohesion depends on a separate complex, Scc2(NIPBL)/Scc4(Mau2) (Scc2/4), which loads cohesin onto DNA and determines its localization across the genome. Proper cohesin loading is essential for cell division, and partial defects cause chromosome missegregation and aberrant transcriptional regulation, leading to severe developmental defects in multicellular organisms. We present here a crystal structure showing the interaction between Scc2 and Scc4. Scc4 is a TPR array that envelops an extended Scc2 peptide. Using budding yeast, we demonstrate that a conserved patch on the surface of Scc4 is required to recruit Scc2/4 to centromeres and to build pericentromeric cohesion. These findings reveal the role of Scc4 in determining the localization of cohesin loading and establish a molecular basis for Scc2/4 recruitment to centromeres.
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Affiliation(s)
- Stephen M Hinshaw
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Vasso Makrantoni
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair Kerr
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Adèle L Marston
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
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Agarwal M, Mehta G, Ghosh SK. Role of Ctf3 and COMA subcomplexes in meiosis: Implication in maintaining Cse4 at the centromere and numeric spindle poles. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:671-84. [PMID: 25562757 DOI: 10.1016/j.bbamcr.2014.12.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/24/2014] [Accepted: 12/29/2014] [Indexed: 12/16/2022]
Abstract
During mitosis and meiosis, kinetochore, a conserved multi-protein complex, connects microtubule with the centromere and promotes segregation of the chromosomes. In budding yeast, central kinetochore complex named Ctf19 has been implicated in various functions and is believed to be made up of three biochemically distinct subcomplexes: COMA, Ctf3 and Iml3-Chl4. In this study, we aimed to identify whether Ctf3 and COMA subcomplexes have any unshared function at the kinetochore. Our data suggests that both these subcomplexes may work as a single functional unit without any unique functions, which we tested. Analysis of severity of the defects in the mutants suggests that COMA is epistatic to Ctf3 subcomplex. Interestingly, we noticed that these subcomplexes affect the organization of mitotic and meiotic kinetochores with subtle differences and they promote maintenance of Cse4 at the centromeres specifically during meiosis which is similar to the role of Mis6 (Ctf3 homolog) in fission yeast during mitosis. Interestingly, analysis of ctf3Δ and ctf19Δ mutants revealed a novel role of Ctf19 complex in regulation of SPB cohesion and duplication in meiosis.
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Affiliation(s)
- Meenakshi Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 40076, India
| | - Gunjan Mehta
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 40076, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 40076, India.
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Nerusheva OO, Galander S, Fernius J, Kelly D, Marston AL. Tension-dependent removal of pericentromeric shugoshin is an indicator of sister chromosome biorientation. Genes Dev 2014; 28:1291-309. [PMID: 24939933 PMCID: PMC4066400 DOI: 10.1101/gad.240291.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/20/2014] [Indexed: 12/24/2022]
Abstract
During mitosis and meiosis, sister chromatid cohesion resists the pulling forces of microtubules, enabling the generation of tension at kinetochores upon chromosome biorientation. How tension is read to signal the bioriented state remains unclear. Shugoshins form a pericentromeric platform that integrates multiple functions to ensure proper chromosome biorientation. Here we show that budding yeast shugoshin Sgo1 dissociates from the pericentromere reversibly in response to tension. The antagonistic activities of the kinetochore-associated Bub1 kinase and the Sgo1-bound phosphatase protein phosphatase 2A (PP2A)-Rts1 underlie a tension-dependent circuitry that enables Sgo1 removal upon sister kinetochore biorientation. Sgo1 dissociation from the pericentromere triggers dissociation of condensin and Aurora B from the centromere, thereby stabilizing the bioriented state. Conversely, forcing sister kinetochores to be under tension during meiosis I leads to premature Sgo1 removal and precocious loss of pericentromeric cohesion. Overall, we show that the pivotal role of shugoshin is to build a platform at the pericentromere that attracts activities that respond to the absence of tension between sister kinetochores. Disassembly of this platform in response to intersister kinetochore tension signals the bioriented state. Therefore, tension sensing by shugoshin is a central mechanism by which the bioriented state is read.
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Affiliation(s)
- Olga O. Nerusheva
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Stefan Galander
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Josefin Fernius
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - David Kelly
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Adele L. Marston
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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