1
|
Sacristan C, Samejima K, Ruiz LA, Deb M, Lambers MLA, Buckle A, Brackley CA, Robertson D, Hori T, Webb S, Kiewisz R, Bepler T, van Kwawegen E, Risteski P, Vukušić K, Tolić IM, Müller-Reichert T, Fukagawa T, Gilbert N, Marenduzzo D, Earnshaw WC, Kops GJPL. Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin. Cell 2024:S0092-8674(24)00409-4. [PMID: 38744280 DOI: 10.1016/j.cell.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/30/2024] [Accepted: 04/14/2024] [Indexed: 05/16/2024]
Abstract
Centromeres are scaffolds for the assembly of kinetochores that ensure chromosome segregation during cell division. How vertebrate centromeres obtain a three-dimensional structure to accomplish their primary function is unclear. Using super-resolution imaging, capture-C, and polymer modeling, we show that vertebrate centromeres are partitioned by condensins into two subdomains during mitosis. The bipartite structure is found in human, mouse, and chicken cells and is therefore a fundamental feature of vertebrate centromeres. Super-resolution imaging and electron tomography reveal that bipartite centromeres assemble bipartite kinetochores, with each subdomain binding a distinct microtubule bundle. Cohesin links the centromere subdomains, limiting their separation in response to spindle forces and avoiding merotelic kinetochore-spindle attachments. Lagging chromosomes during cancer cell divisions frequently have merotelic attachments in which the centromere subdomains are separated and bioriented. Our work reveals a fundamental aspect of vertebrate centromere biology with implications for understanding the mechanisms that guarantee faithful chromosome segregation.
Collapse
Affiliation(s)
- Carlos Sacristan
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), and University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Kumiko Samejima
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Lorena Andrade Ruiz
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Moonmoon Deb
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Maaike L A Lambers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Adam Buckle
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Chris A Brackley
- SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Daniel Robertson
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Tetsuya Hori
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Shaun Webb
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Robert Kiewisz
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY 10027, USA; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, Cantoblanco, Madrid 28049, Spain
| | - Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Eloïse van Kwawegen
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Tatsuo Fukagawa
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Davide Marenduzzo
- SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), and University Medical Center Utrecht, Utrecht, the Netherlands.
| |
Collapse
|
2
|
Kixmoeller K, Chang YW, Black BE. Centromeric chromatin clearings demarcate the site of kinetochore formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591177. [PMID: 38712116 PMCID: PMC11071481 DOI: 10.1101/2024.04.26.591177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The centromere is the chromosomal locus that recruits the kinetochore, directing faithful propagation of the genome during cell division. The kinetochore has been interrogated by electron microscopy since the middle of the last century, but with methodologies that compromised fine structure. Using cryo-ET on human mitotic chromosomes, we reveal a distinctive architecture at the centromere: clustered 20-25 nm nucleosome-associated complexes within chromatin clearings that delineate them from surrounding chromatin. Centromere components CENP-C and CENP-N are each required for the integrity of the complexes, while CENP-C is also required to maintain the chromatin clearing. We further visualize the scaffold of the fibrous corona, a structure amplified at unattached kinetochores, revealing crescent-shaped parallel arrays of fibrils that extend >1 μm. Thus, we reveal how the organization of centromeric chromatin creates a clearing at the site of kinetochore formation as well as the nature of kinetochore amplification mediated by corona fibrils.
Collapse
Affiliation(s)
- Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA, USA
| |
Collapse
|
3
|
Di Tommaso E, Giunta S. Dynamic interplay between human alpha-satellite DNA structure and centromere functions. Semin Cell Dev Biol 2024; 156:130-140. [PMID: 37926668 DOI: 10.1016/j.semcdb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Maintenance of genome stability relies on functional centromeres for correct chromosome segregation and faithful inheritance of the genetic information. The human centromere is the primary constriction within mitotic chromosomes made up of repetitive alpha-satellite DNA hierarchically organized in megabase-long arrays of near-identical higher order repeats (HORs). Centromeres are epigenetically specified by the presence of the centromere-specific histone H3 variant, CENP-A, which enables the assembly of the kinetochore for microtubule attachment. Notably, centromeric DNA is faithfully inherited as intact haplotypes from the parents to the offspring without intervening recombination, yet, outside of meiosis, centromeres are akin to common fragile sites (CFSs), manifesting crossing-overs and ongoing sequence instability. Consequences of DNA changes within the centromere are just starting to emerge, with unclear effects on intra- and inter-generational inheritance driven by centromere's essential role in kinetochore assembly. Here, we review evidence of meiotic selection operating to mitigate centromere drive, as well as recent reports on centromere damage, recombination and repair during the mitotic cell division. We propose an antagonistic pleiotropy interpretation to reconcile centromere DNA instability as both driver of aneuploidy that underlies degenerative diseases, while also potentially necessary for the maintenance of homogenized HORs for centromere function. We attempt to provide a framework for this conceptual leap taking into consideration the structural interface of centromere-kinetochore interaction and present case scenarios for its malfunctioning. Finally, we offer an integrated working model to connect DNA instability, chromatin, and structural changes with functional consequences on chromosome integrity.
Collapse
Affiliation(s)
- Elena Di Tommaso
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Simona Giunta
- Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy.
| |
Collapse
|
4
|
Ólafsson G, Haase MAB, Boeke JD. Humanization reveals pervasive incompatibility of yeast and human kinetochore components. G3 (BETHESDA, MD.) 2023; 14:jkad260. [PMID: 37962556 PMCID: PMC10755175 DOI: 10.1093/g3journal/jkad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 06/29/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Kinetochores assemble on centromeres to drive chromosome segregation in eukaryotic cells. Humans and budding yeast share most of the structural subunits of the kinetochore, whereas protein sequences have diverged considerably. The conserved centromeric histone H3 variant, CenH3 (CENP-A in humans and Cse4 in budding yeast), marks the site for kinetochore assembly in most species. A previous effort to complement Cse4 in yeast with human CENP-A was unsuccessful; however, co-complementation with the human core nucleosome was not attempted. Previously, our lab successfully humanized the core nucleosome in yeast; however, this severely affected cellular growth. We hypothesized that yeast Cse4 is incompatible with humanized nucleosomes and that the kinetochore represented a limiting factor for efficient histone humanization. Thus, we argued that including the human CENP-A or a Cse4-CENP-A chimera might improve histone humanization and facilitate kinetochore function in humanized yeast. The opposite was true: CENP-A expression reduced histone humanization efficiency, was toxic to yeast, and disrupted cell cycle progression and kinetochore function in wild-type (WT) cells. Suppressors of CENP-A toxicity included gene deletions of subunits of 3 conserved chromatin remodeling complexes, highlighting their role in CenH3 chromatin positioning. Finally, we attempted to complement the subunits of the NDC80 kinetochore complex, individually and in combination, without success, in contrast to a previous study indicating complementation by the human NDC80/HEC1 gene. Our results suggest that limited protein sequence similarity between yeast and human components in this very complex structure leads to failure of complementation.
Collapse
Affiliation(s)
- Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 14 11201, USA
| |
Collapse
|
5
|
Kyriacou E, Heun P. Centromere structure and function: lessons from Drosophila. Genetics 2023; 225:iyad170. [PMID: 37931172 PMCID: PMC10697814 DOI: 10.1093/genetics/iyad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/01/2023] [Indexed: 11/08/2023] Open
Abstract
The fruit fly Drosophila melanogaster serves as a powerful model organism for advancing our understanding of biological processes, not just by studying its similarities with other organisms including ourselves but also by investigating its differences to unravel the underlying strategies that evolved to achieve a common goal. This is particularly true for centromeres, specialized genomic regions present on all eukaryotic chromosomes that function as the platform for the assembly of kinetochores. These multiprotein structures play an essential role during cell division by connecting chromosomes to spindle microtubules in mitosis and meiosis to mediate accurate chromosome segregation. Here, we will take a historical perspective on the study of fly centromeres, aiming to highlight not only the important similarities but also the differences identified that contributed to advancing centromere biology. We will discuss the current knowledge on the sequence and chromatin organization of fly centromeres together with advances for identification of centromeric proteins. Then, we will describe both the factors and processes involved in centromere organization and how they work together to provide an epigenetic identity to the centromeric locus. Lastly, we will take an evolutionary point of view of centromeres and briefly discuss current views on centromere drive.
Collapse
Affiliation(s)
- Eftychia Kyriacou
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Patrick Heun
- Wellcome Centre of Cell Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF Edinburgh, UK
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
6
|
Gambogi CW, Pandey N, Dawicki-McKenna JM, Arora UP, Liskovykh MA, Ma J, Lamelza P, Larionov V, Lampson MA, Logsdon GA, Dumont BL, Black BE. Centromere innovations within a mouse species. SCIENCE ADVANCES 2023; 9:eadi5764. [PMID: 37967185 PMCID: PMC10651114 DOI: 10.1126/sciadv.adi5764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
Mammalian centromeres direct faithful genetic inheritance and are typically characterized by regions of highly repetitive and rapidly evolving DNA. We focused on a mouse species, Mus pahari, that we found has evolved to house centromere-specifying centromere protein-A (CENP-A) nucleosomes at the nexus of a satellite repeat that we identified and termed π-satellite (π-sat), a small number of recruitment sites for CENP-B, and short stretches of perfect telomere repeats. One M. pahari chromosome, however, houses a radically divergent centromere harboring ~6 mega-base pairs of a homogenized π-sat-related repeat, π-satB, that contains >20,000 functional CENP-B boxes. There, CENP-B abundance promotes accumulation of microtubule-binding components of the kinetochore and a microtubule-destabilizing kinesin of the inner centromere. We propose that the balance of pro- and anti-microtubule binding by the new centromere is what permits it to segregate during cell division with high fidelity alongside the older ones whose sequence creates a markedly different molecular composition.
Collapse
Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nootan Pandey
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennine M. Dawicki-McKenna
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Uma P. Arora
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Mikhail A. Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Piero Lamelza
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael A. Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
7
|
Virant D, Vojnovic I, Winkelmeier J, Endesfelder M, Turkowyd B, Lando D, Endesfelder U. Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color SMLM imaging. J Cell Biol 2023; 222:213836. [PMID: 36705602 PMCID: PMC9930162 DOI: 10.1083/jcb.202209096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023] Open
Abstract
The key to ensuring proper chromosome segregation during mitosis is the kinetochore (KT), a tightly regulated multiprotein complex that links the centromeric chromatin to the spindle microtubules and as such leads the segregation process. Understanding its architecture, function, and regulation is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in structural detail so far. In this study, we construct a nanometer-precise in situ map of the human-like regional KT of Schizosaccharomyces pombe using multi-color single-molecule localization microscopy. We measure each protein of interest (POI) in conjunction with two references, cnp1CENP-A at the centromere and sad1 at the spindle pole. This allows us to determine cell cycle and mitotic plane, and to visualize individual centromere regions separately. We determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI and, consequently, build an in situ KT model with unprecedented precision, providing new insights into the architecture.
Collapse
Affiliation(s)
- David Virant
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Ilijana Vojnovic
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Jannik Winkelmeier
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Marc Endesfelder
- https://ror.org/05591te55Institute for Assyriology and Hittitology, Ludwig-Maximilians-Universität München, München, Germany
| | - Bartosz Turkowyd
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - David Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Endesfelder
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany,Correspondence to Ulrike Endesfelder:
| |
Collapse
|
8
|
Cieslinski K, Wu YL, Nechyporenko L, Hörner SJ, Conti D, Skruzny M, Ries J. Nanoscale structural organization and stoichiometry of the budding yeast kinetochore. J Cell Biol 2023; 222:213833. [PMID: 36705601 PMCID: PMC9929930 DOI: 10.1083/jcb.202209094] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023] Open
Abstract
Proper chromosome segregation is crucial for cell division. In eukaryotes, this is achieved by the kinetochore, an evolutionarily conserved multiprotein complex that physically links the DNA to spindle microtubules and takes an active role in monitoring and correcting erroneous spindle-chromosome attachments. Our mechanistic understanding of these functions and how they ensure an error-free outcome of mitosis is still limited, partly because we lack a complete understanding of the kinetochore structure in the cell. In this study, we use single-molecule localization microscopy to visualize individual kinetochore complexes in situ in budding yeast. For major kinetochore proteins, we measured their abundance and position within the metaphase kinetochore. Based on this comprehensive dataset, we propose a quantitative model of the budding yeast kinetochore. While confirming many aspects of previous reports based on bulk imaging, our results present a unifying nanoscale model of the kinetochore in budding yeast.
Collapse
Affiliation(s)
- Konstanty Cieslinski
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Translational Radiation Oncology Unit, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Yu-Le Wu
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Faculty of Biosciences, Collaboration for Joint PhD Degree Between European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Lisa Nechyporenko
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Sarah Janice Hörner
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,https://ror.org/04p61dj41Institute of Molecular and Cell Biology, Mannheim University of Applied Sciences, Mannheim, Germany,Interdisciplinary Center for Neuroscience, Heidelberg University, Heidelberg, Germany
| | - Duccio Conti
- https://ror.org/03vpj4s62Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Michal Skruzny
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Ries
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| |
Collapse
|
9
|
In situ visualization of a simple bipartite kinetochore with a single microtubule attachment in Giardia intestinalis (Metamonada). Eur J Cell Biol 2022; 101:151217. [DOI: 10.1016/j.ejcb.2022.151217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/17/2022] [Accepted: 03/15/2022] [Indexed: 11/18/2022] Open
|
10
|
Câmara AS, Schubert V, Mascher M, Houben A. A simple model explains the cell cycle-dependent assembly of centromeric nucleosomes in holocentric species. Nucleic Acids Res 2021; 49:9053-9065. [PMID: 34352103 PMCID: PMC8450114 DOI: 10.1093/nar/gkab648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Centromeres are essential for chromosome movement. In independent taxa, species with holocentric chromosomes exist. In contrast to monocentric species, where no obvious dispersion of centromeres occurs during interphase, the organization of holocentromeres differs between condensed and decondensed chromosomes. During interphase, centromeres are dispersed into a large number of CENH3-positive nucleosome clusters in a number of holocentric species. With the onset of chromosome condensation, the centromeric nucleosomes join and form line-like holocentromeres. Using polymer simulations, we propose a mechanism relying on the interaction between centromeric nucleosomes and structural maintenance of chromosomes (SMC) proteins. Different sets of molecular dynamic simulations were evaluated by testing four parameters: (i) the concentration of Loop Extruders (LEs) corresponding to SMCs, (ii) the distribution and number of centromeric nucleosomes, (iii) the effect of centromeric nucleosomes on interacting LEs and (iv) the assembly of kinetochores bound to centromeric nucleosomes. We observed the formation of a line-like holocentromere, due to the aggregation of the centromeric nucleosomes when the chromosome was compacted into loops. A groove-like holocentromere structure formed after a kinetochore complex was simulated along the centromeric line. Similar mechanisms may also organize a monocentric chromosome constriction, and its regulation may cause different centromere types during evolution.
Collapse
Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| |
Collapse
|
11
|
Gerbi SA, Palazzo RE, Earnshaw WC, Schrader WT. William R. Brinkley: A giant in biomedical research and public policy. J Cell Biol 2021; 220:212526. [PMID: 34342638 PMCID: PMC8340550 DOI: 10.1083/jcb.202106102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Susan A Gerbi
- Division of Biology and Medicine, Brown University, Providence, RI
| | - Robert E Palazzo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, UK
| | | |
Collapse
|
12
|
Matveevsky S, Chassovnikarova T, Grishaeva T, Atsaeva M, Malygin V, Bakloushinskaya I, Kolomiets O. Kinase CDK2 in Mammalian Meiotic Prophase I: Screening for Hetero- and Homomorphic Sex Chromosomes. Int J Mol Sci 2021; 22:1969. [PMID: 33671248 PMCID: PMC7922030 DOI: 10.3390/ijms22041969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/13/2021] [Accepted: 02/13/2021] [Indexed: 01/19/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are crucial regulators of the eukaryotic cell cycle. The critical role of CDK2 in the progression of meiosis was demonstrated in a single mammalian species, the mouse. We used immunocytochemistry to study the localization of CDK2 during meiosis in seven rodent species that possess hetero- and homomorphic male sex chromosomes. To compare the distribution of CDK2 in XY and XX male sex chromosomes, we performed multi-round immunostaining of a number of marker proteins in meiotic chromosomes of the rat and subterranean mole voles. Antibodies to the following proteins were used: RAD51, a member of the double-stranded DNA break repair machinery; MLH1, a component of the DNA mismatch repair system; and SUN1, which is involved in the connection between the meiotic telomeres and nuclear envelope, alongside the synaptic protein SYCP3 and kinetochore marker CREST. Using an enhanced protocol, we were able to assess the distribution of as many as four separate proteins in the same meiotic cell. We showed that during prophase I, CDK2 localizes to telomeric and interstitial regions of autosomes in all species investigated (rat, vole, hamster, subterranean mole voles, and mole rats). In sex bivalents following synaptic specificity, the CDK2 signals were distributed in three different modes. In the XY bivalent in the rat and mole rat, we detected numerous CDK2 signals in asynaptic regions and a single CDK2 focus on synaptic segments, similar to the mouse sex chromosomes. In the mole voles, which have unique XX sex chromosomes in males, CDK2 signals were nevertheless distributed similarly to the rat XY sex chromosomes. In the vole, sex chromosomes did not synapse, but demonstrated CDK2 signals of varying intensity, similar to the rat X and Y chromosomes. In female mole voles, the XX bivalent had CDK2 pattern similar to autosomes of all species. In the hamster, CDK2 signals were revealed in telomeric regions in the short synaptic segment of the sex bivalent. We found that CDK2 signals colocalize with SUN1 and MLH1 signals in meiotic chromosomes in rats and mole voles, similar to the mouse. The difference in CDK2 manifestation at the prophase I sex chromosomes can be considered an example of the rapid chromosome evolution in mammals.
Collapse
Affiliation(s)
- Sergey Matveevsky
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (T.G.); (O.K.)
| | - Tsenka Chassovnikarova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, 1000 Sofia, Bulgaria;
- Department of Zoology, Biological Faculty, University “Paisi Hilendarski”, 4000 Plovdiv, Bulgaria
| | - Tatiana Grishaeva
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (T.G.); (O.K.)
| | - Maret Atsaeva
- Department of Cell Biology, Morphology and Microbiology, Chehen State University, 364051 Grozny, Russia;
| | - Vasilii Malygin
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Irina Bakloushinskaya
- Laboratory of Genome Evolution and Speciation, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Oxana Kolomiets
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (T.G.); (O.K.)
| |
Collapse
|
13
|
Kixmoeller K, Allu PK, Black BE. The centromere comes into focus: from CENP-A nucleosomes to kinetochore connections with the spindle. Open Biol 2020; 10:200051. [PMID: 32516549 PMCID: PMC7333888 DOI: 10.1098/rsob.200051] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic chromosome segregation relies upon specific connections from DNA to the microtubule-based spindle that forms at cell division. The chromosomal locus that directs this process is the centromere, where a structure called the kinetochore forms upon entry into mitosis. Recent crystallography and single-particle electron microscopy have provided unprecedented high-resolution views of the molecular complexes involved in this process. The centromere is epigenetically specified by nucleosomes harbouring a histone H3 variant, CENP-A, and we review recent progress on how it differentiates centromeric chromatin from the rest of the chromosome, the biochemical pathway that mediates its assembly and how two non-histone components of the centromere specifically recognize CENP-A nucleosomes. The core centromeric nucleosome complex (CCNC) is required to recruit a 16-subunit complex termed the constitutive centromere associated network (CCAN), and we highlight recent structures reported of the budding yeast CCAN. Finally, the structures of multiple modular sub-complexes of the kinetochore have been solved at near-atomic resolution, providing insight into how connections are made to the CCAN on one end and to the spindle microtubules on the other. One can now build molecular models from the DNA through to the physical connections to microtubules.
Collapse
Affiliation(s)
- Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Praveen Kumar Allu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
14
|
Zielinska AP, Bellou E, Sharma N, Frombach AS, Seres KB, Gruhn JR, Blayney M, Eckel H, Moltrecht R, Elder K, Hoffmann ER, Schuh M. Meiotic Kinetochores Fragment into Multiple Lobes upon Cohesin Loss in Aging Eggs. Curr Biol 2019; 29:3749-3765.e7. [PMID: 31679939 PMCID: PMC6868511 DOI: 10.1016/j.cub.2019.09.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/23/2019] [Accepted: 09/04/2019] [Indexed: 01/02/2023]
Abstract
Chromosome segregation errors during female meiosis are a leading cause of pregnancy loss and human infertility. The segregation of chromosomes is driven by interactions between spindle microtubules and kinetochores. Kinetochores in mammalian oocytes are subjected to special challenges: they need to withstand microtubule pulling forces over multiple hours and are built on centromeric chromatin that in humans is decades old. In meiosis I, sister kinetochores are paired and oriented toward the same spindle pole. It is well established that they progressively separate from each other with advancing female age. However, whether aging also affects the internal architecture of centromeres and kinetochores is currently unclear. Here, we used super-resolution microscopy to study meiotic centromere and kinetochore organization in metaphase-II-arrested eggs from three mammalian species, including humans. We found that centromeric chromatin decompacts with advancing maternal age. Kinetochores built on decompacted centromeres frequently lost their integrity and fragmented into multiple lobes. Fragmentation extended across inner and outer kinetochore regions and affected over 30% of metaphase-II-arrested (MII) kinetochores in aged women and mice, making the lobular architecture a prominent feature of the female meiotic kinetochore. We demonstrate that a partial cohesin loss, as is known to occur in oocytes with advancing maternal age, is sufficient to trigger centromere decompaction and kinetochore fragmentation. Microtubule pulling forces further enhanced the fragmentation and shaped the arrangement of kinetochore lobes. Fragmented kinetochores were frequently abnormally attached to spindle microtubules, suggesting that kinetochore fragmentation could contribute to the maternal age effect in mammalian eggs.
Collapse
Affiliation(s)
- Agata P Zielinska
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Eirini Bellou
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Ninadini Sharma
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Ann-Sophie Frombach
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - K Bianka Seres
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany; Bourn Hall Clinic, High Street, Cambridge CB23 2TN, UK
| | - Jennifer R Gruhn
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | | | - Heike Eckel
- Kinderwunschzentrum, Kasseler Landstraße 25A, Göttingen 37081, Germany
| | - Rüdiger Moltrecht
- Kinderwunschzentrum, Kasseler Landstraße 25A, Göttingen 37081, Germany
| | - Kay Elder
- Bourn Hall Clinic, High Street, Cambridge CB23 2TN, UK
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Melina Schuh
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
| |
Collapse
|
15
|
French BT, Straight AF. The Power of Xenopus Egg Extract for Reconstitution of Centromere and Kinetochore Function. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 56:59-84. [PMID: 28840233 DOI: 10.1007/978-3-319-58592-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Faithful transmission of genetic information during cell division requires attachment of chromosomes to the mitotic spindle via the kinetochore. In vitro reconstitution studies are beginning to uncover how the kinetochore is assembled upon the underlying centromere, how the kinetochore couples chromosome movement to microtubule dynamics, and how cells ensure the site of kinetochore assembly is maintained from one generation to the next. Here we give special emphasis to advances made in Xenopus egg extract, which provides a unique, biochemically tractable in vitro system that affords the complexity of cytoplasm and nucleoplasm to permit reconstitution of the dynamic, cell cycle-regulated functions of the centromere and kinetochore.
Collapse
Affiliation(s)
- Bradley T French
- Department of Biochemistry, Stanford University, 279 Campus Drive, Beckman 409, Stanford, CA, 94305, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, 279 Campus Drive, Beckman 409, Stanford, CA, 94305, USA.
| |
Collapse
|
16
|
Kyriacou E, Heun P. High-resolution mapping of centromeric protein association using APEX-chromatin fibers. Epigenetics Chromatin 2018; 11:68. [PMID: 30445992 PMCID: PMC6238281 DOI: 10.1186/s13072-018-0237-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/26/2018] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND The centromere is a specialized chromosomal locus that forms the basis for the assembly of a multi-protein complex, the kinetochore and ensures faithful chromosome segregation during every cell division. The repetitive nature of the underlying centromeric sequence represents a major obstacle for high-resolution mapping of protein binding using methods that rely on annotated genomes. Here, we present a novel microscopy-based approach called "APEX-chromatin fibers" for localizing protein binding over the repetitive centromeric sequences at kilobase resolution. RESULTS By fusing centromere factors of interest to ascorbate peroxidase, we were able to label their binding profiles on extended chromatin fibers with biotin marks. We applied APEX-chromatin fibers to at least one member of each CCAN complex, most of which show a localization pattern different from CENP-A but within the CENP-A delineated centromeric domain. Interestingly, we describe here a novel characteristic of CENP-I and CENP-B that display extended localization beyond the CENP-A boundaries. CONCLUSIONS Our approach was successfully applied for mapping protein association over centromeric chromatin, revealing previously undescribed localization patterns. In this study, we focused on centromeric factors, but we believe that this approach could be useful for mapping protein binding patterns in other repetitive regions.
Collapse
Affiliation(s)
- Eftychia Kyriacou
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.,Faculty of Biology, Albert-Ludwigs Universität Freiburg, Freiburg im Breisgau, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Patrick Heun
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
17
|
Drpic D, Almeida AC, Aguiar P, Renda F, Damas J, Lewin HA, Larkin DM, Khodjakov A, Maiato H. Chromosome Segregation Is Biased by Kinetochore Size. Curr Biol 2018; 28:1344-1356.e5. [PMID: 29706521 PMCID: PMC5954971 DOI: 10.1016/j.cub.2018.03.023] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 11/30/2022]
Abstract
Chromosome missegregation during mitosis or meiosis is a hallmark of cancer and the main cause of prenatal death in humans. The gain or loss of specific chromosomes is thought to be random, with cell viability being essentially determined by selection. Several established pathways including centrosome amplification, sister-chromatid cohesion defects, or a compromised spindle assembly checkpoint can lead to chromosome missegregation. However, how specific intrinsic features of the kinetochore—the critical chromosomal interface with spindle microtubules—impact chromosome segregation remains poorly understood. Here we used the unique cytological attributes of female Indian muntjac, the mammal with the lowest known chromosome number (2n = 6), to characterize and track individual chromosomes with distinct kinetochore size throughout mitosis. We show that centromere and kinetochore functional layers scale proportionally with centromere size. Measurement of intra-kinetochore distances, serial-section electron microscopy, and RNAi against key kinetochore proteins confirmed a standard structural and functional organization of the Indian muntjac kinetochores and revealed that microtubule binding capacity scales with kinetochore size. Surprisingly, we found that chromosome segregation in this species is not random. Chromosomes with larger kinetochores bi-oriented more efficiently and showed a 2-fold bias to congress to the equator in a motor-independent manner. Despite robust correction mechanisms during unperturbed mitosis, chromosomes with larger kinetochores were also strongly biased to establish erroneous merotelic attachments and missegregate during anaphase. This bias was impervious to the experimental attenuation of polar ejection forces on chromosome arms by RNAi against the chromokinesin Kif4a. Thus, kinetochore size is an important determinant of chromosome segregation fidelity. Centromere/kinetochore functional layers scale proportionally with centromere size Kinetochore microtubule binding capacity scales with kinetochore size Chromosome congression and bi-orientation are biased by kinetochore size Error formation leading to chromosome missegregation is biased by kinetochore size
Collapse
Affiliation(s)
- Danica Drpic
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Graduate Program in Areas of Basic and Applied Biology (GABBA), Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ana C Almeida
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Paulo Aguiar
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto Nacional de Engenharia Biomédica (INEB), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Fioranna Renda
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
| | - Harris A Lewin
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
| | - Alexey Khodjakov
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA; Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Helder Maiato
- Chromosome Instability & Dynamics Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Cell Division Group, Experimental Biology Unit, Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
| |
Collapse
|
18
|
Lakshmi RB, Nair VM, Manna TK. Regulators of spindle microtubules and their mechanisms: Living together matters. IUBMB Life 2018; 70:101-111. [DOI: 10.1002/iub.1708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/16/2017] [Indexed: 12/23/2022]
Affiliation(s)
- R. Bhagya Lakshmi
- School of Biology; Indian Institute of Science Education and Research, CET Campus; Thiruvananthapuram Kerala India
| | - Vishnu M. Nair
- School of Biology; Indian Institute of Science Education and Research, CET Campus; Thiruvananthapuram Kerala India
| | - Tapas K. Manna
- School of Biology; Indian Institute of Science Education and Research, CET Campus; Thiruvananthapuram Kerala India
| |
Collapse
|
19
|
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.
Collapse
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
| | | |
Collapse
|
20
|
Expanded Satellite Repeats Amplify a Discrete CENP-A Nucleosome Assembly Site on Chromosomes that Drive in Female Meiosis. Curr Biol 2017; 27:2365-2373.e8. [PMID: 28756949 DOI: 10.1016/j.cub.2017.06.069] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/23/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022]
Abstract
Female meiosis provides an opportunity for selfish genetic elements to violate Mendel's law of segregation by increasing the chance of segregating to the egg [1]. Centromeres and other repetitive sequences can drive in meiosis by cheating the segregation process [2], but the underlying mechanisms are unknown. Here, we show that centromeres with more satellite repeats house more nucleosomes that confer centromere identity, containing the histone H3 variant CENP-A, and bias their segregation to the egg relative to centromeres with fewer repeats. CENP-A nucleosomes predominantly occupy a single site within the repeating unit that becomes limiting for centromere assembly on smaller centromeres. We propose that amplified repetitive sequences act as selfish elements by promoting expansion of CENP-A chromatin and increased transmission through the female germline.
Collapse
|
21
|
Xie J, Wooten M, Tran V, Chen X. Breaking Symmetry - Asymmetric Histone Inheritance in Stem Cells. Trends Cell Biol 2017; 27:527-540. [PMID: 28268050 DOI: 10.1016/j.tcb.2017.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 01/17/2023]
Abstract
Asymmetric cell division (ACD) gives rise to two daughter cells with distinct fates. ACD is widely used during development and by many types of adult stem cells during tissue homeostasis and regeneration. ACD can be regulated by extrinsic cues, such as signaling molecules, as well as by intrinsic factors, such as organelles and cortex proteins. The recent discovery of asymmetric histone inheritance during stem cell ACD has revealed another intrinsic mechanism by which ACD produces two distinct daughters. In this review we discuss these findings in the context of cell-cycle regulation, as well as other studies of ACD, to begin understanding the underlying mechanisms and biological relevance of this phenomenon.
Collapse
Affiliation(s)
- Jing Xie
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vuong Tran
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Current address: Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North Seattle, Seattle, WA 98109, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
| |
Collapse
|
22
|
Stepwise unfolding supports a subunit model for vertebrate kinetochores. Proc Natl Acad Sci U S A 2017; 114:3133-3138. [PMID: 28265097 DOI: 10.1073/pnas.1614145114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
During cell division, interactions between microtubules and chromosomes are mediated by the kinetochore, a proteinaceous structure located at the primary constriction of chromosomes. In addition to the centromere histone centromere protein A (CENP-A), 15 other members of the constitutive centromere associated network (CCAN) participate in the formation of a chromatin-associated scaffold that supports kinetochore structure. We performed a targeted screen analyzing unfolded centrochromatin from CENP-depleted chromosomes. Our results revealed that CENP-C and CENP-S are critical for the stable folding of mitotic kinetochore chromatin. Multipeak fitting algorithms revealed the presence of an organized pattern of centrochromatin packing consistent with arrangement of CENP-A-containing nucleosomes into up to five chromatin "subunits"-each containing roughly 20-30 nucleosomes. These subunits could be either layers of a boustrophedon or small loops of centromeric chromatin.
Collapse
|
23
|
Asbury CL. Anaphase A: Disassembling Microtubules Move Chromosomes toward Spindle Poles. BIOLOGY 2017; 6:E15. [PMID: 28218660 PMCID: PMC5372008 DOI: 10.3390/biology6010015] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/04/2017] [Accepted: 02/10/2017] [Indexed: 11/16/2022]
Abstract
The separation of sister chromatids during anaphase is the culmination of mitosis and one of the most strikingly beautiful examples of cellular movement. It consists of two distinct processes: Anaphase A, the movement of chromosomes toward spindle poles via shortening of the connecting fibers, and anaphase B, separation of the two poles from one another via spindle elongation. I focus here on anaphase A chromosome-to-pole movement. The chapter begins by summarizing classical observations of chromosome movements, which support the current understanding of anaphase mechanisms. Live cell fluorescence microscopy studies showed that poleward chromosome movement is associated with disassembly of the kinetochore-attached microtubule fibers that link chromosomes to poles. Microtubule-marking techniques established that kinetochore-fiber disassembly often occurs through loss of tubulin subunits from the kinetochore-attached plus ends. In addition, kinetochore-fiber disassembly in many cells occurs partly through 'flux', where the microtubules flow continuously toward the poles and tubulin subunits are lost from minus ends. Molecular mechanistic models for how load-bearing attachments are maintained to disassembling microtubule ends, and how the forces are generated to drive these disassembly-coupled movements, are discussed.
Collapse
Affiliation(s)
- Charles L Asbury
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
24
|
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: 305] [Impact Index Per Article: 43.6] [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.
Collapse
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.
| |
Collapse
|
25
|
Friedman S, Freitag M. Centrochromatin of Fungi. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:85-109. [PMID: 28840234 DOI: 10.1007/978-3-319-58592-5_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The centromere is an essential chromosomal locus that dictates the nucleation point for assembly of the kinetochore and subsequent attachment of spindle microtubules during chromosome segregation. Research over the last decades demonstrated that centromeres are defined by a combination of genetic and epigenetic factors. Recent work showed that centromeres are quite diverse and flexible and that many types of centromere sequences and centromeric chromatin ("centrochromatin") have evolved. The kingdom of the fungi serves as an outstanding example of centromere plasticity, including organisms with centromeres as diverse as 0.15-300 kb in length, and with different types of chromatin states for most species examined thus far. Some of the species in the less familiar taxa provide excellent opportunities to help us better understand centromere biology in all eukaryotes, which may improve treatment options against fungal infection, and biotechnologies based on fungi. This review summarizes the current knowledge of fungal centromeres and centrochromatin, including an outlook for future research.
Collapse
Affiliation(s)
- Steven Friedman
- Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Bldg, Corvallis, OR, 97331, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Bldg, Corvallis, OR, 97331, USA.
| |
Collapse
|
26
|
García Del Arco A, Erhardt S. Post-translational Modifications of Centromeric Chromatin. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:213-231. [PMID: 28840239 DOI: 10.1007/978-3-319-58592-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Regulation of chromatin structures is important for the control of DNA processes such as gene expression, and misregulation of chromatin is implicated in diverse diseases. Covalent post-translational modifications of histones are a prominent way to regulate chromatin structure and different chromatin regions bear their specific signature of histone modifications. The composition of centromeric chromatin is significantly different from other chromatin structures and mainly defined by the presence of the histone H3-variant CENP-A. Here we summarize the composition of centromeric chromatin and what we know about its differential regulation by post-translational modifications.
Collapse
Affiliation(s)
- Ana García Del Arco
- Center for Molecular Biology of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
- Cell Networks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
| |
Collapse
|
27
|
Stankovic A, Jansen LET. Quantitative Microscopy Reveals Centromeric Chromatin Stability, Size, and Cell Cycle Mechanisms to Maintain Centromere Homeostasis. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:139-162. [PMID: 28840236 DOI: 10.1007/978-3-319-58592-5_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Centromeres are chromatin domains specified by nucleosomes containing the histone H3 variant, CENP-A. This unique centromeric structure is at the heart of a strong self-templating epigenetic mechanism that renders centromeres heritable. We review how specific quantitative microscopy approaches have contributed to the determination of the copy number, architecture, size, and dynamics of centromeric chromatin and its associated centromere complex and kinetochore. These efforts revealed that the key to long-term centromere maintenance is the slow turnover of CENP-A nucleosomes, a critical size of the chromatin domain and its cell cycle-coupled replication. These features come together to maintain homeostasis of a chromatin locus that directs its own epigenetic inheritance and facilitates the assembly of the mitotic kinetochore.
Collapse
Affiliation(s)
- Ana Stankovic
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Lars E T Jansen
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal.
| |
Collapse
|
28
|
Dimitrova YN, Jenni S, Valverde R, Khin Y, Harrison SC. Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly. Cell 2016; 167:1014-1027.e12. [PMID: 27881300 PMCID: PMC5856483 DOI: 10.1016/j.cell.2016.10.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/02/2016] [Accepted: 10/03/2016] [Indexed: 11/25/2022]
Abstract
Kinetochores connect centromeric nucleosomes with mitotic-spindle microtubules through conserved, cross-interacting protein subassemblies. In budding yeast, the heterotetrameric MIND complex (Mtw1, Nnf1, Nsl1, Dsn1), ortholog of the metazoan Mis12 complex, joins the centromere-proximal components, Mif2 and COMA, with the principal microtubule-binding component, the Ndc80 complex (Ndc80C). We report the crystal structure of Kluyveromyces lactis MIND and examine its partner interactions, to understand the connection from a centromeric nucleosome to a much larger microtubule. MIND resembles an elongated, asymmetric Y; two globular heads project from a coiled-coil shaft. An N-terminal extension of Dsn1 from one head regulates interactions of the other head, blocking binding of Mif2 and COMA. Dsn1 phosphorylation by Ipl1/Aurora B relieves this autoinhibition, enabling MIND to join an assembling kinetochore. A C-terminal extension of Dsn1 recruits Ndc80C to the opposite end of the shaft. The structure and properties of MIND show how it integrates phospho-regulatory inputs for kinetochore assembly and disassembly.
Collapse
Affiliation(s)
- Yoana N Dimitrova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Roberto Valverde
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Yadana Khin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA; Howard Hughes Medical Institute, 250 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
29
|
Abstracts. Toxicol Pathol 2016. [DOI: 10.1177/019262339202000415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
30
|
Wynne DJ, Funabiki H. Heterogeneous architecture of vertebrate kinetochores revealed by three-dimensional superresolution fluorescence microscopy. Mol Biol Cell 2016; 27:3395-3404. [PMID: 27170176 PMCID: PMC5221576 DOI: 10.1091/mbc.e16-02-0130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/04/2016] [Indexed: 11/11/2022] Open
Abstract
Superresolution fluorescence microscopy of vertebrate kinetochore proteins reveals that outer kinetochore components assume diverse distribution patterns, including a ring-like configuration encircling the CENP-A–marked centromeric chromatin on the metaphase spindle in Xenopus egg extracts. The kinetochore is often depicted as having a disk-like architecture in which the outer layer of proteins, which engage microtubules and control checkpoint signaling, are built on a static inner layer directly linked to CENP-A chromatin. Here, applying three-dimensional (3D) structural illumination microscopy (SIM) and stochastic optical reconstruction microscopy (STORM) to Xenopus egg extracts and tissue culture cells, we report various distribution patterns of inner and outer kinetochore proteins. In egg extracts, a configuration in which outer kinetochore proteins surround the periphery of CENP-A chromatin is common, forming an ∼200-nm ring-like organization that may engage a bundle of microtubule ends. Similar rings are observed in Xenopus tissue culture cells at a lower frequency but are enriched in conditions in which the spindle is disorganized. Although rings are rare in human cells, the distribution of both inner and outer kinetochore proteins elongates in the absence of microtubule attachment in a manner dependent on Aurora B. We propose a model in which the 3D organization of both the outer and inner kinetochore regions respond to the progression from lateral to end-on microtubule attachments by coalescing into a tight disk from less uniform distributions early in prometaphase.
Collapse
Affiliation(s)
- David J Wynne
- Laboratory of Chromosome and Cell Biology, Rockefeller University, New York, NY 10065.,Department of Biology, College of New Jersey, Ewing, NJ 08628
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, Rockefeller University, New York, NY 10065
| |
Collapse
|
31
|
Rošić S, Erhardt S. No longer a nuisance: long non-coding RNAs join CENP-A in epigenetic centromere regulation. Cell Mol Life Sci 2016; 73:1387-98. [PMID: 26748759 PMCID: PMC11108473 DOI: 10.1007/s00018-015-2124-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/08/2015] [Accepted: 12/17/2015] [Indexed: 01/02/2023]
Abstract
Centromeres represent the basis for kinetochore formation, and are essential for proper chromosome segregation during mitosis. Despite these essential roles, centromeres are not defined by specific DNA sequences, but by epigenetic means. The histone variant CENP-A controls centromere identity epigenetically and is essential for recruiting kinetochore components that attach the chromosomes to the mitotic spindle during mitosis. Recently, a new player in centromere regulation has emerged: long non-coding RNAs transcribed from repetitive regions of centromeric DNA function in regulating centromeres epigenetically. This review summarizes recent findings on the essential roles that transcription, pericentromeric transcripts, and centromere-derived RNAs play in centromere biology.
Collapse
Affiliation(s)
- Silvana Rošić
- Medical Research Council Clinical Sciences Centre, Imperial College London, London, UK
| | - Sylvia Erhardt
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks Excellence Cluster, University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
| |
Collapse
|
32
|
Etemad B, Kops GJPL. Attachment issues: kinetochore transformations and spindle checkpoint silencing. Curr Opin Cell Biol 2016; 39:101-8. [PMID: 26947988 DOI: 10.1016/j.ceb.2016.02.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 12/21/2022]
Abstract
Cell division culminates in the segregation of duplicated chromosomes in opposite directions prior to cellular fission. This process is guarded by the spindle assembly checkpoint (SAC), which prevents the anaphase of cell division until stable connections between spindle microtubules and the kinetochores of all chromosomes are established. The anaphase inhibitor is generated at unattached kinetochores and inhibitor production is prevented when microtubules are captured. Understanding the molecular changes in the kinetochore that are evoked by microtubule attachments is crucial for understanding the mechanisms of SAC signaling and silencing. Here, we highlight the most recent findings on these events, pinpoint some remaining mysteries, and argue for incorporating holistic views of kinetochore dynamics in order to understand SAC silencing.
Collapse
Affiliation(s)
- Banafsheh Etemad
- Hubrecht Institute - KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Geert J P L Kops
- Hubrecht Institute - KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands; Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands.
| |
Collapse
|
33
|
Freitag M. The kinetochore interaction network (KIN) of ascomycetes. Mycologia 2016; 108:485-505. [PMID: 26908646 DOI: 10.3852/15-182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 01/13/2023]
Abstract
Chromosome segregation relies on coordinated activity of a large assembly of proteins, the kinetochore interaction network (KIN). How conserved the underlying mechanisms driving the epigenetic phenomenon of centromere and kinetochore assembly and maintenance are remains unclear, even though various eukaryotic models have been studied. More than 50 different proteins, many in multiple copies, comprise the KIN or are associated with fungal centromeres and kinetochores. Proteins isolated from immune sera recognized centromeric regions on chromosomes and thus were named centromere proteins (CENPs). CENP-A, sometimes called centromere-specific H3 (CenH3), is incorporated into nucleosomes within or near centromeres. The constitutive centromere-associated network (CCAN) assembles on this specialized chromatin, likely based on specific interactions with and requiring presence of CENP-C. The outer kinetochore comprises the Knl1-Mis12-Ndc80 (KMN) protein complexes that connect CCAN to spindles, accomplished by binding and stabilizing microtubules (MTs) and in the process generating load-bearing assemblies for chromatid segregation. In most fungi the Dam1/DASH complex connects the KMN complexes to MTs. Fungi present a rich resource to investigate mechanistic commonalities but also differences in kinetochore architecture. While ascomycetes have sets of CCAN and KMN proteins that are conserved with those of budding yeast or metazoans, searching other major branches of the fungal kingdom revealed that CCAN proteins are poorly conserved at the primary sequence level. Several conserved binding motifs or domains within KMN complexes have been described recently, and these features of ascomycete KIN proteins are shared with most metazoan proteins. In addition, several ascomycete-specific domains have been identified here.
Collapse
Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305
| |
Collapse
|
34
|
Scott KC, Bloom KS. Lessons learned from counting molecules: how to lure CENP-A into the kinetochore. Open Biol 2015; 4:rsob.140191. [PMID: 25500356 PMCID: PMC4281711 DOI: 10.1098/rsob.140191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Kristin C Scott
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Kerry S Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
35
|
Abendroth C, Hofmeister A, Hake SB, Kamweru PK, Miess E, Dornblut C, Küffner I, Deng W, Leonhardt H, Orthaus S, Hoischen C, Diekmann S. The CENP-T C-terminus is exclusively proximal to H3.1 and not to H3.2 or H3.3. Int J Mol Sci 2015; 16:5839-63. [PMID: 25775162 PMCID: PMC4394509 DOI: 10.3390/ijms16035839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 12/17/2022] Open
Abstract
The kinetochore proteins assemble onto centromeric chromatin and regulate DNA segregation during cell division. The inner kinetochore proteins bind centromeres while most outer kinetochore proteins assemble at centromeres during mitosis, connecting the complex to microtubules. The centromere-kinetochore complex contains specific nucleosomes and nucleosomal particles. CENP-A replaces canonical H3 in centromeric nucleosomes, defining centromeric chromatin. Next to CENP-A, the CCAN multi-protein complex settles which contains CENP-T/W/S/X. These four proteins are described to form a nucleosomal particle at centromeres. We had found the CENP-T C-terminus and the CENP-S termini next to histone H3.1 but not to CENP-A, suggesting that the Constitutive Centromere-Associated Network (CCAN) bridges a CENP-A- and a H3-containing nucleosome. Here, we show by in vivo FRET that this proximity between CENP-T and H3 is specific for H3.1 but neither for the H3.1 mutants H3.1(C96A) and H3.1(C110A) nor for H3.2 or H3.3. We also found CENP-M next to H3.1 but not to these H3.1 mutants. Consistently, we detected CENP-M next to CENP-S. These data elucidate the local molecular neighborhood of CCAN proteins next to a H3.1-containing centromeric nucleosome. They also indicate an exclusive position of H3.1 clearly distinct from H3.2, thus documenting a local, and potentially also functional, difference between H3.1 and H3.2.
Collapse
Affiliation(s)
- Christian Abendroth
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Antje Hofmeister
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Sandra B Hake
- Department of Molecular Biology, Center for Integrated Protein Science Munich (CIPSM), Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität Munich, Schillerstr. 44, D-80336 Munich, Germany.
| | - Paul K Kamweru
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Elke Miess
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Carsten Dornblut
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Isabell Küffner
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Wen Deng
- Department of Biology II, Center for Integrated Protein Science, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, D-82152 Munich, Germany.
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, D-82152 Munich, Germany.
| | | | - Christian Hoischen
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Stephan Diekmann
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| |
Collapse
|
36
|
Westhorpe FG, Straight AF. The centromere: epigenetic control of chromosome segregation during mitosis. Cold Spring Harb Perspect Biol 2014; 7:a015818. [PMID: 25414369 DOI: 10.1101/cshperspect.a015818] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A fundamental challenge for the survival of all organisms is maintaining the integrity of the genome in all cells. Cells must therefore segregate their replicated genome equally during each cell division. Eukaryotic organisms package their genome into a number of physically distinct chromosomes, which replicate during S phase and condense during prophase of mitosis to form paired sister chromatids. During mitosis, cells form a physical connection between each sister chromatid and microtubules of the mitotic spindle, which segregate one copy of each chromatid to each new daughter cell. The centromere is the DNA locus on each chromosome that creates the site of this connection. In this review, we present a brief history of centromere research and discuss our current knowledge of centromere establishment, maintenance, composition, structure, and function in mitosis.
Collapse
Affiliation(s)
- Frederick G Westhorpe
- Department of Biochemistry, Stanford University Medical School, Stanford, California 94305
| | - Aaron F Straight
- Department of Biochemistry, Stanford University Medical School, Stanford, California 94305
| |
Collapse
|
37
|
Bodor DL, Mata JF, Sergeev M, David AF, Salimian KJ, Panchenko T, Cleveland DW, Black BE, Shah JV, Jansen LE. The quantitative architecture of centromeric chromatin. eLife 2014; 3:e02137. [PMID: 25027692 PMCID: PMC4091408 DOI: 10.7554/elife.02137] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The centromere, responsible for chromosome segregation during mitosis, is epigenetically defined by CENP-A containing chromatin. The amount of centromeric CENP-A has direct implications for both the architecture and epigenetic inheritance of centromeres. Using complementary strategies, we determined that typical human centromeres contain ∼400 molecules of CENP-A, which is controlled by a mass-action mechanism. This number, despite representing only ∼4% of all centromeric nucleosomes, forms a ∼50-fold enrichment to the overall genome. In addition, although pre-assembled CENP-A is randomly segregated during cell division, this amount of CENP-A is sufficient to prevent stochastic loss of centromere function and identity. Finally, we produced a statistical map of CENP-A occupancy at a human neocentromere and identified nucleosome positions that feature CENP-A in a majority of cells. In summary, we present a quantitative view of the centromere that provides a mechanistic framework for both robust epigenetic inheritance of centromeres and the paucity of neocentromere formation. DOI:http://dx.doi.org/10.7554/eLife.02137.001 The genetic information in a cell is packed into structures called chromosomes. These contain strands of DNA wrapped around proteins called histones, which helps the long DNA chains to fit inside the relatively small nucleus of the cell. When a cell divides, it is important that both of the new cells contain all of the genetic information found in the parent cell. Therefore, the chromosomes duplicate during cell division, with the two copies held together at a single region of the chromosome called the centromere. The centromere then recruits and coordinates the molecular machinery that separates the two copies into different cells. Centromeres are inherited in an epigenetic manner. This means that there is no specific DNA sequence that defines the location of this structure on the chromosomes. Rather, a special type of histone, called CENP-A, is involved in defining its location. Bodor et al. use multiple techniques to show that human centromeres normally contain around 400 molecules of CENP-A, and that this number is crucial for ensuring that centromeres form in the right place. Interestingly, only a minority of the CENP-A molecules are located at centromeres; yet this is more than at any other region of the chromosome. This explains why centromeres are only formed at a single position on each chromosome. When the chromosomes separate, the CENP-A molecules at the centromere are randomly divided between the two copies. In this way memory of the centromere location is maintained. If the number of copies of CENP-A inherited by one of the chromosomes drops below a threshold value, a centromere will not form. However, Bodor et al. found that the number of CENP-A molecules in a centromere is large enough, not only to support the formation of the centromere structure, but also to keep it above the threshold value in nearly all cases. This threshold is also high enough to make it unlikely that a centromere will form in the wrong place because of a random fluctuation in the number of CENP-A molecules. Therefore, the number of CENP-A molecules is crucial for controlling both the formation and the inheritance of the centromere. DOI:http://dx.doi.org/10.7554/eLife.02137.002
Collapse
Affiliation(s)
- Dani L Bodor
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - João F Mata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Mikhail Sergeev
- Department of Systems Biology, Harvard Medical School, Boston, United States Renal Division, Brigham and Women's Hospital, Boston, United States
| | | | - Kevan J Salimian
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Tanya Panchenko
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, United States Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Jagesh V Shah
- Department of Systems Biology, Harvard Medical School, Boston, United States Renal Division, Brigham and Women's Hospital, Boston, United States
| | | |
Collapse
|
38
|
Zaytsev AV, Sundin LJR, DeLuca KF, Grishchuk EL, DeLuca JG. Accurate phosphoregulation of kinetochore-microtubule affinity requires unconstrained molecular interactions. ACTA ACUST UNITED AC 2014; 206:45-59. [PMID: 24982430 PMCID: PMC4085703 DOI: 10.1083/jcb.201312107] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Accurate regulation of kinetochore–microtubule affinity is driven by incremental phosphorylation of an NDC80 molecular “lawn,” in which NDC80–microtubule bonds reorganize dynamically in response to the number and stability of microtubule attachments. Accurate chromosome segregation relies on dynamic interactions between microtubules (MTs) and the NDC80 complex, a major kinetochore MT-binding component. Phosphorylation at multiple residues of its Hec1 subunit may tune kinetochore–MT binding affinity for diverse mitotic functions, but molecular details of such phosphoregulation remain elusive. Using quantitative analyses of mitotic progression in mammalian cells, we show that Hec1 phosphorylation provides graded control of kinetochore–MT affinity. In contrast, modeling the kinetochore interface with repetitive MT binding sites predicts a switchlike response. To reconcile these findings, we hypothesize that interactions between NDC80 complexes and MTs are not constrained, i.e., the NDC80 complexes can alternate their binding between adjacent kinetochore MTs. Experiments using cells with phosphomimetic Hec1 mutants corroborate predictions of such a model but not of the repetitive sites model. We propose that accurate regulation of kinetochore–MT affinity is driven by incremental phosphorylation of an NDC80 molecular “lawn,” in which the NDC80–MT bonds reorganize dynamically in response to the number and stability of MT attachments.
Collapse
Affiliation(s)
- Anatoly V Zaytsev
- Physiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lynsie J R Sundin
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523
| | - Keith F DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523
| | - Ekaterina L Grishchuk
- Physiology Department, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523
| |
Collapse
|
39
|
Cieśliński K, Ries J. The yeast kinetochore - structural insights from optical microscopy. Curr Opin Chem Biol 2014; 20:1-8. [PMID: 24763395 DOI: 10.1016/j.cbpa.2014.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/26/2014] [Indexed: 11/19/2022]
Abstract
In eukaryotic organisms each chromosome is captured by spindle microtubules. This interaction is mediated by an evolutionarily conserved, multi-protein complex called kinetochore. The main function of the kinetochore is to maintain correct chromosome segregation during cell division by transporting each sister chromatid to the spindle pole bodies localized at the opposite sites of the yeast nucleus. The kinetochore of budding yeast (Saccharomyces cerevisiae) is often used as a model system due to its simple composition compared to higher eukaryotes. This review highlights results obtained using optical imaging that revealed relative positions and stoichiometry of the major components of the budding yeast kinetochore.
Collapse
Affiliation(s)
- Konstanty Cieśliński
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| |
Collapse
|
40
|
Graham AN, Kalitsis P. Chromosome Y centromere array deletion leads to impaired centromere function. PLoS One 2014; 9:e86875. [PMID: 24466276 PMCID: PMC3899357 DOI: 10.1371/journal.pone.0086875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/17/2013] [Indexed: 11/18/2022] Open
Abstract
The centromere is an essential chromosomal structure that is required for the faithful distribution of replicated chromosomes to daughter cells. Defects in the centromere can compromise the stability of chromosomes resulting in segregation errors. We have characterised the centromeric structure of the spontaneous mutant mouse strain, BALB/cWt, which exhibits a high rate of Y chromosome instability. The Y centromere DNA array shows a de novo interstitial deletion and a reduction in the level of the foundation centromere protein, CENP-A, when compared to the non-deleted centromere array in the progenitor strain. These results suggest there is a lower threshold limit of centromere size that ensures full kinetochore function during cell division.
Collapse
Affiliation(s)
- Alison N. Graham
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Paul Kalitsis
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| |
Collapse
|
41
|
Miller MP, Amon A, Ünal E. Meiosis I: when chromosomes undergo extreme makeover. Curr Opin Cell Biol 2013; 25:687-96. [PMID: 23916768 PMCID: PMC3836829 DOI: 10.1016/j.ceb.2013.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/02/2013] [Accepted: 07/15/2013] [Indexed: 12/01/2022]
Abstract
The ultimate success of cell division relies on the accurate partitioning of the genetic material. Errors in this process occur in nearly all tumors and are the leading cause of miscarriages and congenital birth defects in humans. Two cell divisions, mitosis and meiosis, use common as well as unique mechanisms to ensure faithful chromosome segregation. In mitosis, alternating rounds of DNA replication and chromosome segregation preserve the chromosome complement of the progenitor cell. In contrast, during meiosis two consecutive rounds of nuclear division, meiosis I and meiosis II, follow a single round of DNA replication to reduce the chromosome complement by half. Meiosis likely evolved through changes to the mitotic cell division program. This review will focus on the recent findings describing the modifications that transform mitosis into meiosis.
Collapse
Affiliation(s)
- Matthew P. Miller
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge MA, USA
- Howard Hughes Medical Institute
| | - Angelika Amon
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge MA, USA
- Howard Hughes Medical Institute
| | - Elçin Ünal
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge MA, USA
- Howard Hughes Medical Institute
| |
Collapse
|
42
|
Zaytsev AV, Ataullakhanov FI, Grishchuk EL. Highly Transient Molecular Interactions Underlie the Stability of Kinetochore-Microtubule Attachment During Cell Division. Cell Mol Bioeng 2013; 6. [PMID: 24376473 DOI: 10.1007/s12195-013-0309-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Chromosome segregation during mitosis is mediated by spindle microtubules that attach to chromosomal kinetochores with strong yet labile links. The exact molecular composition of the kinetochore-microtubule interface is not known but microtubules are thought to bind to kinetochores via the specialized microtubule-binding sites, which contain multiple microtubule-binding proteins. During prometaphase the lifetime of microtubule attachments is short but in metaphase it increases 3-fold, presumably owing to dephosphorylation of the microtubule-binding proteins that increases their affinity. Here, we use mathematical modeling to examine in quantitative and systematic manner the general relationships between the molecular properties of microtubule-binding proteins and the resulting stability of microtubule attachment to the protein-containing kinetochore site. We show that when the protein connections are stochastic, the physiological rate of microtubule turnover is achieved only if these molecular interactions are very transient, each lasting fraction of a second. This "microscopic" time is almost four orders of magnitude shorter than the characteristic time of kinetochore-microtubule attachment. Cooperativity of the microtubule-binding events further increases the disparity of these time scales. Furthermore, for all values of kinetic parameters the microtubule stability is very sensitive to the minor changes in the molecular constants. Such sensitivity of the lifetime of microtubule attachment to the kinetics and cooperativity of molecular interactions at the microtubule-binding site may hinder the accurate regulation of kinetochore-microtubule stability during mitotic progression, and it necessitates detailed experimental examination of the microtubule-binding properties of kinetochore-localized proteins.
Collapse
Affiliation(s)
- Anatoly V Zaytsev
- Physiology Department, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, A401 Richards Building, Philadelphia, PA 19104, USA
| | - Fazly I Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology, RAS, Moscow, Russia, 119991 ; Physics Department, Moscow State University, Moscow, Russia, 119899 ; Laboratory of Biophysics, Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia, 117198
| | - Ekaterina L Grishchuk
- Physiology Department, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, A401 Richards Building, Philadelphia, PA 19104, USA
| |
Collapse
|
43
|
Gan L, Ladinsky MS, Jensen GJ. Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes. Chromosoma 2013; 122:377-86. [PMID: 23818178 PMCID: PMC3777167 DOI: 10.1007/s00412-013-0423-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/26/2013] [Accepted: 06/12/2013] [Indexed: 01/08/2023]
Abstract
Chromatin organization is central to many conserved biological processes, but it is generally unknown how the underlying nucleosomes are arranged in situ. Here, we have used electron cryotomography to study chromatin in the picoplankton Ostreococcus tauri, the smallest known free-living eukaryote. By visualizing the nucleosome densities directly, we find that O. tauri chromosomes do not arrange into discrete, compact bodies or any other higher level of order. In contrast to the textbook 30-nm fiber model, O. tauri chromatin resembles a disordered assemblage of nucleosomes akin to the polymer melt model. This disorganized nucleosome arrangement has important implications for potentially conserved functions in tiny eukaryotes such as the clustering of nonhomologous chromosomes at the kinetochore during mitosis and the independent regulation of closely positioned adjacent genes.
Collapse
Affiliation(s)
- Lu Gan
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA,
| | | | | |
Collapse
|
44
|
Affiliation(s)
- Bill R Brinkley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
45
|
Heckmann S, Macas J, Kumke K, Fuchs J, Schubert V, Ma L, Novák P, Neumann P, Taudien S, Platzer M, Houben A. The holocentric species Luzula elegans shows interplay between centromere and large-scale genome organization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:555-65. [PMID: 23078243 DOI: 10.1111/tpj.12054] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/11/2012] [Accepted: 10/16/2012] [Indexed: 05/18/2023]
Abstract
In higher plants, the large-scale structure of monocentric chromosomes consists of distinguishable eu- and heterochromatic regions, the proportions and organization of which depend on a species' genome size. To determine whether the same interplay is maintained for holocentric chromosomes, we investigated the distribution of repetitive sequences and epigenetic marks in the woodrush Luzula elegans (3.81 Gbp/1C). Sixty-one per cent of the L. elegans genome is characterized by highly repetitive DNA, with over 30 distinct sequence families encoding an exceptionally high diversity of satellite repeats. Over 33% of the genome is composed of the Angela clade of Ty1/copia LTR retrotransposons, which are uniformly dispersed along the chromosomes, while the satellite repeats occur as bands whose distribution appears to be biased towards the chromosome termini. No satellite showed an almost chromosome-wide distribution pattern as expected for a holocentric chromosome and no typical centromere-associated LTR retrotransposons were found either. No distinguishable large-scale patterns of eu- and heterochromatin-typical epigenetic marks or early/late DNA replicating domains were found along mitotic chromosomes, although super-high-resolution light microscopy revealed distinguishable interspersed units of various chromatin types. Our data suggest a correlation between the centromere and overall genome organization in species with holocentric chromosomes.
Collapse
Affiliation(s)
- Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Akiyoshi B, Biggins S. Reconstituting the kinetochore–microtubule interface: what, why, and how. Chromosoma 2012; 121:235-50. [PMID: 22289864 DOI: 10.1007/s00412-012-0362-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/15/2012] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
Abstract
The kinetochore is the proteinaceous complex that governs the movement of duplicated chromosomes by interacting with spindle microtubules during mitosis and meiosis. Faithful chromosome segregation requires that kinetochores form robust load-bearing attachments to the tips of dynamic spindle microtubules, correct microtubule attachment errors, and delay the onset of anaphase until all chromosomes have made proper attachments. To understand how this macromolecular machine operates to segregate duplicated chromosomes with exquisite accuracy, it is critical to reconstitute and study kinetochore–microtubule interactions in vitro using defined components. Here, we review the current status of reconstitution as well as recent progress in understanding the microtubule-binding functions of kinetochores in vivo.
Collapse
Affiliation(s)
- Bungo Akiyoshi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
| | | |
Collapse
|
47
|
Gonen S, Akiyoshi B, Iadanza MG, Shi D, Duggan N, Biggins S, Gonen T. The structure of purified kinetochores reveals multiple microtubule-attachment sites. Nat Struct Mol Biol 2012; 19:925-9. [PMID: 22885327 PMCID: PMC3443262 DOI: 10.1038/nsmb.2358] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/09/2012] [Indexed: 01/21/2023]
Abstract
Chromosomes must be accurately partitioned to daughter cells to prevent aneuploidy, a hallmark of many tumors and birth defects. Kinetochores are the macromolecular machines that segregate chromosomes by maintaining load-bearing attachments to the dynamic tips of microtubules. Here, we present the structure of isolated budding yeast kinetochore particles as visualized by electron microscopy (EM) and electron tomography of negatively stained preparations. The kinetochore appears as a ~126 nm particle containing a large central hub surrounded by multiple outer globular domains. In the presence of microtubules, some particles also have a ring that encircles the microtubule. Our data show that kinetochores bind to microtubules via multivalent attachments and lay the foundation to uncover the key mechanical and regulatory mechanisms by which kinetochores control chromosome segregation and cell division.
Collapse
Affiliation(s)
- Shane Gonen
- Howard Hughes Medical Institute, Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
The Saccharomyces cerevisiae mitotic spindle in budding yeast is exemplified by its simplicity and elegance. Microtubules are nucleated from a crystalline array of proteins organized in the nuclear envelope, known as the spindle pole body in yeast (analogous to the centrosome in larger eukaryotes). The spindle has two classes of nuclear microtubules: kinetochore microtubules and interpolar microtubules. One kinetochore microtubule attaches to a single centromere on each chromosome, while approximately four interpolar microtubules emanate from each pole and interdigitate with interpolar microtubules from the opposite spindle to provide stability to the bipolar spindle. On the cytoplasmic face, two to three microtubules extend from the spindle pole toward the cell cortex. Processes requiring microtubule function are limited to spindles in mitosis and to spindle orientation and nuclear positioning in the cytoplasm. Microtubule function is regulated in large part via products of the 6 kinesin gene family and the 1 cytoplasmic dynein gene. A single bipolar kinesin (Cin8, class Kin-5), together with a depolymerase (Kip3, class Kin-8) or minus-end-directed kinesin (Kar3, class Kin-14), can support spindle function and cell viability. The remarkable feature of yeast cells is that they can survive with microtubules and genes for just two motor proteins, thus providing an unparalleled system to dissect microtubule and motor function within the spindle machine.
Collapse
|
49
|
The evolutionary life cycle of the resilient centromere. Chromosoma 2012; 121:327-40. [PMID: 22527114 DOI: 10.1007/s00412-012-0369-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 03/20/2012] [Accepted: 03/20/2012] [Indexed: 12/13/2022]
Abstract
The centromere is a chromosomal structure that is essential for the accurate segregation of replicated eukaryotic chromosomes to daughter cells. In most centromeres, the underlying DNA is principally made up of repetitive DNA elements, such as tandemly repeated satellite DNA and retrotransposable elements. Paradoxically, for such an essential genomic region, the DNA is rapidly evolving both within and between species. In this review, we show that the centromere locus is a resilient structure that can undergo evolutionary cycles of birth, growth, maturity, death and resurrection. The birth phase is highlighted by examples in humans and other organisms where centromere DNA deletions or chromosome rearrangements can trigger the epigenetic assembly of neocentromeres onto genomic sites without typical features of centromere DNA. In addition, functional centromeres can be generated in the laboratory using various methodologies. Recent mapping of the foundation centromere mark, the histone H3 variant CENP-A, onto near-complete genomes has uncovered examples of new centromeres which have not accumulated centromere repeat DNA. During the growth period of the centromere, repeat DNA begins to appear at some, but not all, loci. The maturity stage is characterised by centromere repeat accumulation, expansions and contractions and the rapid evolution of the centromere DNA between chromosomes of the same species and between species. This stage provides inherent centromere stability, facilitated by repression of gene activity and meiotic recombination at and around the centromeres. Death to a centromere can result from genomic instability precipitating rearrangements, deletions, accumulation of mutations and the loss of essential centromere binding proteins. Surprisingly, ancestral centromeres can undergo resurrection either in the field or in the laboratory, via as yet poorly understood mechanisms. The underlying principle for the preservation of a centromeric evolutionary life cycle is to provide resilience and perpetuity for the all-important structure and function of the centromere.
Collapse
|
50
|
Lee MH, Lin L, Equilibrina I, Uchiyama S, Matsunaga S, Fukui K. ASURA (PHB2) Is Required for Kinetochore Assembly and Subsequent Chromosome Congression. Acta Histochem Cytochem 2011; 44:247-58. [PMID: 22282585 PMCID: PMC3263857 DOI: 10.1267/ahc.11033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/25/2011] [Indexed: 01/24/2023] Open
Abstract
ASURA (PHB2) knockdown has been known to cause premature loss of sister chromatid cohesion, and disrupt the localization of several outer plate proteins to the kinetochore. As a result, cells are arrested at mitotic phase and chromosomes fail to congress to the metaphase plate. In this study, we further clarified the mechanism underlying ASURA function on chromosome congression. Interestingly, ASURA is not specifically localized at the kinetochore during mitotic phase, unlike other kinetochore proteins which construct the kinetochore. Electron microscopy (EM) observation showed that ASURA is required for proper kinetochore formation. By the partial depletion of ASURA, kinetochore maturation is impaired, and kinetochores showing fibrillar balls without a well-defined outer plates are often observed. Moreover, even when the outer plates of kinetochores are constructed, most showed structures stretched and/or distended from the centromere, which resembled premature kinetochores at prometaphase, indicating that the constructed kinetochore plates are less rigid against tension derived from kinetochore microtubule pulling forces. We concluded that ASURA is an essential protein for complete kinetochore development, although ASURA is not being integrated to the kinetochore. These results highlight the uniqueness of ASURA as a kinetochore protein.
Collapse
Affiliation(s)
- Mei Hann Lee
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Linyen Lin
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University
| | - Ilma Equilibrina
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Sachihiro Matsunaga
- Department of Biotechnology, Graduate School of Engineering, Osaka University
- Present address: Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Kiichi Fukui
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| |
Collapse
|