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Shukla S, Bhattacharya A, Sehrawat P, Agarwal P, Shobhawat R, Malik N, Duraisamy K, Rangan NS, Hosur RV, Kumar A. Disorder in CENP-A Cse4 tail-chaperone interaction facilitates binding with Ame1/Okp1 at the kinetochore. Structure 2024; 32:690-705.e6. [PMID: 38565139 DOI: 10.1016/j.str.2024.03.002] [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: 02/06/2023] [Revised: 11/16/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The centromere is epigenetically marked by a histone H3 variant-CENP-A. The budding yeast CENP-A called Cse4, consists of an unusually long N-terminus that is known to be involved in kinetochore assembly. Its disordered chaperone, Scm3 is responsible for the centromeric deposition of Cse4 as well as in the maintenance of a segregation-competent kinetochore. In this study, we show that the Cse4 N-terminus is intrinsically disordered and interacts with Scm3 at multiple sites, and the complex does not gain any substantial structure. Additionally, the complex forms a synergistic association with an essential inner kinetochore component (Ctf19-Mcm21-Okp1-Ame1), and a model has been suggested to this effect. Thus, our study provides mechanistic insights into the Cse4 N-terminus-chaperone interaction and also illustrates how intrinsically disordered proteins mediate assembly of complex multiprotein networks, in general.
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Affiliation(s)
- Shivangi Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | | | - Parveen Sehrawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Prakhar Agarwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Rahul Shobhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Nikita Malik
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Kalaiyarasi Duraisamy
- Centre for Advanced Protein Studies, Syngene International Limited, Bangalore, India
| | | | - Ramakrishna V Hosur
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Ashutosh Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India.
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2
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Malik N, Dantu SC, Shukla S, Kombrabail M, Ghosh SK, Krishnamoorthy G, Kumar A. Conformational flexibility of histone variant CENP-A Cse4 is regulated by histone H4: A mechanism to stabilize soluble Cse4. J Biol Chem 2018; 293:20273-20284. [PMID: 30381395 PMCID: PMC6311523 DOI: 10.1074/jbc.ra118.004141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/23/2018] [Indexed: 11/06/2022] Open
Abstract
The histone variant CENP-ACse4 is a core component of the specialized nucleosome at the centromere in budding yeast and is required for genomic integrity. Accordingly, the levels of Cse4 in cells are tightly regulated, primarily by ubiquitin-mediated proteolysis. However, structural transitions in Cse4 that regulate its centromeric localization and interaction with regulatory components are poorly understood. Using time-resolved fluorescence, NMR, and molecular dynamics simulations, we show here that soluble Cse4 can exist in a "closed" conformation, inaccessible to various regulatory components. We further determined that binding of its obligate partner, histone H4, alters the interdomain interaction within Cse4, enabling an "open" state that is susceptible to proteolysis. This dynamic model allows kinetochore formation only in the presence of H4, as the Cse4 N terminus, which is required for interaction with other centromeric components, is unavailable in the absence of H4. The specific requirement of H4 binding for the conformational regulation of Cse4 suggests a structure-based regulatory mechanism for Cse4 localization. Our data suggested a novel structural transition-based mechanism where conformational flexibility of the Cse4 N terminus can control Cse4 levels in the yeast cell and prevent Cse4 from interacting with kinetochore components at ectopic locations for formation of premature kinetochore assembly.
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Affiliation(s)
- Nikita Malik
- From the Departments of Biosciences and Bioengineering and
| | | | | | - Mamta Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Guruswamy Krishnamoorthy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India; Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India and.
| | - Ashutosh Kumar
- From the Departments of Biosciences and Bioengineering and.
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3
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A Failsafe for Sensing Chromatid Tension in Mitosis with the Histone H3 Tail in Saccharomyces cerevisiae. Genetics 2017; 208:565-578. [PMID: 29242290 DOI: 10.1534/genetics.117.300606] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/08/2017] [Indexed: 01/01/2023] Open
Abstract
Mitotic fidelity is ensured by achieving biorientation on all paired chromosomes. The key signal for proper chromosome alignment is the tension between sister chromatids created by opposing poleward force from the spindles. In the budding yeast, the tension-sensing function requires that the Shugoshin protein, Shugoshin 1, be recruited to the centromeres and the neighboring pericentric regions. Concerted actions integrating proteins at centromeres and pericentromeres create highly specific Shugoshin 1 domains on mitotic chromosomes. We have previously reported that an important regulatory region on histone H3, termed the tension-sensing motif (TSM), is responsible for retaining Shugoshin 1 at pericentromeres. The TSM is negatively regulated by the acetyltransferase Gcn5p, but the underlying mechanism was elusive. In this work, we provide evidence that, when the TSM function is impaired, the histone H3 tail adopts a role that complements the damaged TSM to ensure faithful mitosis. This novel function of the H3 tail is controlled by Gcn5p, which targets selective lysine residues. Mutations to K14 and K23 ameliorate the mitotic defects resulting from TSM mutations. The restoration of faithful segregation is accompanied by regaining Shugoshin 1 access to the pericentric regions. Our data reveal a novel pathway for mitotic Shugoshin 1 recruitment and further reinforce the active role played by chromatins during their segregation in mitosis.
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Identification of Tension Sensing Motif of Histone H3 in Saccharomyces cerevisiae and Its Regulation by Histone Modifying Enzymes. Genetics 2016; 204:1029-1043. [PMID: 27672091 DOI: 10.1534/genetics.116.192443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/14/2016] [Indexed: 11/18/2022] Open
Abstract
To ensure genome stability during cell division, all chromosomes must attach to spindles emanating from the opposite spindle pole bodies before segregation. The tension between sister chromatids generated by the poleward pulling force is an integral part of chromosome biorientation. In budding yeast, the residue Gly44 of histone H3 is critical for retaining the conserved Shugoshin protein Sgo1p at the pericentromeres for monitoring the tension status during mitosis. Studies carried out in this work showed that Lys42, Gly44, and Thr45 of H3 form the core of a tension sensing motif (TSM). Similar to the previously reported G44S mutant, K42A, G44A, and T45A alleles all rendered cells unable to respond to erroneous spindle attachment, a phenotype suppressed by Sgo1p overexpression. TSM functions by physically recruiting or retaining Sgo1p at pericentromeres as evidenced by chromatin immunoprecipitation and by in vitro pulldown experiments. Intriguingly, the function of TSM is likely regulated by multiple histone modifying enzymes, including the histone acetyltransferase Gcn5p, and deacetylases Rpd3p and Hos2p Defects caused by TSM mutations can be suppressed by the expression of a catalytically inactive mutant of Gcn5p Conversely, G44S mutant cells exhibit prominent chromatin instability phenotype in the absence of RPD3 Importantly, the gcn5- suppressor restores the tension sensing function in tsm- background in a fashion that bypasses the need of stably associating Sgo1p with chromatin. These results demonstrate that the TSM of histone H3 is a key component of a mechanism that ensures faithful segregation, and that interaction with chromatin modifying enzymes may be an important part of the mitotic quality control process.
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5
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Dokholyan NV. Physical microscopic model of proteins under force. J Phys Chem B 2012; 116:6806-9. [PMID: 22375559 DOI: 10.1021/jp212543m] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nature has evolved proteins to counteract forces applied on living cells, and has designed proteins that can sense forces. One can appreciate Nature's ingenuity in evolving these proteins to be highly sensitive to force and to have a high dynamic force range at which they operate. To achieve this level of sensitivity, many of these proteins are composed of multiple domains and linking peptides connecting these domains, each of them having their own force response regimes. Here, using a simple model of a protein, we address the question of how each individual domain responds to force. We also ask how multidomain proteins respond to forces. We find that the end-to-end distance of individual domains under force scales linearly with force. In multidomain proteins, we find that the force response has a rich range: at low force, extension is predominantly governed by "weaker" linking peptides or domain intermediates, while at higher force, the extension is governed by unfolding of individual domains. Overall, the force extension curve comprises multiple sigmoidal transitions governed by unfolding of linking peptides and domains. Our study provides a basic framework for the understanding of protein response to force, and allows for interpretation experiments in which force is used to study the mechanical properties of multidomain proteins.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, School of Medicine, Chapel Hill, North Carolina 27599, USA.
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6
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Assembly of Drosophila centromeric nucleosomes requires CID dimerization. Mol Cell 2011; 45:263-9. [PMID: 22209075 DOI: 10.1016/j.molcel.2011.12.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 08/16/2011] [Accepted: 11/23/2011] [Indexed: 11/24/2022]
Abstract
Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four-helix bundle, which mediates intranucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly.
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Shivaraju M, Camahort R, Mattingly M, Gerton JL. Scm3 is a centromeric nucleosome assembly factor. J Biol Chem 2011; 286:12016-23. [PMID: 21317428 PMCID: PMC3069404 DOI: 10.1074/jbc.m110.183640] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Cse4 nucleosome at each budding yeast centromere must be faithfully assembled each cell cycle to specify the site of kinetochore assembly and microtubule attachment for chromosome segregation. Although Scm3 is required for the localization of the centromeric H3 histone variant Cse4 to centromeres, its role in nucleosome assembly has not been tested. We demonstrate that Scm3 is able to mediate the assembly of Cse4 nucleosomes in vitro, but not H3 nucleosomes, as measured by a supercoiling assay. Localization of Cse4 to centromeres and the assembly activity depend on an evolutionarily conserved core motif in Scm3, but localization of the CBF3 subunit Ndc10 to centromeres does not depend on this motif. The centromere targeting domain of Cse4 is sufficient for Scm3 nucleosome assembly activity. Assembly does not depend on centromeric sequence. We propose that Scm3 plays an active role in centromeric nucleosome assembly.
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Abstract
Chromosome cohesion is the term used to describe the cellular process in which sister chromatids are held together from the time of their replication until the time of separation at the metaphase to anaphase transition. In this capacity, chromosome cohesion, especially at centromeric regions, is essential for chromosome segregation. However, cohesion of noncentromeric DNA sequences has been shown to occur during double-strand break (DSB) repair and the transcriptional regulation of genes. Cohesion for the purposes of accurate chromosome segregation, DSB repair, and gene regulation are all achieved through a similar network of proteins, but cohesion for each purpose may be regulated differently. In this review, we focus on recent developments regarding the regulation of this multipurpose network for tying DNA sequences together. In particular, regulation via effectors and posttranslational modifications are reviewed. A picture is emerging in which complex regulatory networks are capable of differential regulation of cohesion in various contexts.
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Affiliation(s)
- Bo Xiong
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.
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Matsson L. Spindle checkpoint regulated by nonequilibrium collective spindle-chromosome interaction; relationship to single DNA molecule force-extension formula. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:502101. [PMID: 21836210 DOI: 10.1088/0953-8984/21/50/502101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The spindle checkpoint, which blocks segregation until all sister chromatid pairs have been stably connected to the two spindle poles, is perhaps the biggest mystery of the cell cycle. The main reason seems to be that the spatial correlations imposed by microtubules between stably attached kinetochores and the nonlinear dependence of the system on the increasing number of such kinetochores have been disregarded in earlier spindle checkpoint studies. From these missing parts a non-equilibrium collective spindle-chromosome interaction is obtained here for budding yeast (Saccharomyces cerevisiae) cells. The interaction, which is based on a non-equilibrium statistical mechanics, can sense and count the number of stably attached kinetochores and sense the threshold for segregation. It blocks segregation until all sister chromatids pairs have been bi-oriented and regulates tension such that segregation becomes synchronized, thus explaining how the cell might decide to segregate replicated chromosomes. The model also predicts kinetochore oscillations at a frequency which agrees well with observation. Finally, a relationship between this spindle-chromosome dynamics and the force-extension formula obtained in a single DNA molecule experiment is obtained.
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Affiliation(s)
- Leif Matsson
- Department of Physics, University of Gothenburg, SE-412 96 Göteborg, Sweden
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10
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Abstract
It has been firmly established that many interphase nuclear functions, including transcriptional regulation, are regulated by chromatin and histones. How mitotic progression and quality control might be influenced by histones is less well characterized. We show that histone H3 plays a crucial role in activating the spindle assembly checkpoint in response to a defect in mitosis. Prior to anaphase, all chromosomes must attach to spindles emanating from the opposite spindle pole bodies. The tension between sister chromatids generated by the poleward pulling force is an integral part of chromosome biorientation. Lack of tension due to erroneous attachment activates the spindle assembly checkpoint, which corrects the mistakes and ensures segregation fidelity. A histone H3 mutation impairs the ability of yeast cells to activate the checkpoint in a tensionless crisis, leading to missegregation and aneuploidy. The defects in tension sensing result directly from an attenuated H3-Sgo1p interaction essential for pericentric recruitment of Sgo1p. Reinstating the pericentric enrichment of Sgo1p alleviates the mitotic defects. Histone H3, and hence the chromatin, is thus a key factor transmitting the tension status to the spindle assembly checkpoint.
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11
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Camahort R, Shivaraju M, Mattingly M, Li B, Nakanishi S, Zhu D, Shilatifard A, Workman JL, Gerton JL. Cse4 is part of an octameric nucleosome in budding yeast. Mol Cell 2009; 35:794-805. [PMID: 19782029 DOI: 10.1016/j.molcel.2009.07.022] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 03/26/2009] [Accepted: 07/31/2009] [Indexed: 01/16/2023]
Abstract
The budding yeast CenH3 histone variant Cse4 localizes to centromeric nucleosomes and is required for kinetochore assembly and chromosome segregation. The exact composition of centromeric Cse4-containing nucleosomes is a subject of debate. Using unbiased biochemical, cell-biological, and genetic approaches, we have tested the composition of Cse4-containing nucleosomes. Using micrococcal nuclease-treated chromatin, we find that Cse4 is associated with the histones H2A, H2B, and H4, but not H3 or the nonhistone protein Scm3. Overexpression of Cse4 rescues the lethality of a scm3 deletion, indicating that Scm3 is not essential for the formation of functional centromeric chromatin. We also find that octameric Cse4 nucleosomes can be reconstituted in vitro. Furthermore, Cse4-Cse4 dimerization occurs in vivo at the centromeric nucleosome, and this requires the predicted Cse4-Cse4 dimerization interface. Taken together, our experimental evidence supports the model that the Cse4 nucleosome is an octamer, containing two copies each of Cse4, H2A, H2B, and H4.
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Affiliation(s)
- Raymond Camahort
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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12
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Abstract
Kinetochores are large protein assemblies built on chromosomal loci named centromeres. The main functions of kinetochores can be grouped under four modules. The first module, in the inner kinetochore, contributes a sturdy interface with centromeric chromatin. The second module, the outer kinetochore, contributes a microtubule-binding interface. The third module, the spindle assembly checkpoint, is a feedback control mechanism that monitors the state of kinetochore-microtubule attachment to control the progression of the cell cycle. The fourth module discerns correct from improper attachments, preventing the stabilization of the latter and allowing the selective stabilization of the former. In this review, we discuss how the molecular organization of the four modules allows a dynamic integration of kinetochore-microtubule attachment with the prevention of chromosome segregation errors and cell-cycle progression.
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Affiliation(s)
- Stefano Santaguida
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Andrea Musacchio
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Research Unit of the Italian Institute of Technology at the IFOM-IEO Campus, Milan, Italy
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13
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Bouck DC, Joglekar AP, Bloom KS. Design features of a mitotic spindle: balancing tension and compression at a single microtubule kinetochore interface in budding yeast. Annu Rev Genet 2009; 42:335-59. [PMID: 18680435 DOI: 10.1146/annurev.genet.42.110807.091620] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Accurate segregation of duplicated chromosomes ensures that daughter cells get one and only one copy of each chromosome. Errors in chromosome segregation result in aneuploidy and have severe consequences on human health. Incorrect chromosome number and chromosomal instability are hallmarks of tumor cells. Hence, segregation errors are thought to be a major cause of tumorigenesis. A study of the physical mechanical basis of chromosome segregation is essential to understand the processes that can lead to errors. Tremendous progress has been made in recent years in identifying the proteins necessary for chromosome movement and segregation, but the mechanism and structure of critical force generating components and the molecular basis of centromere stiffness remain poorly understood.
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Affiliation(s)
- David C Bouck
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA.
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14
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Song JS, Liu X, Liu XS, He X. A high-resolution map of nucleosome positioning on a fission yeast centromere. Genes Dev 2008; 18:1064-72. [PMID: 18411404 PMCID: PMC2493395 DOI: 10.1101/gr.075374.107] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 04/03/2008] [Indexed: 11/25/2022]
Abstract
A key element for defining the centromere identity is the incorporation of a specific histone H3, CENPA, known as Cnp1p in Schizosaccharomyces pombe. Previous studies have suggested that functional S. pombe centromeres lack regularly positioned nucleosomes and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are, in fact, positioned in regular intervals in the core of centromere 2, providing the first high-resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore protein genes cnp1, mis18, mis12, nuf2, mal2; overexpression of cnp1; or the deletion of ams2, which encodes a GATA-like factor participating in CENPA incorporation. Bioinformatics analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence bias in nucleosome positioning. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites of Ams2p. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence.
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Affiliation(s)
- Jun S. Song
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey 08540, USA
| | - Xingkun Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Xiangwei He
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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15
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Abstract
Establishment of proper attachments between chromosomes and microtubules is essential for the accurate division of the genome. Two recent studies indicate that these attachments are facilitated by the geometry of chromosomes and the bipolar arrangement of spindle microtubules.
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Affiliation(s)
- Jason Stumpff
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA.
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16
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Dorn JF, Maddox PS. Chromosome segregation: centromeres get bent. Curr Biol 2008; 18:R159-61. [PMID: 18302916 DOI: 10.1016/j.cub.2007.12.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Work over the last several decades has shown that kinetochores play an active part in chromosome segregation, while the chromatin and, more to the point, the DNA have gathered little attention. In two intriguing papers, the Bloom and Khodjakov groups show that intercentromeric chromatin plays a much more active part in chromosome segregation than previously suspected.
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Affiliation(s)
- Jonas F Dorn
- Department of Pathology and Cell Biology, Université de Montreal, Montréal, Quebec H3C 3J7, Canada
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17
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Yeh E, Haase J, Paliulis LV, Joglekar A, Bond L, Bouck D, Salmon ED, Bloom KS. Pericentric chromatin is organized into an intramolecular loop in mitosis. Curr Biol 2008; 18:81-90. [PMID: 18211850 PMCID: PMC2238682 DOI: 10.1016/j.cub.2007.12.019] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 11/28/2007] [Accepted: 12/07/2007] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cohesin proteins link sister chromatids and provide the basis for tension between bioriented sister chomatids in mitosis. Cohesin is concentrated at the centromere region of the chromosome despite the fact that sister centromeres can be separated by 800 nm in vivo. The function of cohesin at sites of separated DNA is unknown. RESULTS We provide evidence that the kinetochore promotes the organization of pericentric chromatin into a cruciform in mitosis such that centromere-flanking DNA adopts an intramolecular loop, whereas sister-chromatid arms are paired intermolecularly. Visualization of cohesin subunits by fluorescence microscopy revealed a cylindrical structure that encircles the central spindle and spans the distance between sister kinetochores. Kinetochore assembly at the apex of the loop initiates intrastrand loop formation that extends approximately 25 kb (12.5 kb on either side of the centromere). Two centromere loops (one from each sister chromatid) are stretched between the ends of sister-kinetochore microtubules along the spindle axis. At the base of the loop there is a transition to intermolecular sister-chromatid pairing. CONCLUSIONS The C loop conformation reveals the structural basis for sister-kinetochore clustering in budding yeast and for kinetochore biorientation and thus resolves the paradox of maximal interstrand separation in regions of highest cohesin concentration.
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Affiliation(s)
- Elaine Yeh
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
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18
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Black BE, Bassett EA. The histone variant CENP-A and centromere specification. Curr Opin Cell Biol 2008; 20:91-100. [PMID: 18226513 DOI: 10.1016/j.ceb.2007.11.007] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 10/29/2007] [Accepted: 11/26/2007] [Indexed: 12/01/2022]
Abstract
The centromere is the chromosomal locus that guides faithful inheritance. Centromeres are specified epigenetically, and the histone H3 variant CENP-A has emerged as the best candidate to carry the epigenetic centromere mark. Recent advances demonstrate the physical basis for this epigenetic mark whereby CENP-A confers conformational rigidity to the nucleosome it forms with other core histones. This nucleosome is recognized by a multisubunit complex of constitutive centromere proteins, termed the CENP-A(NAC). Evidence from two CENP-A relatives in diverse eukaryotes suggests that the histone complexes they form adopt highly unconventional arrangements on DNA. Centromere identity, itself, is propagated during mitotic exit and early G1, and it relies upon a cis-acting targeting domain within CENP-A and a proposed centromere 'priming' reaction.
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Affiliation(s)
- Ben E Black
- Department of Biochemistry and Biophysics and Program in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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19
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Bloom KS. Beyond the code: the mechanical properties of DNA as they relate to mitosis. Chromosoma 2007; 117:103-10. [PMID: 18060422 DOI: 10.1007/s00412-007-0138-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 11/06/2007] [Accepted: 11/07/2007] [Indexed: 11/26/2022]
Affiliation(s)
- Kerry S Bloom
- Department of Biology, University of North Carolina at Chapel Hill, 623 Fordham Hall CB#3280, Chapel Hill, NC 27599-3280, USA.
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Persistence of DNA threads in human anaphase cells suggests late completion of sister chromatid decatenation. Chromosoma 2007; 117:123-35. [PMID: 17989990 PMCID: PMC2755729 DOI: 10.1007/s00412-007-0131-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 10/11/2007] [Accepted: 10/12/2007] [Indexed: 11/17/2022]
Abstract
PICH (Plk1-interacting checkpoint helicase) was recently identified as an essential component of the spindle assembly checkpoint and shown to localize to kinetochores, inner centromeres, and thin threads connecting separating chromosomes even during anaphase. In this paper, we have used immuno-fiber fluorescence in situ hybridization and chromatin-immunoprecipitation to demonstrate that PICH associates with centromeric chromatin during anaphase. Furthermore, by careful analysis of PICH-positive anaphase threads through FISH as well as bromo-deoxyurdine and CREST labeling, we strengthen the evidence that these threads comprise mainly alphoid centromere deoxyribonucleic acid. Finally, by timing the addition of ICRF-193 (a specific inhibitor of topoisomerase-II alpha) to cells synchronized in anaphase, we demonstrate that topoisomerase activity is required specifically to resolve PICH-positive threads during anaphase (as opposed to being required to prevent the formation of such threads during earlier cell cycle stages). These data indicate that PICH associates with centromeres during anaphase and that most PICH-positive threads evolve from inner centromeres as these stretch in response to tension. Moreover, they show that topoisomerase activity is required during anaphase for the resolution of PICH-positive threads, implying that the complete separation of sister chromatids occurs later than previously assumed.
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Dalal Y, Furuyama T, Vermaak D, Henikoff S. Structure, dynamics, and evolution of centromeric nucleosomes. Proc Natl Acad Sci U S A 2007; 104:15974-81. [PMID: 17893333 PMCID: PMC1993840 DOI: 10.1073/pnas.0707648104] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Indexed: 12/18/2022] Open
Abstract
Centromeres are defining features of eukaryotic chromosomes, providing sites of attachment for segregation during mitosis and meiosis. The fundamental unit of centromere structure is the centromeric nucleosome, which differs from the conventional nucleosome by the presence of a centromere-specific histone variant (CenH3) in place of canonical H3. We have shown that the CenH3 nucleosome core found in interphase Drosophila cells is a heterotypic tetramer, a "hemisome" consisting of one molecule each of CenH3, H4, H2A, and H2B, rather than the octamer of canonical histones that is found in bulk nucleosomes. The surprising discovery of hemisomes at centromeres calls for a reevaluation of evidence that has long been interpreted in terms of a more conventional nucleosome. We describe how the hemisome structure of centromeric nucleosomes can account for enigmatic properties of centromeres, including kinetochore accessibility, epigenetic inheritance, rapid turnover of misincorporated CenH3, and transcriptional quiescence of pericentric heterochromatin. Structural differences mediated by loop 1 are proposed to account for the formation of stable tetramers containing CenH3 rather than stable octamers containing H3. Asymmetric CenH3 hemisomes might interrupt the global condensation of octameric H3 arrays and present an asymmetric surface for kinetochore formation. We suggest that this simple mechanism for differentiation between centromeric and packaging nucleosomes evolved from an archaea-like ancestor at the dawn of eukaryotic evolution.
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Affiliation(s)
| | - Takehito Furuyama
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109
| | | | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109
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Abstract
The kinetochore is a key cell division organelle that enables high-fidelity transmission of genetic information by coupling chromosomes to spindle microtubules during mitosis and meiosis. Despite its cytological description more than a century ago, remarkably little information is available on kinetochore function at a molecular level. Recently, important advances elucidating the overall organization of kinetochores, as well as information about the structures and molecular mechanisms of kinetochore function, have been achieved through a detailed analysis of the kinetochores of the budding yeast Saccharomyces cerevisiae. Here we review the current understanding of kinetochore function in budding yeast and draw comparisons to recent findings in other organisms.
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Affiliation(s)
- Stefan Westermann
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
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Mizuguchi G, Xiao H, Wisniewski J, Smith MM, Wu C. Nonhistone Scm3 and histones CenH3-H4 assemble the core of centromere-specific nucleosomes. Cell 2007; 129:1153-64. [PMID: 17574026 DOI: 10.1016/j.cell.2007.04.026] [Citation(s) in RCA: 237] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 02/28/2007] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
The budding yeast histone H3 variant, Cse4, replaces conventional histone H3 in centromeric chromatin and, together with centromere-specific DNA-binding factors, directs assembly of the kinetochore, a multiprotein complex mediating chromosome segregation. We have identified Scm3, a nonhistone protein that colocalizes with Cse4 and is required for its centromeric association. Bacterially expressed Scm3 binds directly to and reconstitutes a stoichiometric complex with Cse4 and histone H4 but not with conventional histone H3 and H4. A conserved acidic domain of Scm3 is responsible for directing the Cse4-specific interaction. Strikingly, binding of Scm3 can replace histones H2A-H2B from preassembled Cse4-containing histone octamers. This incompatibility between Scm3 and histones H2A-H2B is correlated with diminished in vivo occupancy of histone H2B, H2A, and H2AZ at centromeres. Our findings indicate that nonhistone Scm3 serves to assemble and maintain Cse4-H4 at centromeres and may replace histone H2A-H2B dimers in a centromere-specific nucleosome core.
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Affiliation(s)
- Gaku Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 6068, Bethesda, MD 20892-4255, USA
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Abstract
At the foundation of all eukaryotic kinetochores is a unique histone variant, known as CenH3 (centromere histone H3). We are starting to identify the histone chaperones responsible for CenH3 deposition at centromere DNA, and the mechanisms that restrict CenH3 from chromosome arms. The specialized nucleosome that contains CenH3 in place of canonical histone H3 lies at the interface between microtubules and chromosomes and directs kinetochore protein assembly. By contrast, pericentric chromatin is highly elastic and can stretch or recoil in response to microtubule shortening or growth in mitosis. The variety in histone modification is likely to play a key role in regulating the behavior of these distinct chromatin domains.
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Affiliation(s)
- Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
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Affiliation(s)
- Jennifer L Gerton
- Stowers Institute for Medical Research, University of Kansas Medical Center, Kansas City, Missouri 64110, USA.
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Sharma S, Ding F, Dokholyan NV. Multiscale modeling of nucleosome dynamics. Biophys J 2007; 92:1457-70. [PMID: 17142268 PMCID: PMC1796817 DOI: 10.1529/biophysj.106.094805] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 11/02/2006] [Indexed: 01/16/2023] Open
Abstract
Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid discrete molecular dynamics simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperatures, suggesting a mechanism of chromatin structural organization whereby histone tails regulate inter- and intranucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed "cold sites", which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A interhistone interfaces, indicating the necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows that bending across the H3-H3 is a prominent mode of intranucleosomal dynamics. We postulate that effects of salts on mononucleosomes can be modeled in discrete molecular dynamics by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mononucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin structure, mediated by salt-bridge interactions with adjacent DNA.
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Affiliation(s)
- Shantanu Sharma
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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Eckert CA, Gravdahl DJ, Megee PC. The enhancement of pericentromeric cohesin association by conserved kinetochore components promotes high-fidelity chromosome segregation and is sensitive to microtubule-based tension. Genes Dev 2007; 21:278-91. [PMID: 17242156 PMCID: PMC1785119 DOI: 10.1101/gad.1498707] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 12/05/2006] [Indexed: 02/02/2023]
Abstract
Sister chromatid cohesion, conferred by the evolutionarily conserved cohesin complex, is essential for proper chromosome segregation. Cohesin binds to discrete sites along chromosome arms, and is especially enriched surrounding centromeres, but past studies have not clearly defined the roles of arm and pericentromeric cohesion in chromosome segregation. To address this issue, we developed a technique that specifically reduced pericentromeric cohesin association on a single chromosome without affecting arm cohesin binding. Under these conditions, we observed more extensive stretching of centromeric chromatin and elevated frequencies of chromosome loss, suggesting that pericentromeric cohesin enrichment is essential for high-fidelity chromosome transmission. The magnitude of pericentromeric cohesin association was negatively correlated with tension between sister kinetochores, with the highest levels of association in cells lacking kinetochore-microtubule attachments. Pericentromeric cohesin recruitment required evolutionarily conserved components of the inner and central kinetochore. Together, these observations suggest that pericentromeric cohesin levels reflect the balance of opposing forces: the kinetochore-mediated enhancement of cohesin binding and the disruption of binding by mechanical tension at kinetochores. The involvement of conserved kinetochore components suggests that this pathway for pericentromeric cohesin enrichment may have been retained in higher eukaryotes to promote chromosome biorientation and accurate sister chromatid segregation.
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Affiliation(s)
- Carrie A. Eckert
- Program in Molecular Biology, University of Colorado Health Sciences Center, Aurora, Colorado 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, Colorado 80045, USA
| | - Daniel J. Gravdahl
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, Colorado 80045, USA
| | - Paul C. Megee
- Program in Molecular Biology, University of Colorado Health Sciences Center, Aurora, Colorado 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, Colorado 80045, USA
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Gardner MK, Odde DJ. Modeling of chromosome motility during mitosis. Curr Opin Cell Biol 2007; 18:639-47. [PMID: 17046231 DOI: 10.1016/j.ceb.2006.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 10/03/2006] [Indexed: 11/19/2022]
Abstract
Chromosome motility is a highly regulated and complex process that ultimately achieves proper segregation of the replicated genome. Recent modeling studies provide a computational framework for investigating how microtubule assembly dynamics, motor protein activity and mitotic spindle mechanical properties are integrated to drive chromosome motility. Among other things, these studies show that metaphase chromosome oscillations can be explained by a range of assumptions, and that non-oscillatory states can be achieved with modest changes to the model parameters. In addition, recent microscopy studies provide new insight into the nature of the coupling between force on the kinetochore and kinetochore-microtubule assembly/disassembly. Together, these studies facilitate advancement toward a unified model that quantitatively predicts chromosome motility.
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Affiliation(s)
- Melissa K Gardner
- Department of Biomedical Engineering, University of Minnesota, 7-132 Hasselmo Hall, 312 Church Street S.E., Minneapolis, Minnesota 55455, USA
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Affiliation(s)
- Elaine Yeh
- Elaine Yeh & Kerry Bloom are in the Department of Biology, University of North Carolina at Chapel Hill, 623 Fordham Hall CB#3280, Chapel Hill, North Carolina 27599-3280, USA
| | - Kerry Bloom
- Elaine Yeh & Kerry Bloom are in the Department of Biology, University of North Carolina at Chapel Hill, 623 Fordham Hall CB#3280, Chapel Hill, North Carolina 27599-3280, USA
- Tel: +1 919 962 1182; Fax: +1 919 962 8461;
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Rockmill B, Voelkel-Meiman K, Roeder GS. Centromere-proximal crossovers are associated with precocious separation of sister chromatids during meiosis in Saccharomyces cerevisiae. Genetics 2006; 174:1745-54. [PMID: 17028345 PMCID: PMC1698618 DOI: 10.1534/genetics.106.058933] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 09/24/2006] [Indexed: 11/18/2022] Open
Abstract
In most organisms, meiotic chromosome segregation is dependent on crossovers (COs), which enable pairs of homologous chromosomes to segregate to opposite poles at meiosis I. In mammals, the majority of meiotic chromosome segregation errors result from a lack of COs between homologs. Observations in Homo sapiens and Drosophila melanogaster have revealed a second class of exceptional events in which a CO occurred near the centromere of the missegregated chromosome. We show that in wild-type strains of Saccharomyces cerevisiae, most spore inviability is due to precocious separation of sister chromatids (PSSC) and that PSSC is often associated with centromere-proximal crossing over. COs, as opposed to nonreciprocal recombination events (NCOs), are preferentially associated with missegregation. Strains mutant for the RecQ homolog, SGS1, display reduced spore viability and increased crossing over. Much of the spore inviability in sgs1 results from PSSC, and these events are often associated with centromere-proximal COs, just as in wild type. When crossing over in sgs1 is reduced by the introduction of a nonnull allele of SPO11, spore viability is improved, suggesting that the increased PSSC is due to increased crossing over. We present a model for PSSC in which a centromere-proximal CO promotes local loss of sister-chromatid cohesion.
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Affiliation(s)
- Beth Rockmill
- Howard Hughes Medical Institute, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
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